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{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'gather_categories'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'imap'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'categories'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '31', '52', '58', '65', '124', '147', '208', '214', '236', '248', '330']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '14']}, {'id': '11', 'type': 'comparison_operator', 'children': ['12', '13'], 'value': 'is'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'categories'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'block', 'children': ['15']}, {'id': '15', 'type': 'return_statement', 'children': ['16']}; {'id': '16', 'type': 'dictionary', 'children': ['17']}, {'id': '17', 'type': 'pair', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"default"'}, {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'DataCategory'}, {'id': '21', 'type': 'argument_list', 'children': ['22', '30']}; {'id': '22', 'type': 'call', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'imap'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '29', 'type': 'argument_list', 'children': []}; {'id': '30', 'type': 'dictionary', 'children': []}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'cat_ids'}; {'id': '34', 'type': 'list_comprehension', 'children': ['35', '41', '44']}, {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'cat'}, {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'cat'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'categories'}; {'id': '44', 'type': 'if_clause', 'children': ['45']}, {'id': '45', 'type': 'boolean_operator', 'children': ['46', '49'], 'value': 'and'}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'in'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': 'not'}; {'id': '50', 'type': 'string', 'children': [], 'value': '"="'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '55', 'type': 'call', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'}, {'id': '57', 'type': 'argument_list', 'children': []}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'conditions'}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '65', 'type': 'for_statement', 'children': ['66', '69', '73']}; {'id': '66', 'type': 'pattern_list', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'cat'}, {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'categories'}, {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'if_statement', 'children': ['75', '89']}, {'id': '75', 'type': 'boolean_operator', 'children': ['76', '79'], 'value': 'and'}; {'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': 'in'}, {'id': '77', 'type': 'string', 'children': [], 'value': '"="'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'cat'}, {'id': '79', 'type': 'comparison_operator', 'children': ['80', '88'], 'value': 'in'}; {'id': '80', 'type': 'subscript', 'children': ['81', '87']}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'string', 'children': [], 'value': '"="'}, {'id': '87', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '89', 'type': 'block', 'children': ['90', '108']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'cat_name'}, {'id': '93', 'type': 'subscript', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '95', 'type': 'call', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'subscript', 'children': ['101', '107']}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'string', 'children': [], 'value': '"="'}, {'id': '107', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'call', 'children': ['110', '115']}; {'id': '110', 'type': 'attribute', 'children': ['111', '114']}, {'id': '111', 'type': 'subscript', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'conditions'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'cat_name'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'subscript', 'children': ['117', '123']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'string', 'children': [], 'value': '"="'}, {'id': '123', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '124', 'type': 'if_statement', 'children': ['125', '130']}, {'id': '125', 'type': 'boolean_operator', 'children': ['126', '128'], 'value': 'and'}; {'id': '126', 'type': 'not_operator', 'children': ['127']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'cat_ids'}; {'id': '128', 'type': 'not_operator', 'children': ['129']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '130', 'type': 'block', 'children': ['131']}, {'id': '131', 'type': 'return_statement', 'children': ['132']}; {'id': '132', 'type': 'dictionary', 'children': ['133']}, {'id': '133', 'type': 'pair', 'children': ['134', '135']}; {'id': '134', 'type': 'string', 'children': [], 'value': '"default"'}, {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'DataCategory'}, {'id': '137', 'type': 'argument_list', 'children': ['138', '146']}; {'id': '138', 'type': 'call', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'call', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'imap'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '145', 'type': 'argument_list', 'children': []}; {'id': '146', 'type': 'dictionary', 'children': []}, {'id': '147', 'type': 'if_statement', 'children': ['148', '152']}; {'id': '148', 'type': 'boolean_operator', 'children': ['149', '150'], 'value': 'and'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'cat_ids'}; {'id': '150', 'type': 'not_operator', 'children': ['151']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '152', 'type': 'block', 'children': ['153', '206']}, {'id': '153', 'type': 'for_statement', 'children': ['154', '157', '162']}; {'id': '154', 'type': 'pattern_list', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'sid'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '157', 'type': 'call', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'imap'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '161', 'type': 'argument_list', 'children': []}; {'id': '162', 'type': 'block', 'children': ['163', '178', '195']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'cat_name'}; {'id': '166', 'type': 'call', 'children': ['167', '170']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'string', 'children': [], 'value': '"_"'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '170', 'type': 'argument_list', 'children': ['171']}, {'id': '171', 'type': 'list_comprehension', 'children': ['172', '175']}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '175', 'type': 'for_in_clause', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'cat_ids'}; {'id': '178', 'type': 'if_statement', 'children': ['179', '182']}, {'id': '179', 'type': 'comparison_operator', 'children': ['180', '181'], 'value': 'not'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'cat_name'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '182', 'type': 'block', 'children': ['183']}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '188']}, {'id': '185', 'type': 'subscript', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'cat_name'}; {'id': '188', 'type': 'call', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'DataCategory'}; {'id': '190', 'type': 'argument_list', 'children': ['191', '194']}, {'id': '191', 'type': 'call', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '193', 'type': 'argument_list', 'children': []}; {'id': '194', 'type': 'dictionary', 'children': []}, {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'call', 'children': ['197', '204']}, {'id': '197', 'type': 'attribute', 'children': ['198', '203']}; {'id': '198', 'type': 'attribute', 'children': ['199', '202']}, {'id': '199', 'type': 'subscript', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'cat_name'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'sids'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'sid'}; {'id': '206', 'type': 'return_statement', 'children': ['207']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'assignment', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'cond_ids'}, {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '213', 'type': 'argument_list', 'children': []}; {'id': '214', 'type': 'for_statement', 'children': ['215', '216', '217']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'conditions'}, {'id': '217', 'type': 'block', 'children': ['218']}; {'id': '218', 'type': 'try_statement', 'children': ['219', '232']}, {'id': '219', 'type': 'block', 'children': ['220']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'cond_ids'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '225', 'type': 'argument_list', 'children': ['226']}; {'id': '226', 'type': 'call', 'children': ['227', '230']}, {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '230', 'type': 'argument_list', 'children': ['231']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '232', 'type': 'except_clause', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '234', 'type': 'block', 'children': ['235']}, {'id': '235', 'type': 'continue_statement', 'children': []}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'idx_to_test'}, {'id': '239', 'type': 'call', 'children': ['240', '246']}; {'id': '240', 'type': 'attribute', 'children': ['241', '245']}, {'id': '241', 'type': 'call', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'cat_ids'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'union'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'cond_ids'}; {'id': '248', 'type': 'for_statement', 'children': ['249', '252', '257']}, {'id': '249', 'type': 'pattern_list', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'sid'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '252', 'type': 'call', 'children': ['253', '256']}, {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'imap'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '256', 'type': 'argument_list', 'children': []}, {'id': '257', 'type': 'block', 'children': ['258']}; {'id': '258', 'type': 'if_statement', 'children': ['259', '278']}, {'id': '259', 'type': 'call', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'all'}, {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'list_comprehension', 'children': ['263', '275']}, {'id': '263', 'type': 'comparison_operator', 'children': ['264', '272'], 'value': 'in'}; {'id': '264', 'type': 'subscript', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '266', 'type': 'call', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '272', 'type': 'subscript', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '275', 'type': 'for_in_clause', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '278', 'type': 'block', 'children': ['279', '294', '319']}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'assignment', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '282', 'type': 'call', 'children': ['283', '286']}, {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'string', 'children': [], 'value': '"_"'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '286', 'type': 'argument_list', 'children': ['287']}, {'id': '287', 'type': 'list_comprehension', 'children': ['288', '291']}; {'id': '288', 'type': 'subscript', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '291', 'type': 'for_in_clause', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'idx_to_test'}; {'id': '294', 'type': 'try_statement', 'children': ['295', '304']}, {'id': '295', 'type': 'block', 'children': ['296']}; {'id': '296', 'type': 'assert_statement', 'children': ['297']}, {'id': '297', 'type': 'comparison_operator', 'children': ['298', '299'], 'value': 'in'}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '299', 'type': 'call', 'children': ['300', '303']}; {'id': '300', 'type': 'attribute', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '303', 'type': 'argument_list', 'children': []}; {'id': '304', 'type': 'except_clause', 'children': ['305', '306']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'AssertionError'}; {'id': '306', 'type': 'block', 'children': ['307']}, {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'assignment', 'children': ['309', '312']}, {'id': '309', 'type': 'subscript', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '312', 'type': 'call', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'DataCategory'}; {'id': '314', 'type': 'argument_list', 'children': ['315', '318']}, {'id': '315', 'type': 'call', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '317', 'type': 'argument_list', 'children': []}; {'id': '318', 'type': 'dictionary', 'children': []}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'call', 'children': ['321', '328']}, {'id': '321', 'type': 'attribute', 'children': ['322', '327']}; {'id': '322', 'type': 'attribute', 'children': ['323', '326']}, {'id': '323', 'type': 'subscript', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'sids'}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '328', 'type': 'argument_list', 'children': ['329']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'sid'}; {'id': '330', 'type': 'try_statement', 'children': ['331', '339', '358']}, {'id': '331', 'type': 'block', 'children': ['332']}; {'id': '332', 'type': 'assert_statement', 'children': ['333']}, {'id': '333', 'type': 'comparison_operator', 'children': ['334', '338'], 'value': '>'}; {'id': '334', 'type': 'call', 'children': ['335', '336']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '336', 'type': 'argument_list', 'children': ['337']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '338', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '339', 'type': 'except_clause', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'AssertionError'}, {'id': '341', 'type': 'block', 'children': ['342']}; {'id': '342', 'type': 'return_statement', 'children': ['343']}, {'id': '343', 'type': 'dictionary', 'children': ['344']}; {'id': '344', 'type': 'pair', 'children': ['345', '346']}, {'id': '345', 'type': 'string', 'children': [], 'value': '"default"'}; {'id': '346', 'type': 'call', 'children': ['347', '348']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'DataCategory'}; {'id': '348', 'type': 'argument_list', 'children': ['349', '357']}, {'id': '349', 'type': 'call', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '351', 'type': 'argument_list', 'children': ['352']}; {'id': '352', 'type': 'call', 'children': ['353', '356']}, {'id': '353', 'type': 'attribute', 'children': ['354', '355']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'imap'}, {'id': '355', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '356', 'type': 'argument_list', 'children': []}, {'id': '357', 'type': 'dictionary', 'children': []}; {'id': '358', 'type': 'else_clause', 'children': ['359']}, {'id': '359', 'type': 'block', 'children': ['360']}; {'id': '360', 'type': 'return_statement', 'children': ['361']}, {'id': '361', 'type': 'identifier', 'children': [], 'value': 'table'} | def gather_categories(imap, header, categories=None):
if categories is None:
return {"default": DataCategory(set(imap.keys()), {})}
cat_ids = [header.index(cat)
for cat in categories if cat in header and "=" not in cat]
table = OrderedDict()
conditions = defaultdict(set)
for i, cat in enumerate(categories):
if "=" in cat and cat.split("=")[0] in header:
cat_name = header[header.index(cat.split("=")[0])]
conditions[cat_name].add(cat.split("=")[1])
if not cat_ids and not conditions:
return {"default": DataCategory(set(imap.keys()), {})}
if cat_ids and not conditions:
for sid, row in imap.items():
cat_name = "_".join([row[cid] for cid in cat_ids])
if cat_name not in table:
table[cat_name] = DataCategory(set(), {})
table[cat_name].sids.add(sid)
return table
cond_ids = set()
for k in conditions:
try:
cond_ids.add(header.index(k))
except ValueError:
continue
idx_to_test = set(cat_ids).union(cond_ids)
for sid, row in imap.items():
if all([row[header.index(c)] in conditions[c] for c in conditions]):
key = "_".join([row[idx] for idx in idx_to_test])
try:
assert key in table.keys()
except AssertionError:
table[key] = DataCategory(set(), {})
table[key].sids.add(sid)
try:
assert len(table) > 0
except AssertionError:
return {"default": DataCategory(set(imap.keys()), {})}
else:
return table |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'color_mapping'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sample_map'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'group_column'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'color_column'}, {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '17', '27', '99']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'group_colors'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'}; {'id': '16', 'type': 'argument_list', 'children': []}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'group_gather'}; {'id': '20', 'type': 'call', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'gather_categories'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '24', '25']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'sample_map'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '25', 'type': 'list', 'children': ['26'], 'value': '[group_column]'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'group_column'}, {'id': '27', 'type': 'if_statement', 'children': ['28', '31', '72']}; {'id': '28', 'type': 'comparison_operator', 'children': ['29', '30'], 'value': 'is'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'color_column'}; {'id': '30', 'type': 'None', 'children': []}, {'id': '31', 'type': 'block', 'children': ['32', '42']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'color_gather'}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'gather_categories'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '39', '40']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'sample_map'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '40', 'type': 'list', 'children': ['41'], 'value': '[color_column]'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'color_column'}; {'id': '42', 'type': 'for_statement', 'children': ['43', '44', '45']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'group_gather'}, {'id': '45', 'type': 'block', 'children': ['46']}; {'id': '46', 'type': 'for_statement', 'children': ['47', '48', '49']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'color_gather'}, {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'if_statement', 'children': ['51', '65']}, {'id': '51', 'type': 'call', 'children': ['52', '59']}; {'id': '52', 'type': 'attribute', 'children': ['53', '58']}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'subscript', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'group_gather'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'sids'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'intersection'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'attribute', 'children': ['61', '64']}, {'id': '61', 'type': 'subscript', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'color_gather'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'sids'}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'assignment', 'children': ['68', '71']}; {'id': '68', 'type': 'subscript', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'group_colors'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '72', 'type': 'else_clause', 'children': ['73']}, {'id': '73', 'type': 'block', 'children': ['74', '85']}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'bcolors'}, {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'cycle'}, {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'Set3_12'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'hex_colors'}, {'id': '85', 'type': 'for_statement', 'children': ['86', '87', '88']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'group_gather'}; {'id': '88', 'type': 'block', 'children': ['89']}, {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '94']}, {'id': '91', 'type': 'subscript', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'group_colors'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '94', 'type': 'call', 'children': ['95', '98']}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'bcolors'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '98', 'type': 'argument_list', 'children': []}, {'id': '99', 'type': 'return_statement', 'children': ['100']} | def color_mapping(sample_map, header, group_column, color_column=None):
group_colors = OrderedDict()
group_gather = gather_categories(sample_map, header, [group_column])
if color_column is not None:
color_gather = gather_categories(sample_map, header, [color_column])
for group in group_gather:
for color in color_gather:
if group_gather[group].sids.intersection(color_gather[color].sids):
group_colors[group] = color
else:
bcolors = itertools.cycle(Set3_12.hex_colors)
for group in group_gather:
group_colors[group] = bcolors.next()
return group_colors |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '29']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'shuffle_genome'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '12', '15', '16', '19', '22', '23', '26']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'genome'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'fraction'}; {'id': '8', 'type': 'call', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '10', 'type': 'argument_list', 'children': ['11']}, {'id': '11', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'plot'}; {'id': '14', 'type': 'True', 'children': []}, {'id': '15', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'alpha'}; {'id': '18', 'type': 'float', 'children': [], 'value': '0.1'}, {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'beta'}, {'id': '21', 'type': 'integer', 'children': [], 'value': '100000'}; {'id': '22', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'min_length'}, {'id': '25', 'type': 'integer', 'children': [], 'value': '1000'}; {'id': '26', 'type': 'default_parameter', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'max_length'}; {'id': '28', 'type': 'integer', 'children': [], 'value': '200000'}, {'id': '29', 'type': 'block', 'children': ['30', '39', '60', '67', '71', '152', '159', '242']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '33', 'type': 'binary_operator', 'children': ['34', '35'], 'value': '%'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'>randomized_%s'"}, {'id': '35', 'type': 'parenthesized_expression', 'children': ['36'], 'value': '()'}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'genome'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}, {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'string', 'children': [], 'value': "''"}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'list_comprehension', 'children': ['51', '54']}, {'id': '51', 'type': 'subscript', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '53', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '54', 'type': 'for_in_clause', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'parse_fasta'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'genome'}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'length'}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'sequence'}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'shuffled'}; {'id': '70', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '71', 'type': 'while_statement', 'children': ['72', '75']}; {'id': '72', 'type': 'comparison_operator', 'children': ['73', '74'], 'value': 'is'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '74', 'type': 'False', 'children': []}, {'id': '75', 'type': 'block', 'children': ['76', '89', '99', '126', '134', '146']}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '79', 'type': 'call', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'random'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'gammavariate'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'alpha'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'beta'}, {'id': '89', 'type': 'if_statement', 'children': ['90', '97']}; {'id': '90', 'type': 'boolean_operator', 'children': ['91', '94'], 'value': 'or'}, {'id': '91', 'type': 'comparison_operator', 'children': ['92', '93'], 'value': '<='}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'min_length'}; {'id': '94', 'type': 'comparison_operator', 'children': ['95', '96'], 'value': '>='}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'max_length'}, {'id': '97', 'type': 'block', 'children': ['98']}; {'id': '98', 'type': 'continue_statement', 'children': []}, {'id': '99', 'type': 'if_statement', 'children': ['100', '106', '115']}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '105'], 'value': '<'}, {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'sequence'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '106', 'type': 'block', 'children': ['107']}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '112', 'type': 'slice', 'children': ['113', '114']}, {'id': '113', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '114', 'type': 'colon', 'children': []}, {'id': '115', 'type': 'else_clause', 'children': ['116']}; {'id': '116', 'type': 'block', 'children': ['117']}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '122', 'type': 'slice', 'children': ['123', '124', '125']}, {'id': '123', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '124', 'type': 'colon', 'children': []}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'sequence'}, {'id': '129', 'type': 'subscript', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'sequence'}, {'id': '131', 'type': 'slice', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '133', 'type': 'colon', 'children': []}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'call', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'shuffled'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'string', 'children': [], 'value': "''"}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '146', 'type': 'if_statement', 'children': ['147', '150']}, {'id': '147', 'type': 'comparison_operator', 'children': ['148', '149'], 'value': '=='}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'sequence'}, {'id': '149', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'break_statement', 'children': []}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'random'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'shuffle'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'shuffled'}, {'id': '159', 'type': 'if_statement', 'children': ['160', '166', '171']}; {'id': '160', 'type': 'comparison_operator', 'children': ['161', '162'], 'value': '=='}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'fraction'}; {'id': '162', 'type': 'call', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}, {'id': '165', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '166', 'type': 'block', 'children': ['167']}, {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'subset'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'shuffled'}, {'id': '171', 'type': 'else_clause', 'children': ['172']}; {'id': '172', 'type': 'block', 'children': ['173', '184', '192']}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'max_pieces'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'binary_operator', 'children': ['180', '183'], 'value': '/'}; {'id': '180', 'type': 'binary_operator', 'children': ['181', '182'], 'value': '*'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'length'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'fraction'}, {'id': '183', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '189']}; {'id': '186', 'type': 'pattern_list', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'subset'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'total'}, {'id': '189', 'type': 'expression_list', 'children': ['190', '191']}; {'id': '190', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '191', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '192', 'type': 'for_statement', 'children': ['193', '194', '195']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'fragment'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'shuffled'}, {'id': '195', 'type': 'block', 'children': ['196', '203']}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'length'}, {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'fragment'}, {'id': '203', 'type': 'if_statement', 'children': ['204', '209', '221']}; {'id': '204', 'type': 'comparison_operator', 'children': ['205', '208'], 'value': '<='}, {'id': '205', 'type': 'binary_operator', 'children': ['206', '207'], 'value': '+'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'total'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'length'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'max_pieces'}, {'id': '209', 'type': 'block', 'children': ['210', '217']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'call', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'subset'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '215', 'type': 'argument_list', 'children': ['216']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'fragment'}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'augmented_assignment', 'children': ['219', '220'], 'value': '+='}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'length'}, {'id': '221', 'type': 'else_clause', 'children': ['222']}; {'id': '222', 'type': 'block', 'children': ['223', '229', '241']}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'diff'}; {'id': '226', 'type': 'binary_operator', 'children': ['227', '228'], 'value': '-'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'max_pieces'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'total'}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'subset'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}, {'id': '235', 'type': 'subscript', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'fragment'}, {'id': '237', 'type': 'slice', 'children': ['238', '239', '240']}; {'id': '238', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '239', 'type': 'colon', 'children': []}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'diff'}, {'id': '241', 'type': 'break_statement', 'children': []}; {'id': '242', 'type': 'if_statement', 'children': ['243', '246', '257']}, {'id': '243', 'type': 'comparison_operator', 'children': ['244', '245'], 'value': 'is'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'cat'}, {'id': '245', 'type': 'True', 'children': []}; {'id': '246', 'type': 'block', 'children': ['247']}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'yield', 'children': ['249']}, {'id': '249', 'type': 'list', 'children': ['250', '251'], 'value': "[header, ''.join(subset)]"}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '251', 'type': 'call', 'children': ['252', '255']}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}, {'id': '253', 'type': 'string', 'children': [], 'value': "''"}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '255', 'type': 'argument_list', 'children': ['256']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'subset'}, {'id': '257', 'type': 'else_clause', 'children': ['258']}; {'id': '258', 'type': 'block', 'children': ['259']}, {'id': '259', 'type': 'for_statement', 'children': ['260', '263', '267']}; {'id': '260', 'type': 'pattern_list', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'subset'}, {'id': '267', 'type': 'block', 'children': ['268']}; {'id': '268', 'type': 'expression_statement', 'children': ['269']}, {'id': '269', 'type': 'yield', 'children': ['270']}; {'id': '270', 'type': 'list', 'children': ['271', '276'], 'value': "['%s fragment:%s' % (header, i), seq]"}, {'id': '271', 'type': 'binary_operator', 'children': ['272', '273'], 'value': '%'}; {'id': '272', 'type': 'string', 'children': [], 'value': "'%s fragment:%s'"}, {'id': '273', 'type': 'tuple', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'i'} | def shuffle_genome(genome, cat, fraction = float(100), plot = True, \
alpha = 0.1, beta = 100000, \
min_length = 1000, max_length = 200000):
header = '>randomized_%s' % (genome.name)
sequence = list(''.join([i[1] for i in parse_fasta(genome)]))
length = len(sequence)
shuffled = []
while sequence is not False:
s = int(random.gammavariate(alpha, beta))
if s <= min_length or s >= max_length:
continue
if len(sequence) < s:
seq = sequence[0:]
else:
seq = sequence[0:s]
sequence = sequence[s:]
shuffled.append(''.join(seq))
if sequence == []:
break
random.shuffle(shuffled)
if fraction == float(100):
subset = shuffled
else:
max_pieces = int(length * fraction/100)
subset, total = [], 0
for fragment in shuffled:
length = len(fragment)
if total + length <= max_pieces:
subset.append(fragment)
total += length
else:
diff = max_pieces - total
subset.append(fragment[0:diff])
break
if cat is True:
yield [header, ''.join(subset)]
else:
for i, seq in enumerate(subset):
yield ['%s fragment:%s' % (header, i), seq] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sam2fastq'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'singles'}, {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'force'}; {'id': '10', 'type': 'False', 'children': []}, {'id': '11', 'type': 'block', 'children': ['12', '20']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}, {'id': '13', 'type': 'assignment', 'children': ['14', '17']}; {'id': '14', 'type': 'pattern_list', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '17', 'type': 'expression_list', 'children': ['18', '19']}; {'id': '18', 'type': 'None', 'children': []}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'for_statement', 'children': ['21', '22', '23']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '23', 'type': 'block', 'children': ['24', '35', '47', '82', '97', '109', '126', '170', '258']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '33']}, {'id': '25', 'type': 'comparison_operator', 'children': ['26', '32'], 'value': 'is'}; {'id': '26', 'type': 'call', 'children': ['27', '30']}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}, {'id': '31', 'type': 'string', 'children': [], 'value': "'@'"}; {'id': '32', 'type': 'True', 'children': []}, {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'continue_statement', 'children': []}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '38', 'type': 'call', 'children': ['39', '46']}, {'id': '39', 'type': 'attribute', 'children': ['40', '45']}; {'id': '40', 'type': 'call', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'strip'}; {'id': '44', 'type': 'argument_list', 'children': []}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '46', 'type': 'argument_list', 'children': []}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '50', 'type': 'list_comprehension', 'children': ['51', '57', '58']}, {'id': '51', 'type': 'conditional_expression', 'children': ['52', '53', '56'], 'value': 'if'}; {'id': '52', 'type': 'True', 'children': []}, {'id': '53', 'type': 'comparison_operator', 'children': ['54', '55'], 'value': '=='}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '55', 'type': 'string', 'children': [], 'value': "'1'"}; {'id': '56', 'type': 'False', 'children': []}, {'id': '57', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '58', 'type': 'for_in_clause', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '60', 'type': 'subscript', 'children': ['61', '77']}, {'id': '61', 'type': 'subscript', 'children': ['62', '76']}; {'id': '62', 'type': 'call', 'children': ['63', '74']}, {'id': '63', 'type': 'attribute', 'children': ['64', '73']}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'bin'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'string', 'children': [], 'value': "'b'"}; {'id': '76', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '77', 'type': 'slice', 'children': ['78', '79', '80']}; {'id': '78', 'type': 'colon', 'children': []}, {'id': '79', 'type': 'colon', 'children': []}; {'id': '80', 'type': 'unary_operator', 'children': ['81'], 'value': '-'}, {'id': '81', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '82', 'type': 'while_statement', 'children': ['83', '89']}, {'id': '83', 'type': 'comparison_operator', 'children': ['84', '88'], 'value': '<'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '88', 'type': 'integer', 'children': [], 'value': '8'}, {'id': '89', 'type': 'block', 'children': ['90']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'False', 'children': []}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '108']}, {'id': '99', 'type': 'pattern_list', 'children': ['100', '101', '102', '103', '104', '105', '106', '107']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'pair'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'proper'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'na'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'nap'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'rev'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'mrev'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'left'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'bit'}, {'id': '109', 'type': 'if_statement', 'children': ['110', '113']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'is'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '112', 'type': 'False', 'children': []}, {'id': '113', 'type': 'block', 'children': ['114', '125']}; {'id': '114', 'type': 'if_statement', 'children': ['115', '118']}, {'id': '115', 'type': 'comparison_operator', 'children': ['116', '117'], 'value': 'is'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'singles'}, {'id': '117', 'type': 'True', 'children': []}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'print_single'}; {'id': '122', 'type': 'argument_list', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'rev'}, {'id': '125', 'type': 'continue_statement', 'children': []}; {'id': '126', 'type': 'if_statement', 'children': ['127', '130', '156']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '129'], 'value': 'is'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'rev'}, {'id': '129', 'type': 'True', 'children': []}; {'id': '130', 'type': 'block', 'children': ['131', '144']}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '134', 'type': 'subscript', 'children': ['135', '143']}, {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'rc'}, {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'list', 'children': ['139', '140'], 'value': "['', line[9]]"}, {'id': '139', 'type': 'string', 'children': [], 'value': "''"}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '9'}, {'id': '143', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'qual'}, {'id': '147', 'type': 'subscript', 'children': ['148', '151']}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '150', 'type': 'integer', 'children': [], 'value': '10'}, {'id': '151', 'type': 'slice', 'children': ['152', '153', '154']}; {'id': '152', 'type': 'colon', 'children': []}, {'id': '153', 'type': 'colon', 'children': []}; {'id': '154', 'type': 'unary_operator', 'children': ['155'], 'value': '-'}, {'id': '155', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '156', 'type': 'else_clause', 'children': ['157']}, {'id': '157', 'type': 'block', 'children': ['158', '164']}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'assignment', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '161', 'type': 'subscript', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '163', 'type': 'integer', 'children': [], 'value': '9'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'qual'}, {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '169', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '170', 'type': 'if_statement', 'children': ['171', '174']}, {'id': '171', 'type': 'comparison_operator', 'children': ['172', '173'], 'value': 'is'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'left'}, {'id': '173', 'type': 'True', 'children': []}; {'id': '174', 'type': 'block', 'children': ['175', '213', '223', '239']}, {'id': '175', 'type': 'if_statement', 'children': ['176', '183']}; {'id': '176', 'type': 'boolean_operator', 'children': ['177', '180'], 'value': 'and'}, {'id': '177', 'type': 'comparison_operator', 'children': ['178', '179'], 'value': 'is'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'L'}, {'id': '179', 'type': 'None', 'children': []}; {'id': '180', 'type': 'comparison_operator', 'children': ['181', '182'], 'value': 'is'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'force'}; {'id': '182', 'type': 'False', 'children': []}, {'id': '183', 'type': 'block', 'children': ['184', '194', '209']}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'call', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '187', 'type': 'argument_list', 'children': ['188', '189']}; {'id': '188', 'type': 'string', 'children': [], 'value': "'sam file is not sorted'"}, {'id': '189', 'type': 'keyword_argument', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'stderr'}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'call', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '197', 'type': 'argument_list', 'children': ['198', '204']}; {'id': '198', 'type': 'binary_operator', 'children': ['199', '200'], 'value': '%'}, {'id': '199', 'type': 'string', 'children': [], 'value': "'\\te.g.: %s'"}; {'id': '200', 'type': 'parenthesized_expression', 'children': ['201'], 'value': '()'}, {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '203', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '204', 'type': 'keyword_argument', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'stderr'}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'call', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'exit'}; {'id': '212', 'type': 'argument_list', 'children': []}, {'id': '213', 'type': 'if_statement', 'children': ['214', '217']}; {'id': '214', 'type': 'comparison_operator', 'children': ['215', '216'], 'value': 'is'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '216', 'type': 'None', 'children': []}, {'id': '217', 'type': 'block', 'children': ['218', '222']}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}, {'id': '219', 'type': 'assignment', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'L'}, {'id': '221', 'type': 'None', 'children': []}; {'id': '222', 'type': 'continue_statement', 'children': []}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '226', 'type': 'list', 'children': ['227', '232', '233', '238'], 'value': "['@%s' % line[0], seq, '+%s' % line[0], qual]"}, {'id': '227', 'type': 'binary_operator', 'children': ['228', '229'], 'value': '%'}; {'id': '228', 'type': 'string', 'children': [], 'value': "'@%s'"}, {'id': '229', 'type': 'subscript', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '231', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '233', 'type': 'binary_operator', 'children': ['234', '235'], 'value': '%'}; {'id': '234', 'type': 'string', 'children': [], 'value': "'+%s'"}, {'id': '235', 'type': 'subscript', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '237', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'qual'}, {'id': '239', 'type': 'if_statement', 'children': ['240', '243']}; {'id': '240', 'type': 'comparison_operator', 'children': ['241', '242'], 'value': 'is'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '242', 'type': 'None', 'children': []}, {'id': '243', 'type': 'block', 'children': ['244', '247', '250']}; {'id': '244', 'type': 'expression_statement', 'children': ['245']}, {'id': '245', 'type': 'yield', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'L'}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'yield', 'children': ['249']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}, {'id': '251', 'type': 'assignment', 'children': ['252', '255']}; {'id': '252', 'type': 'pattern_list', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '255', 'type': 'expression_list', 'children': ['256', '257']}; {'id': '256', 'type': 'None', 'children': []}, {'id': '257', 'type': 'None', 'children': []}; {'id': '258', 'type': 'if_statement', 'children': ['259', '262']}, {'id': '259', 'type': 'comparison_operator', 'children': ['260', '261'], 'value': 'is'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'right'}, {'id': '261', 'type': 'True', 'children': []}; {'id': '262', 'type': 'block', 'children': ['263', '301', '311', '327']}, {'id': '263', 'type': 'if_statement', 'children': ['264', '271']}; {'id': '264', 'type': 'boolean_operator', 'children': ['265', '268'], 'value': 'and'}, {'id': '265', 'type': 'comparison_operator', 'children': ['266', '267'], 'value': 'is'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '267', 'type': 'None', 'children': []}; {'id': '268', 'type': 'comparison_operator', 'children': ['269', '270'], 'value': 'is'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'force'}; {'id': '270', 'type': 'False', 'children': []}, {'id': '271', 'type': 'block', 'children': ['272', '282', '297']}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}, {'id': '273', 'type': 'call', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '275', 'type': 'argument_list', 'children': ['276', '277']}; {'id': '276', 'type': 'string', 'children': [], 'value': "'sam file is not sorted'"}, {'id': '277', 'type': 'keyword_argument', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '279', 'type': 'attribute', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'stderr'}; {'id': '282', 'type': 'expression_statement', 'children': ['283']}, {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '285', 'type': 'argument_list', 'children': ['286', '292']}; {'id': '286', 'type': 'binary_operator', 'children': ['287', '288'], 'value': '%'}, {'id': '287', 'type': 'string', 'children': [], 'value': "'\\te.g.: %s'"}; {'id': '288', 'type': 'parenthesized_expression', 'children': ['289'], 'value': '()'}, {'id': '289', 'type': 'subscript', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '291', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '292', 'type': 'keyword_argument', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '294', 'type': 'attribute', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'stderr'}, {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'call', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'exit'}; {'id': '300', 'type': 'argument_list', 'children': []}, {'id': '301', 'type': 'if_statement', 'children': ['302', '305']}; {'id': '302', 'type': 'comparison_operator', 'children': ['303', '304'], 'value': 'is'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '304', 'type': 'None', 'children': []}, {'id': '305', 'type': 'block', 'children': ['306', '310']}; {'id': '306', 'type': 'expression_statement', 'children': ['307']}, {'id': '307', 'type': 'assignment', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '309', 'type': 'None', 'children': []}; {'id': '310', 'type': 'continue_statement', 'children': []}, {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '314', 'type': 'list', 'children': ['315', '320', '321', '326'], 'value': "['@%s' % line[0], seq, '+%s' % line[0], qual]"}, {'id': '315', 'type': 'binary_operator', 'children': ['316', '317'], 'value': '%'}; {'id': '316', 'type': 'string', 'children': [], 'value': "'@%s'"}, {'id': '317', 'type': 'subscript', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '319', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '321', 'type': 'binary_operator', 'children': ['322', '323'], 'value': '%'}; {'id': '322', 'type': 'string', 'children': [], 'value': "'+%s'"}, {'id': '323', 'type': 'subscript', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '325', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'qual'}, {'id': '327', 'type': 'if_statement', 'children': ['328', '331']}; {'id': '328', 'type': 'comparison_operator', 'children': ['329', '330'], 'value': 'is'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '330', 'type': 'None', 'children': []}, {'id': '331', 'type': 'block', 'children': ['332', '335', '338']}; {'id': '332', 'type': 'expression_statement', 'children': ['333']}, {'id': '333', 'type': 'yield', 'children': ['334']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'L'}, {'id': '335', 'type': 'expression_statement', 'children': ['336']}; {'id': '336', 'type': 'yield', 'children': ['337']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '338', 'type': 'expression_statement', 'children': ['339']}, {'id': '339', 'type': 'assignment', 'children': ['340', '343']}; {'id': '340', 'type': 'pattern_list', 'children': ['341', '342']}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '343', 'type': 'expression_list', 'children': ['344', '345']}; {'id': '344', 'type': 'None', 'children': []}, {'id': '345', 'type': 'None', 'children': []} | def sam2fastq(sam, singles = False, force = False):
L, R = None, None
for line in sam:
if line.startswith('@') is True:
continue
line = line.strip().split()
bit = [True if i == '1' else False \
for i in bin(int(line[1])).split('b')[1][::-1]]
while len(bit) < 8:
bit.append(False)
pair, proper, na, nap, rev, mrev, left, right = bit
if pair is False:
if singles is True:
print_single(line, rev)
continue
if rev is True:
seq = rc(['', line[9]])[1]
qual = line[10][::-1]
else:
seq = line[9]
qual = line[10]
if left is True:
if L is not None and force is False:
print('sam file is not sorted', file = sys.stderr)
print('\te.g.: %s' % (line[0]), file = sys.stderr)
exit()
if L is not None:
L = None
continue
L = ['@%s' % line[0], seq, '+%s' % line[0], qual]
if R is not None:
yield L
yield R
L, R = None, None
if right is True:
if R is not None and force is False:
print('sam file is not sorted', file = sys.stderr)
print('\te.g.: %s' % (line[0]), file = sys.stderr)
exit()
if R is not None:
R = None
continue
R = ['@%s' % line[0], seq, '+%s' % line[0], qual]
if L is not None:
yield L
yield R
L, R = None, None |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_sam'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '6', 'type': 'block', 'children': ['7', '29', '141']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'tempdir'}; {'id': '10', 'type': 'binary_operator', 'children': ['11', '12'], 'value': '%'}, {'id': '11', 'type': 'string', 'children': [], 'value': "'%s/'"}; {'id': '12', 'type': 'parenthesized_expression', 'children': ['13'], 'value': '()'}, {'id': '13', 'type': 'subscript', 'children': ['14', '28']}; {'id': '14', 'type': 'call', 'children': ['15', '25']}, {'id': '15', 'type': 'attribute', 'children': ['16', '24']}; {'id': '16', 'type': 'call', 'children': ['17', '22']}, {'id': '17', 'type': 'attribute', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'abspath'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'sam'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'rsplit'}, {'id': '25', 'type': 'argument_list', 'children': ['26', '27']}; {'id': '26', 'type': 'string', 'children': [], 'value': "'/'"}, {'id': '27', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '28', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '29', 'type': 'if_statement', 'children': ['30', '33', '119']}; {'id': '30', 'type': 'comparison_operator', 'children': ['31', '32'], 'value': 'is'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '32', 'type': 'True', 'children': []}, {'id': '33', 'type': 'block', 'children': ['34', '49', '112']}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'mapping'}, {'id': '37', 'type': 'binary_operator', 'children': ['38', '39'], 'value': '%'}; {'id': '38', 'type': 'string', 'children': [], 'value': "'%s.sorted.sam'"}, {'id': '39', 'type': 'parenthesized_expression', 'children': ['40'], 'value': '()'}; {'id': '40', 'type': 'subscript', 'children': ['41', '48']}, {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'sam'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'rsplit'}, {'id': '45', 'type': 'argument_list', 'children': ['46', '47']}; {'id': '46', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '47', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '48', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '49', 'type': 'if_statement', 'children': ['50', '53', '79']}; {'id': '50', 'type': 'comparison_operator', 'children': ['51', '52'], 'value': '!='}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'sam'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'-'"}, {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'if_statement', 'children': ['55', '65']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '64'], 'value': 'is'}; {'id': '56', 'type': 'call', 'children': ['57', '62']}, {'id': '57', 'type': 'attribute', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '64', 'type': 'False', 'children': []}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'system'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'binary_operator', 'children': ['73', '74'], 'value': '%'}, {'id': '73', 'type': 'string', 'children': [], 'value': '"\\\n sort -k1 --buffer-size=%sG -T %s -o %s %s\\\n "'}; {'id': '74', 'type': 'tuple', 'children': ['75', '76', '77', '78']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'sbuffer'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'tempdir'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '79', 'type': 'else_clause', 'children': ['80']}; {'id': '80', 'type': 'block', 'children': ['81', '85', '106']}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '84', 'type': 'string', 'children': [], 'value': "'stdin-sam.sorted.sam'"}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '88', 'type': 'call', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'Popen'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '98', '103']}, {'id': '91', 'type': 'binary_operator', 'children': ['92', '93', '94'], 'value': '%'}; {'id': '92', 'type': 'string', 'children': [], 'value': '"sort -k1 --buffer-size=%sG -T %s -o %s"'}, {'id': '93', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '94', 'type': 'tuple', 'children': ['95', '96', '97']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'sbuffer'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'tempdir'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '98', 'type': 'keyword_argument', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'stdin'}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'stdin'}, {'id': '103', 'type': 'keyword_argument', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'shell'}, {'id': '105', 'type': 'True', 'children': []}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'communicate'}, {'id': '111', 'type': 'argument_list', 'children': []}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'mapping'}, {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'mapping'}, {'id': '119', 'type': 'else_clause', 'children': ['120']}; {'id': '120', 'type': 'block', 'children': ['121']}, {'id': '121', 'type': 'if_statement', 'children': ['122', '125', '132']}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '124'], 'value': '=='}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'sam'}; {'id': '124', 'type': 'string', 'children': [], 'value': "'-'"}, {'id': '125', 'type': 'block', 'children': ['126']}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'mapping'}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'stdin'}; {'id': '132', 'type': 'else_clause', 'children': ['133']}, {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'mapping'}, {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '141', 'type': 'return_statement', 'children': ['142']} | def sort_sam(sam, sort):
tempdir = '%s/' % (os.path.abspath(sam).rsplit('/', 1)[0])
if sort is True:
mapping = '%s.sorted.sam' % (sam.rsplit('.', 1)[0])
if sam != '-':
if os.path.exists(mapping) is False:
os.system("\
sort -k1 --buffer-size=%sG -T %s -o %s %s\
" % (sbuffer, tempdir, mapping, sam))
else:
mapping = 'stdin-sam.sorted.sam'
p = Popen("sort -k1 --buffer-size=%sG -T %s -o %s" \
% (sbuffer, tempdir, mapping), stdin = sys.stdin, shell = True)
p.communicate()
mapping = open(mapping)
else:
if sam == '-':
mapping = sys.stdin
else:
mapping = open(sam)
return mapping |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'crossmap'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fas'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'reads'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'options'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'no_shrink'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'keepDB'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'cluster'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '12', 'type': 'block', 'children': ['13', '22', '26', '213']}, {'id': '13', 'type': 'if_statement', 'children': ['14', '17']}; {'id': '14', 'type': 'comparison_operator', 'children': ['15', '16'], 'value': 'is'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'cluster'}; {'id': '16', 'type': 'True', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'threads'}, {'id': '21', 'type': 'string', 'children': [], 'value': "'48'"}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'btc'}, {'id': '25', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '26', 'type': 'for_statement', 'children': ['27', '28', '29']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'fa'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'fas'}, {'id': '29', 'type': 'block', 'children': ['30', '38', '45']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'btd'}, {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'bowtiedb'}, {'id': '35', 'type': 'argument_list', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'fa'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'keepDB'}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '44']}; {'id': '40', 'type': 'pattern_list', 'children': ['41', '42', '43']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'F'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'U'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'reads'}, {'id': '45', 'type': 'if_statement', 'children': ['46', '49', '142']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'is'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'F'}; {'id': '48', 'type': 'False', 'children': []}, {'id': '49', 'type': 'block', 'children': ['50', '59']}; {'id': '50', 'type': 'if_statement', 'children': ['51', '54']}, {'id': '51', 'type': 'comparison_operator', 'children': ['52', '53'], 'value': 'is'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '53', 'type': 'False', 'children': []}; {'id': '54', 'type': 'block', 'children': ['55']}, {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '58', 'type': 'False', 'children': []}, {'id': '59', 'type': 'for_statement', 'children': ['60', '63', '67']}; {'id': '60', 'type': 'pattern_list', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'F'}, {'id': '67', 'type': 'block', 'children': ['68', '74', '85', '125']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '71', 'type': 'subscript', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '74', 'type': 'if_statement', 'children': ['75', '78']}, {'id': '75', 'type': 'comparison_operator', 'children': ['76', '77'], 'value': 'is'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '77', 'type': 'False', 'children': []}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '82', 'type': 'subscript', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'U'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'sam'}; {'id': '88', 'type': 'binary_operator', 'children': ['89', '90'], 'value': '%'}, {'id': '89', 'type': 'string', 'children': [], 'value': "'%s/%s-vs-%s'"}; {'id': '90', 'type': 'tuple', 'children': ['91', '96', '97', '107']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'getcwd'}, {'id': '95', 'type': 'argument_list', 'children': []}; {'id': '96', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '97', 'type': 'subscript', 'children': ['98', '105']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'fa'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'rsplit'}; {'id': '102', 'type': 'argument_list', 'children': ['103', '104']}, {'id': '103', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '104', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '105', 'type': 'unary_operator', 'children': ['106'], 'value': '-'}; {'id': '106', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '107', 'type': 'subscript', 'children': ['108', '124']}; {'id': '108', 'type': 'call', 'children': ['109', '121']}, {'id': '109', 'type': 'attribute', 'children': ['110', '120']}; {'id': '110', 'type': 'subscript', 'children': ['111', '118']}, {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'rsplit'}, {'id': '115', 'type': 'argument_list', 'children': ['116', '117']}; {'id': '116', 'type': 'string', 'children': [], 'value': "'/'"}, {'id': '117', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '118', 'type': 'unary_operator', 'children': ['119'], 'value': '-'}, {'id': '119', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'rsplit'}, {'id': '121', 'type': 'argument_list', 'children': ['122', '123']}; {'id': '122', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '123', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '124', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'btc'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'bowtie'}, {'id': '133', 'type': 'argument_list', 'children': ['134', '135', '136', '137', '138', '139', '140', '141']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'btd'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'no_shrink'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '142', 'type': 'else_clause', 'children': ['143']}, {'id': '143', 'type': 'block', 'children': ['144', '148', '152']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '147', 'type': 'False', 'children': []}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '151', 'type': 'False', 'children': []}; {'id': '152', 'type': 'for_statement', 'children': ['153', '154', '155']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '155', 'type': 'block', 'children': ['156', '196']}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'sam'}, {'id': '159', 'type': 'binary_operator', 'children': ['160', '161'], 'value': '%'}; {'id': '160', 'type': 'string', 'children': [], 'value': "'%s/%s-vs-%s'"}, {'id': '161', 'type': 'tuple', 'children': ['162', '167', '168', '178']}; {'id': '162', 'type': 'call', 'children': ['163', '166']}, {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'getcwd'}; {'id': '166', 'type': 'argument_list', 'children': []}, {'id': '167', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '168', 'type': 'subscript', 'children': ['169', '176']}, {'id': '169', 'type': 'call', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'fa'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'rsplit'}, {'id': '173', 'type': 'argument_list', 'children': ['174', '175']}; {'id': '174', 'type': 'string', 'children': [], 'value': "'/'"}, {'id': '175', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '176', 'type': 'unary_operator', 'children': ['177'], 'value': '-'}, {'id': '177', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '178', 'type': 'subscript', 'children': ['179', '195']}, {'id': '179', 'type': 'call', 'children': ['180', '192']}; {'id': '180', 'type': 'attribute', 'children': ['181', '191']}, {'id': '181', 'type': 'subscript', 'children': ['182', '189']}; {'id': '182', 'type': 'call', 'children': ['183', '186']}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'rsplit'}; {'id': '186', 'type': 'argument_list', 'children': ['187', '188']}, {'id': '187', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '188', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '189', 'type': 'unary_operator', 'children': ['190'], 'value': '-'}; {'id': '190', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'rsplit'}; {'id': '192', 'type': 'argument_list', 'children': ['193', '194']}, {'id': '193', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '194', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '195', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'btc'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'call', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'bowtie'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206', '207', '208', '209', '210', '211', '212']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'sam'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'btd'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'options'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'no_shrink'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'threads'}, {'id': '213', 'type': 'if_statement', 'children': ['214', '217', '240']}; {'id': '214', 'type': 'comparison_operator', 'children': ['215', '216'], 'value': 'is'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'cluster'}; {'id': '216', 'type': 'False', 'children': []}, {'id': '217', 'type': 'block', 'children': ['218']}; {'id': '218', 'type': 'for_statement', 'children': ['219', '220', '221']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'btc'}, {'id': '221', 'type': 'block', 'children': ['222', '234']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '225', 'type': 'call', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'Popen'}, {'id': '229', 'type': 'argument_list', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '231', 'type': 'keyword_argument', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'shell'}, {'id': '233', 'type': 'True', 'children': []}; {'id': '234', 'type': 'expression_statement', 'children': ['235']}, {'id': '235', 'type': 'call', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'communicate'}, {'id': '239', 'type': 'argument_list', 'children': []}; {'id': '240', 'type': 'else_clause', 'children': ['241']}, {'id': '241', 'type': 'block', 'children': ['242', '273']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '245', 'type': 'call', 'children': ['246', '249']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}, {'id': '247', 'type': 'string', 'children': [], 'value': "''"}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '249', 'type': 'generator_expression', 'children': ['250', '267']}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'random'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'choice'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}, {'id': '255', 'type': 'list_comprehension', 'children': ['256', '260']}; {'id': '256', 'type': 'call', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '260', 'type': 'for_in_clause', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '262', 'type': 'call', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '264', 'type': 'argument_list', 'children': ['265', '266']}, {'id': '265', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '266', 'type': 'integer', 'children': [], 'value': '9'}, {'id': '267', 'type': 'for_in_clause', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': '_'}, {'id': '269', 'type': 'call', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'integer', 'children': [], 'value': '5'}, {'id': '273', 'type': 'for_statement', 'children': ['274', '277', '286']}; {'id': '274', 'type': 'pattern_list', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'commands'}, {'id': '277', 'type': 'call', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '279', 'type': 'argument_list', 'children': ['280', '285']}; {'id': '280', 'type': 'call', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '282', 'type': 'argument_list', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'btc'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'nodes'}, {'id': '285', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '286', 'type': 'block', 'children': ['287', '304', '317', '323', '342']}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'bs'}; {'id': '290', 'type': 'call', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '292', 'type': 'argument_list', 'children': ['293', '303']}, {'id': '293', 'type': 'binary_operator', 'children': ['294', '295'], 'value': '%'}; {'id': '294', 'type': 'string', 'children': [], 'value': "'%s/crossmap-qsub.%s.%s.sh'"}, {'id': '295', 'type': 'tuple', 'children': ['296', '301', '302']}; {'id': '296', 'type': 'call', 'children': ['297', '300']}, {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'getcwd'}; {'id': '300', 'type': 'argument_list', 'children': []}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'ID'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '303', 'type': 'string', 'children': [], 'value': "'w'"}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'call', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '307', 'type': 'argument_list', 'children': ['308', '314']}; {'id': '308', 'type': 'call', 'children': ['309', '312']}, {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'string', 'children': [], 'value': "'\\n'"}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '312', 'type': 'argument_list', 'children': ['313']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'commands'}; {'id': '314', 'type': 'keyword_argument', 'children': ['315', '316']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'bs'}, {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'call', 'children': ['319', '322']}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'bs'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '322', 'type': 'argument_list', 'children': []}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'assignment', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '326', 'type': 'call', 'children': ['327', '330']}, {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'subprocess'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'Popen'}; {'id': '330', 'type': 'argument_list', 'children': ['331', '338', '339']}, {'id': '331', 'type': 'binary_operator', 'children': ['332', '333', '334'], 'value': '%'}; {'id': '332', 'type': 'string', 'children': [], 'value': "'qsub -V -N crossmap %s'"}, {'id': '333', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '334', 'type': 'parenthesized_expression', 'children': ['335'], 'value': '()'}, {'id': '335', 'type': 'attribute', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'bs'}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '338', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '339', 'type': 'keyword_argument', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'shell'}, {'id': '341', 'type': 'True', 'children': []}; {'id': '342', 'type': 'expression_statement', 'children': ['343']}, {'id': '343', 'type': 'call', 'children': ['344', '347']}; {'id': '344', 'type': 'attribute', 'children': ['345', '346']}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'communicate'}, {'id': '347', 'type': 'argument_list', 'children': []} | def crossmap(fas, reads, options, no_shrink, keepDB, threads, cluster, nodes):
if cluster is True:
threads = '48'
btc = []
for fa in fas:
btd = bowtiedb(fa, keepDB)
F, R, U = reads
if F is not False:
if U is False:
u = False
for i, f in enumerate(F):
r = R[i]
if U is not False:
u = U[i]
sam = '%s/%s-vs-%s' % (os.getcwd(), \
fa.rsplit('/', 1)[-1], f.rsplit('/', 1)[-1].rsplit('.', 3)[0])
btc.append(bowtie(sam, btd, f, r, u, options, no_shrink, threads))
else:
f = False
r = False
for u in U:
sam = '%s/%s-vs-%s' % (os.getcwd(), \
fa.rsplit('/', 1)[-1], u.rsplit('/', 1)[-1].rsplit('.', 3)[0])
btc.append(bowtie(sam, btd, f, r, u, options, no_shrink, threads))
if cluster is False:
for i in btc:
p = subprocess.Popen(i, shell = True)
p.communicate()
else:
ID = ''.join(random.choice([str(i) for i in range(0, 9)]) for _ in range(5))
for node, commands in enumerate(chunks(btc, nodes), 1):
bs = open('%s/crossmap-qsub.%s.%s.sh' % (os.getcwd(), ID, node), 'w')
print('\n'.join(commands), file=bs)
bs.close()
p = subprocess.Popen(\
'qsub -V -N crossmap %s' \
% (bs.name), \
shell = True)
p.communicate() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'bit_by_bit'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'in_data'}; {'id': '6', 'type': 'block', 'children': ['7', '25', '31', '97', '135', '152']}, {'id': '7', 'type': 'if_statement', 'children': ['8', '13']}; {'id': '8', 'type': 'call', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '10', 'type': 'argument_list', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'in_data'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'in_data'}, {'id': '17', 'type': 'list_comprehension', 'children': ['18', '22']}; {'id': '18', 'type': 'call', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'ord'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '22', 'type': 'for_in_clause', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'in_data'}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'NonDirectInit'}, {'id': '31', 'type': 'for_statement', 'children': ['32', '33', '34']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'octet'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'in_data'}; {'id': '34', 'type': 'block', 'children': ['35', '50']}, {'id': '35', 'type': 'if_statement', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'ReflectIn'}, {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'octet'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'reflect'}, {'id': '47', 'type': 'argument_list', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'octet'}, {'id': '49', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '50', 'type': 'for_statement', 'children': ['51', '52', '56']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '56', 'type': 'block', 'children': ['57', '65', '88']}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'topbit'}; {'id': '60', 'type': 'binary_operator', 'children': ['61', '62'], 'value': '&'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'MSB_Mask'}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '68', 'type': 'binary_operator', 'children': ['69', '78'], 'value': '|'}, {'id': '69', 'type': 'parenthesized_expression', 'children': ['70'], 'value': '()'}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '75'], 'value': '&'}, {'id': '71', 'type': 'parenthesized_expression', 'children': ['72'], 'value': '()'}; {'id': '72', 'type': 'binary_operator', 'children': ['73', '74'], 'value': '<<'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '74', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'Mask'}; {'id': '78', 'type': 'parenthesized_expression', 'children': ['79'], 'value': '()'}, {'id': '79', 'type': 'binary_operator', 'children': ['80', '87'], 'value': '&'}; {'id': '80', 'type': 'parenthesized_expression', 'children': ['81'], 'value': '()'}, {'id': '81', 'type': 'binary_operator', 'children': ['82', '83'], 'value': '>>'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'octet'}, {'id': '83', 'type': 'parenthesized_expression', 'children': ['84'], 'value': '()'}; {'id': '84', 'type': 'binary_operator', 'children': ['85', '86'], 'value': '-'}, {'id': '85', 'type': 'integer', 'children': [], 'value': '7'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '87', 'type': 'integer', 'children': [], 'value': '0x01'}; {'id': '88', 'type': 'if_statement', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'topbit'}; {'id': '90', 'type': 'block', 'children': ['91']}, {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'augmented_assignment', 'children': ['93', '94'], 'value': '^='}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'Poly'}, {'id': '97', 'type': 'for_statement', 'children': ['98', '99', '105']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'Width'}, {'id': '105', 'type': 'block', 'children': ['106', '114', '126']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'topbit'}, {'id': '109', 'type': 'binary_operator', 'children': ['110', '111'], 'value': '&'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'register'}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'MSB_Mask'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'register'}, {'id': '117', 'type': 'parenthesized_expression', 'children': ['118'], 'value': '()'}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '123'], 'value': '&'}, {'id': '119', 'type': 'parenthesized_expression', 'children': ['120'], 'value': '()'}; {'id': '120', 'type': 'binary_operator', 'children': ['121', '122'], 'value': '<<'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'Mask'}; {'id': '126', 'type': 'if_statement', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'topbit'}; {'id': '128', 'type': 'block', 'children': ['129']}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'augmented_assignment', 'children': ['131', '132'], 'value': '^='}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'register'}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'Poly'}, {'id': '135', 'type': 'if_statement', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'ReflectOut'}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'register'}, {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'reflect'}, {'id': '147', 'type': 'argument_list', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'register'}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'Width'}; {'id': '152', 'type': 'return_statement', 'children': ['153']}, {'id': '153', 'type': 'binary_operator', 'children': ['154', '155'], 'value': '^'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'register'}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'XorOut'} | def bit_by_bit(self, in_data):
if isinstance(in_data, str):
in_data = [ord(c) for c in in_data]
register = self.NonDirectInit
for octet in in_data:
if self.ReflectIn:
octet = self.reflect(octet, 8)
for i in range(8):
topbit = register & self.MSB_Mask
register = ((register << 1) & self.Mask) | ((octet >> (7 - i)) & 0x01)
if topbit:
register ^= self.Poly
for i in range(self.Width):
topbit = register & self.MSB_Mask
register = ((register << 1) & self.Mask)
if topbit:
register ^= self.Poly
if self.ReflectOut:
register = self.reflect(register, self.Width)
return register ^ self.XorOut |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse_ggKbase_tables'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'tables'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'id_type'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '232']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'g2info'}; {'id': '10', 'type': 'dictionary', 'children': []}, {'id': '11', 'type': 'for_statement', 'children': ['12', '13', '14']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'tables'}; {'id': '14', 'type': 'block', 'children': ['15']}, {'id': '15', 'type': 'for_statement', 'children': ['16', '17', '21']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '21', 'type': 'block', 'children': ['22', '35', '62', '76', '87']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '25', 'type': 'call', 'children': ['26', '33']}; {'id': '26', 'type': 'attribute', 'children': ['27', '32']}, {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '31', 'type': 'argument_list', 'children': []}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'string', 'children': [], 'value': "'\\t'"}, {'id': '35', 'type': 'if_statement', 'children': ['36', '44']}; {'id': '36', 'type': 'call', 'children': ['37', '42']}, {'id': '37', 'type': 'attribute', 'children': ['38', '41']}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '40', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '44', 'type': 'block', 'children': ['45', '49', '55', '61']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '54']}, {'id': '51', 'type': 'subscript', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '53', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '54', 'type': 'string', 'children': [], 'value': "'genome size (bp)'"}, {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '60']}, {'id': '57', 'type': 'subscript', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '59', 'type': 'integer', 'children': [], 'value': '12'}; {'id': '60', 'type': 'string', 'children': [], 'value': "'\n header[13] = '"}, {'id': '61', 'type': 'continue_statement', 'children': []}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '68']}; {'id': '64', 'type': 'pattern_list', 'children': ['65', '66', '67']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '68', 'type': 'expression_list', 'children': ['69', '72', '75']}, {'id': '69', 'type': 'subscript', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '71', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '72', 'type': 'subscript', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '74', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '79', 'type': 'list_comprehension', 'children': ['80', '84']}; {'id': '80', 'type': 'call', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'to_int'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '84', 'type': 'for_in_clause', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '87', 'type': 'if_statement', 'children': ['88', '91', '167']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '90'], 'value': 'is'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'id_type'}; {'id': '90', 'type': 'False', 'children': []}, {'id': '91', 'type': 'block', 'children': ['92', '105', '144']}; {'id': '92', 'type': 'if_statement', 'children': ['93', '100']}, {'id': '93', 'type': 'boolean_operator', 'children': ['94', '97'], 'value': 'or'}; {'id': '94', 'type': 'comparison_operator', 'children': ['95', '96'], 'value': 'in'}, {'id': '95', 'type': 'string', 'children': [], 'value': "'UNK'"}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '97', 'type': 'comparison_operator', 'children': ['98', '99'], 'value': 'in'}; {'id': '98', 'type': 'string', 'children': [], 'value': "'unknown'"}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '100', 'type': 'block', 'children': ['101']}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '105', 'type': 'if_statement', 'children': ['106', '117', '143']}; {'id': '106', 'type': 'boolean_operator', 'children': ['107', '111'], 'value': 'and'}, {'id': '107', 'type': 'parenthesized_expression', 'children': ['108'], 'value': '()'}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': '!='}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '111', 'type': 'parenthesized_expression', 'children': ['112'], 'value': '()'}; {'id': '112', 'type': 'boolean_operator', 'children': ['113', '114'], 'value': 'and'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '114', 'type': 'comparison_operator', 'children': ['115', '116'], 'value': 'in'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'g2info'}, {'id': '117', 'type': 'ERROR', 'children': ['118', '123', '130']}; {'id': '118', 'type': 'call', 'children': ['119', '120', '122']}, {'id': '119', 'type': 'string', 'children': [], 'value': "'\n print('"}; {'id': '120', 'type': 'ERROR', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'exit'}; {'id': '122', 'type': 'argument_list', 'children': []}, {'id': '123', 'type': 'ERROR', 'children': ['124', '127']}; {'id': '124', 'type': 'comparison_operator', 'children': ['125', '126'], 'value': 'not'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'g2info'}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'g2info'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '130', 'type': 'dictionary_comprehension', 'children': ['131', '134']}, {'id': '131', 'type': 'pair', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '134', 'type': 'for_in_clause', 'children': ['135', '138']}, {'id': '135', 'type': 'pattern_list', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '138', 'type': 'call', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '143', 'type': 'block', 'children': [], 'value': ''}; {'id': '144', 'type': 'if_statement', 'children': ['145', '148']}, {'id': '145', 'type': 'comparison_operator', 'children': ['146', '147'], 'value': 'not'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'g2info'}; {'id': '148', 'type': 'block', 'children': ['149']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '154']}, {'id': '151', 'type': 'subscript', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'g2info'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '154', 'type': 'dictionary_comprehension', 'children': ['155', '158']}, {'id': '155', 'type': 'pair', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '158', 'type': 'for_in_clause', 'children': ['159', '162']}, {'id': '159', 'type': 'pattern_list', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '162', 'type': 'call', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '164', 'type': 'argument_list', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '167', 'type': 'else_clause', 'children': ['168']}; {'id': '168', 'type': 'block', 'children': ['169']}, {'id': '169', 'type': 'if_statement', 'children': ['170', '173', '178', '187']}; {'id': '170', 'type': 'comparison_operator', 'children': ['171', '172'], 'value': '=='}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'id_type'}; {'id': '172', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '173', 'type': 'block', 'children': ['174']}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}, {'id': '175', 'type': 'assignment', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '178', 'type': 'elif_clause', 'children': ['179', '182']}, {'id': '179', 'type': 'comparison_operator', 'children': ['180', '181'], 'value': '=='}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'id_type'}, {'id': '181', 'type': 'string', 'children': [], 'value': "'code'"}; {'id': '182', 'type': 'block', 'children': ['183']}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'ID'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '187', 'type': 'else_clause', 'children': ['188', '231']}; {'id': '188', 'type': 'ERROR', 'children': ['189', '204', '217', '230']}, {'id': '189', 'type': 'ERROR', 'children': ['190', '193', '194', '201']}; {'id': '190', 'type': 'call', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'exit'}; {'id': '192', 'type': 'argument_list', 'children': []}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'ID'}; {'id': '194', 'type': 'call', 'children': ['195', '198']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '198', 'type': 'argument_list', 'children': ['199', '200']}, {'id': '199', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '200', 'type': 'string', 'children': [], 'value': "''"}, {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'g2info'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'ID'}; {'id': '204', 'type': 'dictionary_comprehension', 'children': ['205', '208']}, {'id': '205', 'type': 'pair', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '208', 'type': 'for_in_clause', 'children': ['209', '212']}, {'id': '209', 'type': 'pattern_list', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '217', 'type': 'ERROR', 'children': ['218', '225']}; {'id': '218', 'type': 'comparison_operator', 'children': ['219', '224'], 'value': '=='}, {'id': '219', 'type': 'subscript', 'children': ['220', '223']}; {'id': '220', 'type': 'subscript', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'g2info'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '223', 'type': 'string', 'children': [], 'value': "'genome size (bp)'"}; {'id': '224', 'type': 'string', 'children': [], 'value': "''"}, {'id': '225', 'type': 'subscript', 'children': ['226', '229']}; {'id': '226', 'type': 'subscript', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'g2info'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '229', 'type': 'string', 'children': [], 'value': "'genome size (bp)'"}; {'id': '230', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '231', 'type': 'block', 'children': [], 'value': ''}; {'id': '232', 'type': 'return_statement', 'children': ['233']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'g2info'} | def parse_ggKbase_tables(tables, id_type):
g2info = {}
for table in tables:
for line in open(table):
line = line.strip().split('\t')
if line[0].startswith('name'):
header = line
header[4] = 'genome size (bp)'
header[12] = '
header[13] = '
continue
name, code, info = line[0], line[1], line
info = [to_int(i) for i in info]
if id_type is False:
if 'UNK' in code or 'unknown' in code:
code = name
if (name != code) and (name and code in g2info):
print('
print('
exit()
if name not in g2info:
g2info[name] = {item:stat for item, stat in zip(header, info)}
if code not in g2info:
g2info[code] = {item:stat for item, stat in zip(header, info)}
else:
if id_type == 'name':
ID = name
elif id_type == 'code':
ID = code
else:
print('
exit()
ID = ID.replace(' ', '')
g2info[ID] = {item:stat for item, stat in zip(header, info)}
if g2info[ID]['genome size (bp)'] == '':
g2info[ID]['genome size (bp)'] = 0
return g2info |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'top_hits'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'hits'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'num'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'column'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '8', 'type': 'block', 'children': ['9', '24']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'call', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'hits'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '21']}, {'id': '15', 'type': 'keyword_argument', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'itemgetter'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'column'}, {'id': '21', 'type': 'keyword_argument', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '24', 'type': 'for_statement', 'children': ['25', '26', '32']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'hit'}; {'id': '26', 'type': 'subscript', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '28', 'type': 'slice', 'children': ['29', '30', '31']}, {'id': '29', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '30', 'type': 'colon', 'children': []}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'num'}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'yield', 'children': ['35']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'hit'} | def top_hits(hits, num, column, reverse):
hits.sort(key = itemgetter(column), reverse = reverse)
for hit in hits[0:num]:
yield hit |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'numBlast_sort'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'blast'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'numHits'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'bitT'}; {'id': '8', 'type': 'block', 'children': ['9', '32', '35', '45', '136', '145']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '12', 'type': 'list', 'children': ['13', '30'], 'value': "['\n 'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']"}, {'id': '13', 'type': 'concatenated_string', 'children': ['14', '15', '17', '18', '20', '21', '23', '24', '26', '27', '29']}; {'id': '14', 'type': 'string', 'children': [], 'value': "'\n '"}, {'id': '15', 'type': 'ERROR', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'qstart'}, {'id': '17', 'type': 'string', 'children': [], 'value': "', '"}; {'id': '18', 'type': 'ERROR', 'children': ['19']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'qend'}; {'id': '20', 'type': 'string', 'children': [], 'value': "', '"}, {'id': '21', 'type': 'ERROR', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'tstart'}, {'id': '23', 'type': 'string', 'children': [], 'value': "', '"}; {'id': '24', 'type': 'ERROR', 'children': ['25']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'tend'}; {'id': '26', 'type': 'string', 'children': [], 'value': "', '"}, {'id': '27', 'type': 'ERROR', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'evalue'}, {'id': '29', 'type': 'string', 'children': [], 'value': "', '"}; {'id': '30', 'type': 'ERROR', 'children': ['31']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'bitscore'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'yield', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'hmm'}; {'id': '38', 'type': 'dictionary_comprehension', 'children': ['39', '42']}, {'id': '39', 'type': 'pair', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'h'}, {'id': '41', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '42', 'type': 'for_in_clause', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '45', 'type': 'for_statement', 'children': ['46', '47', '48']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'blast'}; {'id': '48', 'type': 'block', 'children': ['49', '107', '117']}, {'id': '49', 'type': 'if_statement', 'children': ['50', '53', '105']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'startswith'}, {'id': '53', 'type': 'ERROR', 'children': ['54', '56', '72', '76', '82', '88', '90', '95', '98']}; {'id': '54', 'type': 'ERROR', 'children': ['55']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'continue'}; {'id': '56', 'type': 'keyword_argument', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '58', 'type': 'subscript', 'children': ['59', '69', '71']}, {'id': '59', 'type': 'call', 'children': ['60', '67']}; {'id': '60', 'type': 'attribute', 'children': ['61', '66']}, {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '65', 'type': 'argument_list', 'children': []}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'string', 'children': [], 'value': "'\\t'"}, {'id': '69', 'type': 'ERROR', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '71', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '72', 'type': 'ERROR', 'children': ['73']}, {'id': '73', 'type': 'subscript', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '75', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '76', 'type': 'call', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'subscript', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '81', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'subscript', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '87', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '88', 'type': 'ERROR', 'children': ['89']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'evalue'}; {'id': '90', 'type': 'keyword_argument', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '92', 'type': 'subscript', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '94', 'type': 'integer', 'children': [], 'value': '10'}, {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '97', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '98', 'type': 'boolean_operator', 'children': ['99', '102'], 'value': 'and'}, {'id': '99', 'type': 'comparison_operator', 'children': ['100', '101'], 'value': 'is'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '101', 'type': 'False', 'children': []}; {'id': '102', 'type': 'comparison_operator', 'children': ['103', '104'], 'value': '>'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'evalue'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'continue_statement', 'children': []}, {'id': '107', 'type': 'if_statement', 'children': ['108', '115']}; {'id': '108', 'type': 'boolean_operator', 'children': ['109', '112'], 'value': 'and'}, {'id': '109', 'type': 'comparison_operator', 'children': ['110', '111'], 'value': 'is'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'bitT'}, {'id': '111', 'type': 'False', 'children': []}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': '<'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'bitT'}, {'id': '115', 'type': 'block', 'children': ['116']}; {'id': '116', 'type': 'continue_statement', 'children': []}, {'id': '117', 'type': 'for_statement', 'children': ['118', '121', '126']}; {'id': '118', 'type': 'pattern_list', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'h'}, {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'zip'}, {'id': '123', 'type': 'argument_list', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '134']}, {'id': '129', 'type': 'attribute', 'children': ['130', '133']}; {'id': '130', 'type': 'subscript', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'hmm'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'h'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'hmm'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'DataFrame'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'hmm'}, {'id': '145', 'type': 'for_statement', 'children': ['146', '149', '177']}; {'id': '146', 'type': 'pattern_list', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '149', 'type': 'comparison_operator', 'children': ['150', '164', '167'], 'value': 'in'}; {'id': '150', 'type': 'call', 'children': ['151', '154']}, {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'hmm'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '154', 'type': 'argument_list', 'children': ['155', '161']}, {'id': '155', 'type': 'keyword_argument', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'by'}, {'id': '157', 'type': 'list', 'children': ['158', '159'], 'value': "['\n df = df.sort_values(by = ['bitscore']"}; {'id': '158', 'type': 'string', 'children': [], 'value': "'\n df = df.sort_values(by = ['"}, {'id': '159', 'type': 'ERROR', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'bitscore'}, {'id': '161', 'type': 'keyword_argument', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'ascending'}, {'id': '163', 'type': 'False', 'children': []}; {'id': '164', 'type': 'ERROR', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'for'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'hit'}, {'id': '167', 'type': 'subscript', 'children': ['168', '173']}; {'id': '168', 'type': 'attribute', 'children': ['169', '172']}, {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '173', 'type': 'slice', 'children': ['174', '175', '176']}; {'id': '174', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '175', 'type': 'colon', 'children': []}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'numHits'}, {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}, {'id': '179', 'type': 'yield', 'children': ['180']} | def numBlast_sort(blast, numHits, evalueT, bitT):
header = ['
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
hmm = {h:[] for h in header}
for line in blast:
if line.startswith('
continue
line = line.strip().split('\t')
line[10], line[11] = float(line[10]), float(line[11])
evalue, bit = line[10], line[11]
if evalueT is not False and evalue > evalueT:
continue
if bitT is not False and bit < bitT:
continue
for i, h in zip(line, header):
hmm[h].append(i)
hmm = pd.DataFrame(hmm)
for query, df in hmm.groupby(by = ['
df = df.sort_values(by = ['bitscore'], ascending = False)
for hit in df[header].values[0:numHits]:
yield hit |
{'id': '0', 'type': 'module', 'children': ['1', '64', '67', '75', '267']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9', '47']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'numDomtblout'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'domtblout'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'numHits'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'bitT'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '9', 'type': 'ERROR', 'children': ['10', '29', '30', '40', '42', '43', '44', '45', '46']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '14']}, {'id': '11', 'type': 'comparison_operator', 'children': ['12', '13'], 'value': 'is'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '13', 'type': 'True', 'children': []}; {'id': '14', 'type': 'block', 'children': ['15', '28']}, {'id': '15', 'type': 'for_statement', 'children': ['16', '17', '24']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'hit'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'numDomtblout_sort'}, {'id': '19', 'type': 'argument_list', 'children': ['20', '21', '22', '23']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'domtblout'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'numHits'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'bitT'}; {'id': '24', 'type': 'block', 'children': ['25']}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'yield', 'children': ['27']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'hit'}; {'id': '28', 'type': 'return_statement', 'children': []}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '30', 'type': 'concatenated_string', 'children': ['31', '32', '35', '36', '39']}, {'id': '31', 'type': 'string', 'children': [], 'value': "'\n '"}; {'id': '32', 'type': 'ERROR', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '35', 'type': 'string', 'children': [], 'value': "', '"}; {'id': '36', 'type': 'ERROR', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'accession'}, {'id': '39', 'type': 'string', 'children': [], 'value': "', '"}; {'id': '40', 'type': 'ERROR', 'children': ['41']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'qlen'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'full E-value'"}, {'id': '43', 'type': 'string', 'children': [], 'value': "'full score'"}; {'id': '44', 'type': 'string', 'children': [], 'value': "'full bias'"}, {'id': '45', 'type': 'ERROR', 'children': []}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'domain'}, {'id': '47', 'type': 'block', 'children': ['48', '53', '60']}; {'id': '48', 'type': 'expression_statement', 'children': ['49', '50', '51', '52']}, {'id': '49', 'type': 'string', 'children': [], 'value': "'domain c-Evalue'"}; {'id': '50', 'type': 'string', 'children': [], 'value': "'domain i-Evalue'"}, {'id': '51', 'type': 'string', 'children': [], 'value': "'domain score'"}; {'id': '52', 'type': 'string', 'children': [], 'value': "'domain bias'"}, {'id': '53', 'type': 'expression_statement', 'children': ['54', '55', '56', '57', '58', '59']}; {'id': '54', 'type': 'string', 'children': [], 'value': "'hmm from'"}, {'id': '55', 'type': 'string', 'children': [], 'value': "'hmm to'"}; {'id': '56', 'type': 'string', 'children': [], 'value': "'seq from'"}, {'id': '57', 'type': 'string', 'children': [], 'value': "'seq to'"}; {'id': '58', 'type': 'string', 'children': [], 'value': "'env from'"}, {'id': '59', 'type': 'string', 'children': [], 'value': "'env to'"}; {'id': '60', 'type': 'ERROR', 'children': ['61']}, {'id': '61', 'type': 'expression_statement', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'acc'"}, {'id': '63', 'type': 'string', 'children': [], 'value': "'target description'"}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'yield', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'header'}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '72']}, {'id': '69', 'type': 'pattern_list', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'prev'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '72', 'type': 'expression_list', 'children': ['73', '74']}, {'id': '73', 'type': 'None', 'children': []}; {'id': '74', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '75', 'type': 'for_statement', 'children': ['76', '77', '78']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'domtblout'}; {'id': '78', 'type': 'block', 'children': ['79', '199', '263']}, {'id': '79', 'type': 'if_statement', 'children': ['80', '83', '173']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'startswith'}, {'id': '83', 'type': 'ERROR', 'children': ['84', '86', '134', '138', '144', '150', '152', '157', '164', '167', '169', '170']}; {'id': '84', 'type': 'ERROR', 'children': ['85']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'continue'}; {'id': '86', 'type': 'keyword_argument', 'children': ['87', '88', '123']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '88', 'type': 'ERROR', 'children': ['89', '98', '99', '109', '110', '116', '122']}, {'id': '89', 'type': 'call', 'children': ['90', '97']}; {'id': '90', 'type': 'attribute', 'children': ['91', '96']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '95', 'type': 'argument_list', 'children': []}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '97', 'type': 'argument_list', 'children': []}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'desc'}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'subscript', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '106', 'type': 'slice', 'children': ['107', '108']}, {'id': '107', 'type': 'integer', 'children': [], 'value': '18'}; {'id': '108', 'type': 'colon', 'children': []}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '112', 'type': 'slice', 'children': ['113', '114', '115']}, {'id': '113', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '114', 'type': 'colon', 'children': []}, {'id': '115', 'type': 'integer', 'children': [], 'value': '18'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'desc'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '123', 'type': 'binary_operator', 'children': ['124', '127'], 'value': '+'}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '126', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '127', 'type': 'subscript', 'children': ['128', '131', '133']}; {'id': '128', 'type': 'subscript', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '9'}, {'id': '131', 'type': 'ERROR', 'children': ['132']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '133', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '134', 'type': 'ERROR', 'children': ['135']}, {'id': '135', 'type': 'subscript', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '137', 'type': 'integer', 'children': [], 'value': '13'}; {'id': '138', 'type': 'call', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'subscript', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '143', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '144', 'type': 'call', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'subscript', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '149', 'type': 'integer', 'children': [], 'value': '13'}; {'id': '150', 'type': 'ERROR', 'children': ['151']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'evalue'}; {'id': '152', 'type': 'keyword_argument', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'bitscore'}; {'id': '154', 'type': 'subscript', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '156', 'type': 'integer', 'children': [], 'value': '11'}, {'id': '157', 'type': 'subscript', 'children': ['158', '161', '163']}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '13'}, {'id': '161', 'type': 'ERROR', 'children': ['162']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '163', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '164', 'type': 'subscript', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '166', 'type': 'integer', 'children': [], 'value': '13'}, {'id': '167', 'type': 'ERROR', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'evalue'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'bitscore'}; {'id': '170', 'type': 'comparison_operator', 'children': ['171', '172'], 'value': '!='}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'ID'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'prev'}, {'id': '173', 'type': 'block', 'children': ['174', '195']}; {'id': '174', 'type': 'if_statement', 'children': ['175', '181']}, {'id': '175', 'type': 'comparison_operator', 'children': ['176', '180'], 'value': '>'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '180', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'for_statement', 'children': ['183', '184', '191']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'hit'}; {'id': '184', 'type': 'call', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'top_hits'}; {'id': '186', 'type': 'argument_list', 'children': ['187', '188', '189', '190']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'numHits'}, {'id': '189', 'type': 'integer', 'children': [], 'value': '13'}; {'id': '190', 'type': 'True', 'children': []}, {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'yield', 'children': ['194']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'hit'}, {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '198', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '199', 'type': 'if_statement', 'children': ['200', '207', '215', '231', '247']}; {'id': '200', 'type': 'boolean_operator', 'children': ['201', '204'], 'value': 'and'}, {'id': '201', 'type': 'comparison_operator', 'children': ['202', '203'], 'value': '=='}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '203', 'type': 'False', 'children': []}; {'id': '204', 'type': 'comparison_operator', 'children': ['205', '206'], 'value': '=='}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'bitT'}; {'id': '206', 'type': 'False', 'children': []}, {'id': '207', 'type': 'block', 'children': ['208']}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'call', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '215', 'type': 'elif_clause', 'children': ['216', '223']}; {'id': '216', 'type': 'boolean_operator', 'children': ['217', '220'], 'value': 'and'}, {'id': '217', 'type': 'comparison_operator', 'children': ['218', '219'], 'value': '<='}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'evalue'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'evalueT'}; {'id': '220', 'type': 'comparison_operator', 'children': ['221', '222'], 'value': '=='}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'bitT'}; {'id': '222', 'type': 'False', 'children': []}, {'id': '223', 'type': 'block', 'children': ['224']}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'call', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '229', 'type': 'argument_list', 'children': ['230']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '231', 'type': 'elif_clause', 'children': ['232', '239']}; {'id': '232', 'type': 'boolean_operator', 'children': ['233', '236'], 'value': 'and'}, {'id': '233', 'type': 'comparison_operator', 'children': ['234', '235'], 'value': '<='}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'evalue'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'evalueT'}; {'id': '236', 'type': 'comparison_operator', 'children': ['237', '238'], 'value': '>='}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'bitT'}, {'id': '239', 'type': 'block', 'children': ['240']}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}, {'id': '241', 'type': 'call', 'children': ['242', '245']}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '247', 'type': 'elif_clause', 'children': ['248', '255']}; {'id': '248', 'type': 'boolean_operator', 'children': ['249', '252'], 'value': 'and'}, {'id': '249', 'type': 'comparison_operator', 'children': ['250', '251'], 'value': '=='}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'evalueT'}, {'id': '251', 'type': 'False', 'children': []}; {'id': '252', 'type': 'comparison_operator', 'children': ['253', '254'], 'value': '>='}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'bit'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'bitT'}, {'id': '255', 'type': 'block', 'children': ['256']}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'call', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'assignment', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'prev'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'ID'}, {'id': '267', 'type': 'for_statement', 'children': ['268', '269', '276', '281']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'hit'}, {'id': '269', 'type': 'call', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'top_hits'}, {'id': '271', 'type': 'argument_list', 'children': ['272', '273', '274', '275']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'hits'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'numHits'}; {'id': '274', 'type': 'integer', 'children': [], 'value': '13'}, {'id': '275', 'type': 'True', 'children': []}; {'id': '276', 'type': 'ERROR', 'children': ['277']}, {'id': '277', 'type': 'block', 'children': ['278']}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'yield', 'children': ['280']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'hit'}, {'id': '281', 'type': 'block', 'children': [], 'value': ''} | def numDomtblout(domtblout, numHits, evalueT, bitT, sort):
if sort is True:
for hit in numDomtblout_sort(domtblout, numHits, evalueT, bitT):
yield hit
return
header = ['
'query name', 'query accession', 'qlen',
'full E-value', 'full score', 'full bias',
'domain
'domain c-Evalue', 'domain i-Evalue', 'domain score', 'domain bias',
'hmm from', 'hmm to', 'seq from', 'seq to', 'env from', 'env to',
'acc', 'target description']
yield header
prev, hits = None, []
for line in domtblout:
if line.startswith('
continue
line = line.strip().split()
desc = ' '.join(line[18:])
line = line[0:18]
line.append(desc)
ID = line[0] + line[9]
line[11], line[13] = float(line[11]), float(line[13])
evalue, bitscore = line[11], line[13]
line[11], line[13] = evalue, bitscore
if ID != prev:
if len(hits) > 0:
for hit in top_hits(hits, numHits, 13, True):
yield hit
hits = []
if evalueT == False and bitT == False:
hits.append(line)
elif evalue <= evalueT and bitT == False:
hits.append(line)
elif evalue <= evalueT and bit >= bitT:
hits.append(line)
elif evalueT == False and bit >= bitT:
hits.append(line)
prev = ID
for hit in top_hits(hits, numHits, 13, True):
yield hit |
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