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import ssl
import requests as r
from decimal import *
import numpy as np
def add_annotations(dataframe):
print('Downloading UniProt sequence annotations...\n')
ssl._create_default_https_context = ssl._create_unverified_context
original_annot_name = ['DISULFID', 'INIT_MET', 'INTRAMEM', 'VARIANT', 'DNA_BIND', 'ACT_SITE', 'NP_BIND', 'LIPID',
'SITE',
'TRANSMEM', 'CROSSLNK', 'MUTAGEN', 'STRAND', 'HELIX', 'TURN', 'METAL', 'REPEAT', 'TOPO_DOM',
'CA_BIND', 'BINDING', 'REGION', 'SIGNAL', 'MOD_RES', 'ZN_FING', 'MOTIF', 'COILED', 'PEPTIDE',
'TRANSIT', 'CARBOHYD', 'PROPEP']
annotation_list = ['disulfide', 'intMet', 'intramembrane', 'naturalVariant', 'dnaBinding', 'activeSite',
'nucleotideBinding', 'lipidation', 'site', 'transmembrane', 'crosslink', 'mutagenesis', 'strand',
'helix', 'turn', 'metalBinding', 'repeat', 'topologicalDomain', 'caBinding', 'bindingSite',
'region',
'signalPeptide', 'modifiedResidue', 'zincFinger', 'motif', 'coiledCoil', 'peptide',
'transitPeptide', 'glycosylation', 'propeptide']
dataframe = dataframe.reset_index().drop(['index'], axis=1)
for annot in original_annot_name:
dataframe[annot] = ''
for protein in list(set(dataframe.uniprotID.to_list())):
print('Downloading annotations for ' + protein)
uniprot_entry = r.get("http://www.uniprot.org/uniprot/" + protein + ".txt")
uniprot_entry = uniprot_entry.text.split('\n')
annot_for_protein = []
for annotation in original_annot_name:
for line in uniprot_entry:
if annotation.strip() in line and line.startswith(
'FT') and 'evidence' not in line and 'ECO' not in line and 'note' not in line:
annot_for_protein.append(list(filter(None, line.split(' ')))[1:])
for select in annot_for_protein:
if select[0] not in dataframe.columns:
dataframe.loc[dataframe.uniprotID == protein, select[0]] = str((select[1] + '; '))
else:
dataframe.loc[dataframe.uniprotID == protein, select[0]] += str((select[1] + '; '))
for i in range(len(original_annot_name)):
dataframe = dataframe.rename(columns={original_annot_name[i]: annotation_list[i]})
# Fix annotation positions
print('Processing positions...\n')
for i in dataframe.index:
for annot in dataframe.columns[-30:]:
if annot != 'disulfide':
if dataframe.at[i, annot] != 'nan':
dataframe.at[i, annot] = ([x for x in [k.strip() for k in dataframe.at[i, annot].split(';')] if x])
if '..' not in str(dataframe.at[i, annot]):
pass
elif '..' in str(dataframe.at[i, annot]):
dataframe.at[i, annot] = str(dataframe.at[i, annot]).replace('..', '-')
else:
disulfide_annot = []
if dataframe.at[i, annot] != 'nan':
dataframe.at[i, annot]= dataframe.at[i, annot].split(';')
dataframe.at[i, annot] = [i.split('..') for i in dataframe.at[i, annot]]
dataframe.at[i, annot] =[e for v in dataframe.at[i, annot] for e in v]
dataframe.at[i, annot] = [i for i in dataframe.at[i, annot] if i != ' ']
# Add binary annotations
print('Adding binary annotations...\n')
dataframe = dataframe.astype('str')
for i in dataframe.index:
for k in annotation_list: # get the positions of each attribute as a list
txt = k + 'Binary'
dataframe.at[i, txt] = Decimal('nan')
try:
for positions in dataframe.at[i, k].split(','):
position = positions.strip('[').strip(']').replace("'", "")
if position != 'nan' and position != '' and '-' not in position and int(
dataframe.at[i, 'pos']) == int(position):
dataframe.at[i, txt] = '1'
break
elif position != 'nan' and position != '' and '-' not in position and int(
dataframe.at[i, 'pos']) != int(position):
dataframe.at[i, txt] = '0'
elif position != 'nan' and position != '' and '-' in position:
if int(position.split('-')[0]) < int(dataframe.at[i, 'pos']) < int(position.split('-')[1]):
dataframe.at[i, txt] = '1'
break
else:
dataframe.at[i, txt] = '0'
except:
ValueError
# Final corrections
dataframe = dataframe.replace({'[\'?\']': 'nan'})
dataframe = dataframe.replace({'[]': 'nan'})
return dataframe
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