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import pandas as pd
import numpy as np
from add_sequence import *
def create_isoforms(uniprot_id, isoform_fasta):
if uniprot_id not in isoform_fasta.uniprotID.to_list():
isoform_current = pd.DataFrame(get_isoforms(uniprot_id).items(), columns=['uniprotID', 'isoformSequence'])
isoform_current['whichIsoform'] = isoform_current['uniprotID'].apply(lambda x: x[7:10].strip())
isoform_current['uniprotID'] = isoform_current['uniprotID'].apply(lambda x: x[0:6])
isoform_fasta = pd.concat([isoform_fasta, isoform_current], axis=0)
return isoform_fasta
def add_isoform(isoform_fasta, uniprot_id, variation_position, wild_type):
if len(isoform_fasta) != 0:
isoList = isoform_fasta[isoform_fasta['uniprotID'] == uniprot_id].isoformSequence.to_list()
for k in isoList:
if len(k) >= int(variation_position):
resInIso = k[int(int(variation_position) - 1)]
if wild_type == resInIso:
whichIsoform_ = isoform_fasta[isoform_fasta.isoformSequence == k].whichIsoform.to_list()[0]
wt_sequence_match = 'i'
break
else:
whichIsoform_ = np.NaN
wt_sequence_match = np.NaN
else:
whichIsoform_ = np.NaN
wt_sequence_match = np.NaN
return whichIsoform_, wt_sequence_match
def add_uniprot_sequence(DATAFRAME):
CANONICAL_FASTA = pd.DataFrame(columns=['uniprotID', 'uniprotSequence'])
ISOFORM_FASTA = pd.DataFrame(columns=['uniprotID', 'isoformSequence'])
UNIPROT_ID_LIST = list(set(DATAFRAME['uniprotID'].to_list()))
for i in range(len(UNIPROT_ID_LIST)):
CANONICAL_FASTA.at[i, 'uniprotSequence'] = get_uniprot_seq(UNIPROT_ID_LIST[i])
CANONICAL_FASTA.at[i, 'uniprotID'] = UNIPROT_ID_LIST[i]
canonical_fasta = CANONICAL_FASTA.drop_duplicates()
DATAFRAME = DATAFRAME.merge(canonical_fasta, on='uniprotID', how='left')
DATAFRAME['uniprotSequence'].replace({'': np.NaN}, inplace=True)
for i in DATAFRAME.index:
UNIPROT_ID = DATAFRAME.at[i, 'uniprotID']
VARIATION_POSITION = DATAFRAME.at[i, 'pos']
WILDTYPE = DATAFRAME.at[i, 'wt']
if len(DATAFRAME.loc[i, 'uniprotSequence']) >= int(VARIATION_POSITION):
can = str(DATAFRAME.at[i, 'uniprotSequence'])[int(VARIATION_POSITION) - 1]
if WILDTYPE == can:
DATAFRAME.loc[i, 'wt_sequence_match'] = 'm'
elif WILDTYPE != can:
ISOFORM_FASTA = create_isoforms(UNIPROT_ID, ISOFORM_FASTA)
ISOFORM_NUM, MATCH_STAT = add_isoform(ISOFORM_FASTA, UNIPROT_ID, VARIATION_POSITION, WILDTYPE)
ISOFORM_SEQUENCE = ISOFORM_FASTA[(ISOFORM_FASTA['uniprotID'] == UNIPROT_ID) &
(ISOFORM_FASTA['whichIsoform'] == ISOFORM_NUM)].isoformSequence.values
DATAFRAME.at[i,'whichIsoform'] = ISOFORM_NUM
DATAFRAME.at[i, 'wt_sequence_match'] = MATCH_STAT
DATAFRAME.at[i, 'uniprotSequence'] = ISOFORM_SEQUENCE
elif len(DATAFRAME.at[i, 'uniprotSequence']) < int(VARIATION_POSITION):
ISOFORM_FASTA = create_isoforms(ISOFORM_FASTA, UNIPROT_ID)
ISOFORM_NUM, MATCH_STAT = add_isoform(ISOFORM_FASTA, UNIPROT_ID, VARIATION_POSITION, WILDTYPE)
ISOFORM_SEQUENCE = ISOFORM_FASTA[(ISOFORM_FASTA['uniprotID'] == UNIPROT_ID) &
( ISOFORM_FASTA['whichIsoform'] == ISOFORM_NUM)].isoformSequence.values
DATAFRAME.at[i, 'whichIsoform'] = ISOFORM_NUM
DATAFRAME.at[i, 'wt_sequence_match'] = MATCH_STAT
DATAFRAME.at[i, 'uniprotSequence'] = ISOFORM_SEQUENCE
DATAFRAME['uniprotSequence'] = DATAFRAME['uniprotSequence'].apply(lambda x: x[0] if (type(x) != str and len(x)>0) else x)
DATAFRAME['uniprotSequence'] = DATAFRAME['uniprotSequence'].apply(lambda x: np.NaN if (type(x) != str and len(x) == 0) else x)
print('>> Sequence files created...\n')
return DATAFRAME
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