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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 | |