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| import requests as r | |
| from io import StringIO | |
| from Bio import SeqIO | |
| import xml.etree.ElementTree as ET | |
| def get_uniprot_seq(protein_id): | |
| print('>> Fetching UniProt Sequences for ID: ', protein_id) | |
| baseUrl = "http://www.uniprot.org/uniprot/" | |
| currentUrl = baseUrl + protein_id + ".fasta" | |
| response = r.post(currentUrl) | |
| cData = ''.join(response.text) | |
| Seq = StringIO(cData) | |
| pSeq = list(SeqIO.parse(Seq, 'fasta')) | |
| try: | |
| return str(pSeq[0].seq) | |
| except: | |
| IndexError | |
| return str('') | |
| def get_isoforms(protein_id): | |
| print('>> Fetching UniProt Isoforms for ID: ', protein_id) | |
| try: | |
| # a dictionary storing the sequence of your isoforms, key: accesion number, value: sequence | |
| isoforms = dict() | |
| # make a call to EBI API | |
| req = r.get('https://www.ebi.ac.uk/proteins/api/proteins/{}/isoforms'.format(protein_id)) | |
| # parse the returned XML | |
| uniprot = ET.fromstring(req.text) | |
| for isoform in uniprot: | |
| # get the sequence | |
| seq = isoform.find('{http://uniprot.org/uniprot}sequence') | |
| # get the accession number | |
| iso_accession = isoform.find('{http://uniprot.org/uniprot}accession') | |
| # add the values to the dictionary | |
| if seq.text and iso_accession.text: | |
| isoforms[iso_accession.text] = seq.text | |
| return isoforms | |
| except: | |
| AttributeError | |
| isoforms = {} | |
| return isoforms | |