Source code for bioservices.apps.peptides

from bioservices import UniProt
import re

[docs]class Peptides(object): """ :: >>> p = Peptides() >>> p.get_fasta_sequence("Q8IYB3") >>> p.get_peptide_position("Q8IYB3", "VPKPEPIPEPKEPSPE") 189 Sometimes, peptides are provided with a pattern indicating the phospho site. e.g., :: >>> """ def __init__(self, verbose=False): self.u = UniProt(verbose=verbose) self.sequences = {}
[docs] def get_fasta_sequence(self, uniprot_name): seq = self.u.get_fasta_sequence(uniprot_name) return seq
[docs] def get_phosphosite_position(self, uniprot_name, peptide): if uniprot_name not in self.sequences.keys(): seq = self.get_fasta_sequence(uniprot_name) self.sequences[uniprot_name] = seq[:] else: seq = self.sequences[uniprot_name][:] positions = [x.start() for x in re.finditer("PQS", seq)] return positions