view biopython_parsing.py @ 1:112751823323 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

#!/usr/bin/env python
# Biopython parsing module. Uses in conjunction with the sar_finder script, and potential future scripts down the line.

from Bio import SeqIO


class FASTA_parser:
    """Parses multi fasta file, and zips together header with sequence"""

    def __init__(self, fa):
        self.fa = fa

    def multifasta_dict(self):
        """parses the input multi fasta, and puts results into dictionary"""

        return SeqIO.to_dict(SeqIO.parse(self.fa, "fasta"))


if __name__ == "__main__":
    fa_file = "test-data/mu-proteins.fa"
    d = FASTA_parser(fa_file).multifasta_dict()
    print(d)
    for k, v in d.items():
        print(v.description)