Mercurial > repos > curtisross > remove_fasta_description
view fasta_remove_id.py @ 0:2b42545705fa draft
Uploaded Python Script
author | curtisross |
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date | Thu, 23 Sep 2021 16:24:09 +0000 |
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#!/usr/bin/env python import sys import argparse import logging from Bio import SeqIO logging.basicConfig(level=logging.INFO) log = logging.getLogger() def drop_id(fasta_file=None): for rec in SeqIO.parse(fasta_file, "fasta"): rec.description = "" ind = str(rec.seq).find("##") if ( ind != -1 ): # This method causes mid-file comments (such as from Apollo sequences) to be appended to the end of the previous sequence rec.seq = rec.seq[0:ind] yield rec if __name__ == "__main__": parser = argparse.ArgumentParser(description="Identify shine-dalgarno sequences") parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Genbank file") args = parser.parse_args() for rec in drop_id(**vars(args)): SeqIO.write([rec], sys.stdout, "fasta")