Mercurial > repos > iuc > snpeff
view gbk2fa.py @ 26:5b80f544c67f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51
author | iuc |
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date | Fri, 25 Nov 2022 19:44:27 +0000 |
parents | 5c7b70713fb5 |
children |
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import argparse import bz2 import gzip from Bio import SeqIO def get_opener(gbk_filename): try: bz2.open(gbk_filename).read(1) return bz2.open except OSError: pass try: gzip.open(gbk_filename).read(1) return gzip.open except OSError: return open parser = argparse.ArgumentParser() parser.add_argument( "genbank_file", help="GenBank input file. Can be compressed with gzip or bzip2" ) parser.add_argument( "fasta_file", help="FASTA output datset" ) parser.add_argument( "--remove_version", action="store_true", help="Remove version number from NCBI form formatted accession numbers. " "For example, this would convert 'B000657.2' to 'B000657'" ) args = parser.parse_args() gbk_open = get_opener(args.genbank_file) with gbk_open(args.genbank_file, 'rt') as input_handle, \ open(args.fasta_file, 'w') as output_handle: for seq_record in SeqIO.parse(input_handle, 'genbank'): if args.remove_version: seq_id = seq_record.id.split('.')[0] else: seq_id = seq_record.id print('Writing FASTA record: {}'.format(seq_id)) print('>' + seq_id, file=output_handle) print(seq_record.seq, file=output_handle)