| ''' | |
| Converts fasta files to txt format. | |
| ''' | |
| import argparse | |
| from Bio import SeqIO | |
| if __name__ == '__main__': | |
| parser = argparse.ArgumentParser() | |
| parser.add_argument('input_file', type=str) | |
| parser.add_argument('output_file', type=str) | |
| parser.add_argument('--extract_ids', action='store_true') | |
| args = parser.parse_args() | |
| records = SeqIO.parse(args.input_file, "fasta") | |
| count = 0 | |
| with open(args.output_file, 'w+') as seq_list: | |
| for record in records: | |
| if args.extract_ids: | |
| ids = str(record.id).split('|') | |
| if len(ids) == 1: | |
| seq_list.write(ids[0]) | |
| else: | |
| seq_list.write(ids[1]) | |
| else: | |
| seq_list.write(str(record.seq)) | |
| seq_list.write('\n') | |
| count += 1 | |
| #SeqIO.write(records, args.output_file, "tab") | |
| print("Converted %i records" % count) | |