| ''' | |
| Converts txt file to fasta. | |
| ''' | |
| import argparse | |
| from Bio import SeqIO | |
| import pandas as pd | |
| if __name__ == '__main__': | |
| parser = argparse.ArgumentParser() | |
| parser.add_argument('input_file', type=str) | |
| parser.add_argument('output_file', type=str) | |
| args = parser.parse_args() | |
| count = 0 | |
| if args.input_file.endswith('.csv'): | |
| df = pd.read_csv(args.input_file) | |
| with open(args.output_file, 'w') as out: | |
| for s in df.seq.values: | |
| out.write(f'>id_{count}\n') | |
| out.write(s + '\n') | |
| count += 1 | |
| else: | |
| with open(args.input_file, 'r') as in_file: | |
| with open(args.output_file, 'w') as out: | |
| for line in in_file.readlines(): | |
| out.write(f'>id_{count}\n') | |
| out.write(line) | |
| count += 1 | |
| print("Converted %i records" % count) | |