| ''' | |
| Extracts UniProt ids from .sto alignment files. | |
| ''' | |
| import argparse | |
| from evcouplings.align.alignment import Alignment | |
| from evcouplings.align.protocol import modify_alignment, cut_sequence | |
| import numpy as np | |
| from utils import read_fasta | |
| def main(): | |
| parser = argparse.ArgumentParser() | |
| parser.add_argument('sto_alignment_file', type=str, help='input filepath for .sto') | |
| parser.add_argument('output_file', type=str) | |
| args = parser.parse_args() | |
| with open(args.sto_alignment_file) as a: | |
| ali_raw = Alignment.from_file(a, "stockholm") | |
| ids = np.unique(ali_raw.ids) | |
| with open(args.output_file, 'w') as f: | |
| for i in ids: | |
| f.write(i.split('|')[1]) | |
| f.write('\n') | |
| if __name__ == "__main__": | |
| main() | |