qvextractspecific

#!/usr/bin/env python3
'''
    This is a command-line tool to extract a specific set of PDB files from a Quiver file.

    Usage:
        qvextract <quiver_file> <tag1> <tag2> ...
'''

import sys
import os

from quiver import Quiver

# Thanks to bcov for this code
import stat

quiver_file = sys.argv[1]

tag_buffers = []
if ( stat.S_ISFIFO(os.stat("/dev/stdin").st_mode) ):
    tag_buffers += sys.stdin.readlines()
tag_buffers += sys.argv[2:]

tags = []
for line in tag_buffers:
    line = line.strip()
    if (len(line) == 0):
        continue
    sp = line.split(" ")
    for tag in sp:
        tags.append(tag)

qv = Quiver(quiver_file, 'r')

for tag in tags:
    outfn = f'{tag}.pdb'

    if os.path.exists(outfn):
        print(f'File {outfn} already exists, skipping')
        continue

    try:
        lines = qv.get_pdblines(tag)
    except:
        print(f'Could not find tag {tag} in Quiver file, skipping')
        continue

    with open(outfn, 'w') as f:
        for line in lines:
            f.write(line)

print(f'Successfully extracted {len(tags)} PDB files from {quiver_file}')