File size: 2,266 Bytes
5032722 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import re
import os
import pandas as pd
def split_seed_file(seed_alignment_dir: str,
pfam_seed_file: str,
header: str):
"""
Pfam seed alignments are in one giant file, split into per-pfam
alignment files
inputs:
-------
- seed_alignment_dir (str): where individual .seed files should go
- pfam_seed_file: the single Pfam seed file to split
- header: information to add at the top of the stats file
returns:
--------
(None)
outputs:
--------
- f'{prefix}_INIT-STATS.tsv': some initial stats after splitting
"""
# make the folder
if seed_alignment_dir not in os.listdir():
os.mkdir(seed_alignment_dir)
# split the contents of the main seed file
with open(pfam_seed_file,'r', encoding='latin') as f:
contents = [entry for entry in f.read().split('//\n') if entry != '']
# parse through the contents, gather stats, and output
num_pfams = len(contents)
num_pfams_with_clans = 0
seen_clans = set()
for entry in contents:
match = re.search(rf"^.*#=GF AC.*$", entry, re.MULTILINE)
line_with_pfam_name = match.group(0) if match else None
pfam = line_with_pfam_name.strip().split()[2].split('.')[0]
del match
match = re.search(rf"^.*#=GF CL.*$", entry, re.MULTILINE)
line_with_clan_name = match.group(0) if match else None
if line_with_clan_name != None:
num_pfams_with_clans += 1
clan = line_with_clan_name.strip().split()[-1]
if clan not in seen_clans:
seen_clans.add(clan)
with open(f'./{seed_alignment_dir}/{pfam}.seed','w') as g:
g.write(entry)
# write the final stats
out_dict = {'Number of Pfams': num_pfams,
'Number of Pfams in clans': num_pfams_with_clans,
'Number of Unique clans': len(seen_clans)}
prefix = pfam_seed_file.split('.')[0]
with open(f'{prefix}_INIT-STATS.tsv', 'w') as g:
g.write(f'{header}\n')
[g.write(f'{key}\t{val}\n') for key, val in out_dict.items()]
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