Commit 6a80c032 authored by hmueller's avatar hmueller
Browse files

Implement simple storage of query sequence names. Currently relies on resolution of issue #22.

parent f67b0373
#!/usr/bin/env python3
import env
import argparse
import json
from psot import config
from os import system, makedirs
......@@ -22,3 +23,15 @@ system(hmmscan_tool +
" --domtblout " + args.output + "/domtblout.tsv " +
" --pfamtblout " + args.output + "/pfamtblout.tsv " +
args.database + " " + args.fasta)
# Provide a list of all query sequence names for conversion process
queries = []
with open(args.fasta) as f:
for line in f:
if line.startswith('>'):
queries.append(line.replace('>', '').strip())
query_file = args.output + '/' + 'queries.json'
with open(query_file, 'w') as o:
json.dump(queries, o)
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