Commit c6f18289 authored by hmueller's avatar hmueller
Browse files

Minor code cosmetics

parent 1e084c41
......@@ -38,7 +38,7 @@ with open(filename) as f:
try:
queries.remove(query_id)
except ValueError:
print('HMMER converter: Query ID "' + query_id + '" not present among initial queries!')
print('HMMER converter: Query ID "' + query_id + '" not found among initial queries!')
results = documents[query_id]['computations'][0]["results"]
results.append({
......@@ -57,11 +57,8 @@ with open(filename) as f:
}
})
# Include queries with no matches in results
for query_id in queries:
print("In list: " + query_id)
if not query_id in documents:
print("Recording: " + query_id)
documents[query_id] = {"id": query_id, "computations": [{'tool': tool, 'results':"no match found"}]}
output_filename = args.output
......
......@@ -18,7 +18,7 @@ makedirs(args.output, exist_ok=True)
system(hmmscan_tool +
" -E " + args.evalue +
" -o " +args.output+ "/hmmscan.out " +
" -o " + args.output + "/hmmscan.out " +
" --tblout " + args.output + "/tblout.tsv " +
" --domtblout " + args.output + "/domtblout.tsv " +
" --pfamtblout " + args.output + "/pfamtblout.tsv " +
......@@ -32,6 +32,6 @@ with open(args.fasta) as f:
if line.startswith('>'):
queries.append(line.replace('>', '').strip())
query_file = args.output + '/' + 'queries.json'
query_file = args.output + '/queries.json'
with open(query_file, 'w') as o:
json.dump(queries, o)
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment