Commit ded79224 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Adapted blast json document to the signalp document structure

parent 184e0d46
......@@ -5,7 +5,8 @@ import json
filename = sys.argv[1]
documents = {}
with open(filename) as f:
header = {}
header = None
tool = None
for line in f:
line = line.strip()
if line.startswith('#'):
......@@ -14,10 +15,19 @@ with open(filename) as f:
header = {}
for idx, key in enumerate(header_entries):
header[key] = idx
if line.startswith('# BLASTP'):
split = line.split()
tool = {'name': 'blastp',
'version': split[2]}
if line.startswith('# Database'):
split = line.split()
tool['database'] = split[2]
else:
split = line.split("\t")
if not split[0] in documents:
documents[split[0]] = {"id": split[0], "results": []}
documents[split[0]] = {"id": split[0], "computations": [{'tool':tool, 'results':[]}]}
results = documents[split[0]]['computations'][0]['results']
result = {}
result["dbxref"] = "UniProtKB/Swiss-Prot:"+split[header['subject id']].split("|")[1]
......@@ -32,7 +42,7 @@ with open(filename) as f:
if 'BTOP' in header:
result['btop'] = split[header['BTOP']]
documents[split[0]]["results"].append(result)
results.append(result)
for key in documents:
......
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