Commit 152c2c54 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

hmmscan converter now uses dbxref instead of accessions (fixes #18)

parent c921b071
......@@ -6,6 +6,7 @@ import argparse
parser = argparse.ArgumentParser(description='Convert hmmscan results to json documents')
parser.add_argument('--result', '-r', required=True, help='The run_hmmer result directory')
parser.add_argument('--output', '-o', required=True, help='The converted results json file')
parser.add_argument('--dbxref', '-d', required=True, help='The dbxref prefix that will be prepended to the accession or id')
args = parser.parse_args()
filename = args.result + "/domtblout.tsv"
......@@ -34,7 +35,7 @@ with open(filename) as f:
results.append({
'target': {
'name': split[0],
'accession': split[1],
'dbxref': args.dbxref + ':' + split[1],
'length': split[2],
'score': float(split[13]),
'start': int(split[15]),
......
......@@ -18,3 +18,5 @@ analysis:
# result file from the analysis_script
converter:
script: 'convert_hmmer.py'
parameters:
dbxref: 'PFAM'
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