Added a module that runs hmmscan vs PFAM-A

bin/convert_hmmer.py

+#!/usr/bin/python3
+import sys
+import json
+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')
+args = parser.parse_args()
+
+filename = args.result + "/domtblout.tsv"
+documents = {}
+tool = {'name': None, 'version': None, 'database': None}
+with open(filename) as f:
+    # first scan for tool information
+    for line in f:
+        if line.startswith("# Program:"):
+            tool['name'] = line.split()[2]
+        if line.startswith("# Version:"):
+            tool['version'] = line.split()[2]
+        if line.startswith("# Target file:"):
+            tool['database'] = line.split()[3]
+
+with open(filename) as f:
+    # second scan for data
+    for line in f:
+        if not line.startswith("#"):
+            split = line.split(None, 22)
+            query_id = split[3]
+            if not query_id in documents:
+                documents[query_id] = {"id": query_id, "computations": [{'tool': tool, 'results':[]}]}
+            results =  documents[query_id]['computations'][0]["results"]
+
+            results.append({
+                'target': {
+                    'name': split[0],
+                    'accession': split[1],
+                    'length': split[2],
+                    'score': float(split[13]),
+                    'start': int(split[15]),
+                    'end': int(split[16]),
+                    'description': split[22].rstrip()
+                    },
+                'query': {
+                    'start': int(split[17]),
+                    'end': int(split[19])
+                    }
+                })
+
+output_filename = args.output
+with open(output_filename, 'w') as o:
+    json.dump(documents, o)

bin/run_hmmer.py

+#!/usr/bin/env python3
+import argparse
+import config
+from os import system, makedirs
+
+hmmscan_tool = config.load_config()['tools'].get('hmmscan', 'hmmscan')
+
+parser = argparse.ArgumentParser(description='Search sequences against a profile database')
+parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
+parser.add_argument('--database', '-d', required=True, help='Database to search in')
+parser.add_argument('--output', '-o', required=True, help='The result directory')
+parser.add_argument('--evalue', '-e', default='0.0001', help='Evalue cutoff')
+args = parser.parse_args()
+
+makedirs(args.output, exist_ok=True)
+
+system(hmmscan_tool + 
+        " -E " + args.evalue + 
+        " -o " +args.output+ "/hmmscan.out " + 
+        " --tblout " + args.output + "/tblout.tsv "  + 
+        " --domtblout " + args.output + "/domtblout.tsv " + 
+        " --pfamtblout " + args.output + "/pfamtblout.tsv " + 
+        args.database + " " +  args.fasta)

config.yaml

@@ -14,6 +14,7 @@ profiles:
       modules:
           signalp:
           blastp_swissprot:
+          hmmer_pfam_a:
     - name: 'complete'
       info: 'Profile that uses all available tools'
       modules:

modules/hmmer_vs_PFAM-A.yaml

+# Module manifest for the blastp against swissprot analysis
+
+# The name of the module. Is needed for the list-analyses option, for custom
+# configurations and custom profiles
+name: 'hmmer_pfam_a'
+
+# Short description of the analysis
+info: 'hmmscan analysis against PFAM-A'
+
+# The name of the script for the analysis step. Must take a --fasta parameter
+analysis_script: 'run_hmmer.py'
+
+# The name of the result to json converter script. Must take one parameter, the
+# result file from the analysis_script
+converter_script: 'convert_hmmer.py'
+
+parameters:
+    database: '/vol/biodb/pfam/Pfam-A.hmm'
+    evalue: 1e-10