diff annotateviz.py @ 0:7537482eed36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotateviz.py	Sat Jun 17 13:31:06 2017 -0400
@@ -0,0 +1,30 @@
+import sys
+import os
+import gffutils
+import argparse
+import json
+
+def add_matches(matches,array):
+    for m in matches:
+        trans = {}
+        trans['mRNA'] = '.'.join(m.id.split('.',2)[:2]) #hack to recover mRNA from PFAM gff which doesn't include a query field
+        trans['Contig'] = m.seqid
+        trans['Source'] = m.source
+        trans['Score'] = m.score
+        trans['Prediction']=m["Name"]
+        array.append(trans)
+def main(argv, wayout):
+        if not len(argv):
+                argv.append("-h")
+        parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
+        parser.add_argument('-d','--database', help="gffutils sqlite database")
+        parser.add_argument('-j','--json', help="report in json format")
+        gffutils.constants.always_return_list = False
+        db = gffutils.interface.FeatureDB(args.database)
+        prediction_list = []
+        add_matches(db.features_of_type("protein_match"), prediction_list)
+        add_matches(db.features_of_type("signalpep"), prediction_list)
+        add_matches(db.features_of_type("trans_helix"), prediction_list)
+        add_matches(db.features_of_type("PFAM"), prediction_list)
+        fout=open(args.json, 'w')
+        json.dump(prediction_list,fout)