accept wildcard <group> as parameter to improve usability

workflow/scripts/add_infos_to_vcf.py

@@ -6,22 +6,23 @@
 This script combines multiple vcfs into one vcf. It adds a new INFO field for the group name
 
 Usage:
-python combine_vcf.py '<input_vcfs>' <method> <output_vcf>
+python combine_vcf.py '<input_vcfs>' <method> <group> <output_vcf>
 '''
 
 def main():
     vcf = sys.argv[1]
     # extract the replicate (e.g., {rep1}_*.vcf)
-    if '_call.indel.vcf' in str(Path(vcf).name):
-        rpl = Path(vcf).name.split('_call.indel.vcf')[0]
-    elif '_somatic.short.indels.vcf' in str(Path(vcf).name):
-        rpl = Path(vcf).name.split('_somatic.short.indels.vcf')[0]
-    elif '_somatic.snvs.vcf' in str(Path(vcf).name):
-        rpl = Path(vcf).name.split('_somatic.snvs.vcf')[0]
-    elif '_fusions.vcf' in str(Path(vcf).name):
-        rpl = Path(vcf).name.split('_fusions.vcf')[0]
-    elif '_exitrons.vcf' in str(Path(vcf).name):
-        rpl = Path(vcf).name.split('_exitrons.vcf')[0]
+
+    # if '_call.indel.vcf' in str(Path(vcf).name):
+        # rpl = Path(vcf).name.split('_call.indel.vcf')[0]
+    # elif '_somatic.short.indels.vcf' in str(Path(vcf).name):
+        # rpl = Path(vcf).name.split('_somatic.short.indels.vcf')[0]
+    # elif '_somatic.snvs.vcf' in str(Path(vcf).name):
+        # rpl = Path(vcf).name.split('_somatic.snvs.vcf')[0]
+    # elif '_fusions.vcf' in str(Path(vcf).name):
+        # rpl = Path(vcf).name.split('_fusions.vcf')[0]
+    # elif '_exitrons.vcf' in str(Path(vcf).name):
+        # rpl = Path(vcf).name.split('_exitrons.vcf')[0]
 
     reader = vcfpy.Reader.from_path(vcf)
     reader.header.add_info_line(
@@ -37,12 +38,12 @@ def main():
              ('Type', 'String'),
              ('Description', 'Source of the variant')]))
 
-    writer = vcfpy.Writer.from_path(sys.argv[3], reader.header)
+    writer = vcfpy.Writer.from_path(sys.argv[4], reader.header)
 
     # iterate through all records
     for record in reader:
-        record.INFO['GRP'] = rpl
         record.INFO['SRC'] = sys.argv[2]
+        record.INFO['GRP'] = sys.argv[3]
         writer.write_record(record)
 
 main()