correction of gff attribute modification in bin/reformatGmapWGGFF.py

bin/reformatGmapWGGFF.py

-#!/usr/bin/env python3
+#!/usr/bin/env python3.5
 # coding: utf-8
 import os.path
 from os import path
@@ -23,6 +23,7 @@ class reformatGmapGff (object):
 	def main(self):
 		self.getOptions()
 		self.checkInputs()
+		self.regexlcl=re.compile(r'lcl\|')
 
 		# load inputs
 		self.loadChromosomeMap()
@@ -74,6 +75,9 @@ class reformatGmapGff (object):
 							print("\t".join(map(str, feature)), file=self.errorFH)
 							
 	def reformatGff(self):
+		lastmrna=''
+		featureindex={'CDS':1, 'exon':1}
+
 		with open(self.options.input) as mygff:
 			for line in mygff.readlines():
 				if not line.startswith('#'):
@@ -84,6 +88,7 @@ class reformatGmapGff (object):
 					if featuretype == 'gene':
 						# get only the gene name because here the ID corresponds to the mrna isoform which has been mapped
 						geneId=featureId.split('.')[0]
+						lastmrna=''
 						
 						if geneId not in self.knownGenes:
 							self.knownGenes.append(geneId)
@@ -100,11 +105,13 @@ class reformatGmapGff (object):
 								'attributes': gff_array[8]}
 
 					elif featuretype == 'mRNA':
-						mrna=self.getFeatureAttribute(gff=line, attribute='ID')
+						mrna=self.getFeatureAttribute(gff=line, attribute='Name')
+						lastmrna=mrna
+						featureindex={'CDS':1, 'exon':1}
 						self.knownMrna.append(mrna)
 						parent=mrna.split('.')[0]
 						self.geneIsoforms[parent].append(mrna)
-						gff_array[8] = self.setGffAttributes(attributes=gff_array[8], new={'Parent': parent})
+						gff_array[8] = self.setGffAttributes(attributes=gff_array[8], new={'Parent': parent, 'ID':mrna, 'Name':mrna})
 						self.mrnaFeatures[mrna]=[gff_array]
 
 						# check if this new mrna has start or stop different from the gene feature
@@ -118,9 +125,13 @@ class reformatGmapGff (object):
 							sys.stderr.write(" New gene length: {}\n".format(int(gff_array[4])-int(gff_array[3])+1))
 						
 					else:
-						featureId=self.getFeatureAttribute(gff=line, attribute='ID')
-						featureParent=self.getFeatureAttribute(gff=line, attribute='Parent')
-						self.mrnaFeatures[featureParent].append(line.rstrip('\n').split('\t'))
+						
+						featureId=lastmrna+'.'+featuretype.lower()+str(featureindex[featuretype])
+						featureParent=lastmrna
+						gff_array[8] = self.setGffAttributes(attributes=gff_array[8], new={'ID':featureId, 'Parent': featureParent, 'Name':featureId})
+						self.mrnaFeatures[featureParent].append(gff_array)
+						featureindex[featuretype]+=1
+
 
 		numgenes=len(self.knownGenes)
 		nummrna=len(self.knownMrna)
@@ -154,6 +165,8 @@ class reformatGmapGff (object):
 			(key, val) = attr.split('=')
 			attr_dict[key] = val
 		if attribute in attr_dict.keys():
+			if self.regexlcl.search(attr_dict[attribute]) and attribute in ['ID', 'Parent', 'Name']:
+				attr_dict[attribute] = self.regexlcl.sub('',attr_dict[attribute])
 			return attr_dict[attribute]
 		else:
 			sys.stderr.write(' ERROR: no attribute {} in gff record {}'.format(attribute, gff))
@@ -196,4 +209,4 @@ class reformatGmapGff (object):
 if __name__== "__main__":
 
 	run=reformatGmapGff()
-	run.main()
\ No newline at end of file
+	run.main()