Merge branch...

Merge branch '5-improve-renamegffids-py-build-chromosome-map-based-on-input-gff-and-not-mapping-file' into 'missing_conda_rules'

IMPROVE: initialise chromosomeMap dict while reading input GFF

See merge request !5

bin/renameGffID.py

@@ -24,7 +24,7 @@ class renameIDs (object):
 		self.checkInputs()
 
 		# load inputs
-		self.loadChromosomeMap()
+		#self.loadChromosomeMap()
 
 		# open filehandler for output files
 		self.prepareOutputFiles()
@@ -251,6 +251,14 @@ class renameIDs (object):
 					coord=line.rstrip('\n').split('\t')[3]
 					stop=line.rstrip('\n').split('\t')[4]
 					geneId=self.getFeatureAttribute(gff=line, attribute='ID')
+
+
+					# check if this chromosome is in the mapping dictionaries
+					if (chrom not in self.chromosomeMap.keys()):
+						self.chromosomeMap[chrom] = chrom
+						self.geneMapCoord[chrom] = defaultdict()
+						self.newGeneMapCoord[chrom] = defaultdict()
+						
 					if featureType == 'gene':
 						while coord in self.geneMapCoord[chrom].keys():
 							sys.stderr.write(" WARNING: gene {} has same coordinate as gene {} \n".format(geneId, self.geneMapCoord[chrom][coord]))
@@ -289,9 +297,6 @@ class renameIDs (object):
 			for line in maprecord.readlines():
 				if not line.startswith('#'):
 					(name, id) = line.rstrip('\n').split('\t')
-					#self.chromosomeMap[name] = id
-					#self.geneMapCoord[name] = defaultdict()
-					#self.newGeneMapCoord[name] = defaultdict()
 					self.chromosomeMap[id] = name
 					self.geneMapCoord[id] = defaultdict()
 					self.newGeneMapCoord[id] = defaultdict()