From 5b2c2706555a4ff047c4678e258843c31d6f4940 Mon Sep 17 00:00:00 2001
From: Helene RIMBERT <helene.rimbert@inrae.fr>
Date: Thu, 29 Jun 2023 15:31:50 +0200
Subject: [PATCH] IMPROVE: initialise chromosomeMap dict while reading input
GFF
---
bin/renameGffID.py | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/bin/renameGffID.py b/bin/renameGffID.py
index 22184bf..e80826a 100755
--- a/bin/renameGffID.py
+++ b/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()
--
GitLab