diff kmer_analysis.py @ 18:a121cce43f90 draft

Uploaded

--- a/kmer_analysis.py	Fri May 29 09:17:29 2015 -0400
+++ b/kmer_analysis.py	Tue Jun 09 09:06:17 2015 -0400
@@ -367,12 +367,11 @@
 
     try:
         
-        if os.path.exists(options.dirout):
-            raise
-        try:
-            os.mkdir(options.dirout)
-        except:
-            raise 
+        if not os.path.exists(options.dirout):
+            try:
+                os.mkdir(options.dirout)
+            except Exception, e :
+                stop_err('Error running make directory : ' + str(e)) 
         
         ##testing indexed bam file
         if os.path.isfile(options.bamfile+".bai") :
@@ -404,7 +403,10 @@
         ## check gff reading
         if not GFF['order'] :
             stop_err( 'Incorrect GFF file' )
-        
+        for gene in GFF['order']:
+            if not GFF[gene]['exon'] :
+                del GFF[gene]
+                GFF['order'].remove(gene)  
         ## split bam
         split_bam(options.bamfile,tmpdir)
         ###################################