# HG changeset patch
# User fubar
# Date 1370588389 14400
# Node ID 63eaa64904be19250aa305a1bb1b56fc5b266859
# Parent  9b2f58a260e9e506564d17b0d15277296d380137
Uploaded

diff -r 9b2f58a260e9 -r 63eaa64904be htseq_bams_to_count_matrix/htseqsams2mx.py
--- a/htseq_bams_to_count_matrix/htseqsams2mx.py	Fri Jun 07 02:46:09 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.py	Fri Jun 07 02:59:49 2013 -0400
@@ -303,16 +303,17 @@
     scolnames = [x.split(',')[1].replace("'",'').replace('"','') for x in samdat]
     assert len(samf) == len(scolnames), '##ERROR sams2mx: Count of sam/cname not consistent - %d/%d' % (len(samf),len(scolname))
     for i,b in enumerate(samf):
-        assert os.path.isfile(b),'## Supplied input sam file "%s" not found' % b
-        sam_filenames.append(b)
-        sampName = scolnames[i] # better be unique
-        if sampName == "":
-            sampName = b # for test
-        sampName = sampName.replace('#','') # for R
-        sampName = sampName.replace('(','') # for R
-        sampName = sampName.replace(')','') # for R
-        sampName = sampName.replace(' ','_') # for R
-        colnames.append(sampName)
+        if b != 'None':
+            assert os.path.isfile(b),'## Supplied input sam file "%s" not found' % b
+            sam_filenames.append(b)
+            sampName = scolnames[i] # better be unique
+            if sampName == "":
+                sampName = b # for test
+            sampName = sampName.replace('#','') # for R
+            sampName = sampName.replace('(','') # for R
+            sampName = sampName.replace(')','') # for R
+            sampName = sampName.replace(' ','_') # for R
+            colnames.append(sampName)
     counts,empty,ambiguous,lowqual,notaligned,nonunique = htseqMX(gff_file, sam_filenames,colnames,opts)
     heads = '\t'.join(['Contig',] + colnames)
     res = [heads,]
diff -r 9b2f58a260e9 -r 63eaa64904be htseq_bams_to_count_matrix/htseqsams2mx.xml
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml	Fri Jun 07 02:46:09 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml	Fri Jun 07 02:59:49 2013 -0400
@@ -23,7 +23,7 @@
     --samf "'$fourthsamf','${fourthsamf.name}'"
     #end if
     #for $s in $samfiles:
-      #if $s.samf.name:
+      #if $s.samf != None:
         --samf "'${s.samf}','${s.samf.name}'" 
       #end if
     #end for