From 6a8c4de25a0059d010a2a41420747a849f9214b9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Thu, 2 Mar 2017 11:34:02 -0600
Subject: [PATCH] Update pysam to account for new syntax.
---
rpkm_gro.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rpkm_gro.py b/rpkm_gro.py
index ee3c56a..732206e 100755
--- a/rpkm_gro.py
+++ b/rpkm_gro.py
@@ -62,7 +62,7 @@ def rpkm_strand(peak_file,aln_file,exp_name,columns):
columns.append(exp_name)
## RPKM = numReads / (geneLength/1000 * totalNumReads/1,000,000 )
peak_counts = peak_file.multi_bam_coverage(bams=[aln_file],s=True)
- total_counts = reduce(lambda x, y: x + y, [ int(l.rstrip('\n').split('\t')[2]) for l in pysam.idxstats(aln_file,split_lines=True))])
+ total_counts = reduce(lambda x, y: x + y, [ int(l.rstrip('\n').split('\t')[2]) for l in pysam.idxstats(aln_file,split_lines=True)])
rpkm = peak_counts.each(normalized_to_length, 6, float(math.pow(10,9))/float(total_counts)).saveas("test.bed")
rpkm_df = rpkm.to_dataframe()
#os.remove('test.bed')
--
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