From 47afde44453c583873910a8dbcab782395e8ccb8 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 7 Mar 2017 10:23:38 -0600
Subject: [PATCH] Fix name rpkm values.
---
rpkm_name.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rpkm_name.py b/rpkm_name.py
index 9363f10..6f40d4e 100755
--- a/rpkm_name.py
+++ b/rpkm_name.py
@@ -50,7 +50,7 @@ def rpkm(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])
- total_counts = reduce(lambda x, y: x + y, [ int(l.rstrip('\n').split('\t')[2]) for l in pysam.idxstats(aln_file)])
+ 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, 4, float(math.pow(10,9))/total_counts).saveas("test.bed")
rpkm_df = rpkm.to_dataframe()
#os.remove('test.bed')
--
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