From 202ae5c75ed0b9c6191d4fdf2e86994b86f678c4 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 7 Mar 2017 10:09:44 -0600
Subject: [PATCH] fix syntax.
---
rpkm.py | 4 ++--
rpkm_gro.py | 1 -
2 files changed, 2 insertions(+), 3 deletions(-)
diff --git a/rpkm.py b/rpkm.py
index 77e195a..4895f5f 100755
--- a/rpkm.py
+++ b/rpkm.py
@@ -47,7 +47,7 @@ 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,,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, 3, float(math.pow(10,9))/total_counts).saveas("test.bed")
rpkm_df = rpkm.to_dataframe()
#os.remove('test.bed')
@@ -61,7 +61,7 @@ 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')
diff --git a/rpkm_gro.py b/rpkm_gro.py
index cae162d..4cf65f2 100755
--- a/rpkm_gro.py
+++ b/rpkm_gro.py
@@ -48,7 +48,6 @@ def rpkm(peak_file,aln_file,exp_name,columns):
## 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,split_lines=True)])
- print total_counts
rpkm = peak_counts.each(normalized_to_length, 3, float(math.pow(10,9))/total_counts).saveas("test.bed")
rpkm_df = rpkm.to_dataframe()
#os.remove('test.bed')
--
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