Update pysam to account for new syntax.

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)])
+    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)])
+    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')

rpkm_gro.py

@@ -47,7 +47,8 @@ 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)])
+    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')
@@ -61,7 +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)])
+    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')
@@ -112,7 +113,6 @@ def main():
     # Write out RPKM matrix
     filtered_peaks = filtered_rpkm[columns]
     filtered_rpkm.to_csv(args.factor + '_filtered_peaks.tsv', header=True, index=None, sep='\t')
-    peak_rpkm_only_sum.to_csv(args.factor + '_sum.tsv', header=True, index=True, sep='\t')
     pybedtools.BedTool.from_dataframe(filtered_peaks).saveas(args.factor + '_filtered_peaks.bed')