initial import

SVN: 19218

deep_sequencing_unit/source/Python/bam2wig.py

+#!/usr/bin/env python
+# Manuel Kohler, ETH Zuerich, 12/2010
+
+# Creates a Wiggle file out of a BAM file
+
+# Prerequisite:  BAM index file 
+# Documentation says: 'If an index for a BAM file exists (.bai), it will be opened automatically.
+# Without an index random access to reads via fetch() and pileup() is disabled.'
+
+import sys, pysam
+bamfile_name = sys.argv[1]
+bamfile = pysam.Samfile(bamfile_name,'rb')
+wigfile_name = bamfile_name.replace('.bam', '.wig')
+wigfile = open(wigfile_name, 'w')
+header_full = 'track type=wiggle_0 name=' + wigfile_name
+variable_wig = 'variableStep chrom=chr'
+
+print >> wigfile, header_full
+for gene_names in range(bamfile.nreferences):
+  # UCSC conformity
+  if bamfile.getrname(gene_names) == 'dmel_mitochondrion_genome':
+    print >> wigfile, variable_wig+'M'
+  else:
+    print >> wigfile, variable_wig+bamfile.getrname(gene_names)
+  for pile in bamfile.pileup(bamfile.getrname(gene_names)):
+    print >> wigfile, pile.pos, pile.n 
+
+bamfile.close()
+wigfile.close()