--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_slice_bam.py	Mon Aug 26 14:25:12 2013 -0400
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for slicing a BAM file by provided BED file using SAMTools.
+%prog input_filename.sam output_filename.bam
+"""
+#TODO: Confirm that the sort is necessary e.g. if input regions are out of order
+
+
+import sys, optparse, os, tempfile, subprocess, shutil
+
+CHUNK_SIZE = 2**20 #1mb
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    (options, args) = parser.parse_args()
+    
+    assert len( args ) == 4, "Invalid command line: samtools_slice_bam.py input.bam input.bam.bai input.interval output.bam"
+    input_bam_filename, input_index_filename, input_interval_filename, output_bam_filename = args
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-samtools_slice_bam-' )
+    
+    tmp_input_bam_filename = os.path.join( tmp_dir, 'input_bam.bam' )
+    os.symlink( input_bam_filename, tmp_input_bam_filename )
+    os.symlink( input_index_filename, "%s.bai" % tmp_input_bam_filename )
+    
+    #Slice BAM
+    unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' )
+    unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' )
+    cmd = 'samtools view -b -L "%s" "%s" > "%s"' % ( input_interval_filename, tmp_input_bam_filename, unsorted_bam_filename )
+    proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr = open( unsorted_stderr_filename )
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    #sort sam, so indexing will not fail
+    #TODO: confirm if sorting is necessary (is original BAM order maintained, or does the output follow the order of input intervals?)
+    sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' )
+    sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' )
+    cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_bam_filename )
+    proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr = open( sorted_stderr_filename )
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()