diff tools/samtools/sam_merge.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools/sam_merge.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+
+"""
+Merges any number of BAM files
+usage: %prog [options]
+    input1
+    output1
+    input2
+    [input3[,input4[,input5[,...]]]]
+"""
+
+import os, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def __main__():
+    infile =  sys.argv[1]
+    outfile = sys.argv[2]
+    if len( sys.argv ) < 3:
+        stop_err( 'There are not enough files to merge' )
+    filenames = sys.argv[3:]
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'Samtools %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Samtools version\n' )
+    cmd = 'samtools merge %s %s %s' % ( outfile, infile, ' '.join( filenames ) )
+    tmp = tempfile.NamedTemporaryFile().name
+    try:
+        tmp_stderr = open( tmp, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        tmp_stderr = open( tmp, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        if returncode != 0:
+            raise Exception, stderr
+        if os.path.exists( tmp ):
+            os.unlink( tmp )
+    except Exception, e:
+        if os.path.exists( tmp ):
+            os.unlink( tmp )
+        stop_err( 'Error running SAMtools merge tool\n' + str( e ) )
+    if os.path.getsize( outfile ) > 0:
+        sys.stdout.write( '%s files merged.' % ( len( sys.argv ) - 2 ) )
+    else:
+        stop_err( 'The output file is empty, there may be an error with one of your input files.' )
+
+if __name__ == "__main__" : __main__()