--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/bam_to_sam_parallel.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,172 @@
+#!/usr/bin/env python
+"""
+Converts BAM data to sorted SAM data.
+usage: bam_to_sam.py [options]
+   --input1: SAM file to be converted
+   --output1: output dataset in bam format
+"""
+
+import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random
+#from galaxy import eggs
+#import pkg_resources; pkg_resources.require( "bx-python" )
+#from bx.cookbook import doc_optparse
+#from galaxy import util
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+    
+def toTar(tarFileName, samOutputNames):
+    dir = os.path.dirname(tarFileName)    
+    tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
+    currentPath = os.getcwd()
+    os.chdir(dir)
+    for file in samOutputNames:
+        relativeFileName = os.path.basename(file)
+        tfile.add(relativeFileName)
+    os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
+    tfile.close()
+    os.chdir(currentPath)    
+
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' )
+    parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' )
+    #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' )
+    parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' )
+    #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' )
+    parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
+    ( options, args ) = parser.parse_args()
+
+
+    #Parse the input txt file and read a list of BAM files.
+    file = open(options.input1, "r")
+    lines = file.readlines()
+    inputFileNames = []
+    samOutputNames = []
+    outputName = options.output1
+    resDirName = os.path.dirname(outputName) + '/'
+    #Write output txt file and define all output sam file names.
+    out = open(outputName, "w")
+    for line in lines:
+        tab = line.split()
+        inputFileNames.append(tab[1])
+        samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000)
+        samOutputNames.append(samOutName)
+        out.write(tab[0] + '\t' + samOutName  + '\n')
+    file.close()
+    out.close()
+
+    # output version # of tool
+    try:
+        tmp_files = []
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_files.append(tmp)
+        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' )
+
+
+
+    tmp_dirs = []
+    for i in range(len(inputFileNames)):
+        try:
+            # exit if input file empty
+            if os.path.getsize( inputFileNames[i] ) == 0:
+                raise Exception, 'Initial input txt file is empty.'
+            # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
+            # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
+            # into memory ( controlled by option -m ).
+            tmp_dir = tempfile.mkdtemp()
+            tmp_dirs.append(tmp_dir)
+            tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
+            tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
+            tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
+            tmp_files.append(tmp_sorted_aligns_file_name)
+            tmp_sorted_aligns_file.close()
+            
+            command = 'samtools sort %s %s' % ( inputFileNames[i], tmp_sorted_aligns_file_base )
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, 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
+            # exit if sorted BAM file empty
+            if os.path.getsize( tmp_sorted_aligns_file_name) == 0:
+                raise Exception, 'Intermediate sorted BAM file empty'
+        except Exception, e:
+            stop_err( 'Error sorting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) )
+            
+        try:
+            # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ).
+            if options.header:
+                view_options = "-h"
+            else:
+                view_options = ""
+            command = 'samtools view %s -o %s %s' % ( view_options, samOutputNames[i], tmp_sorted_aligns_file_name )
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, 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
+        except Exception, e:
+            stop_err( 'Error extracting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) )
+        if os.path.getsize( samOutputNames[i] ) > 0:
+            sys.stdout.write( 'BAM file converted to SAM' )
+        else:
+            stop_err( 'The output file is empty, there may be an error with your input file.' )
+     
+    if options.outputTar != None:
+        toTar(options.outputTar, samOutputNames)       
+    #clean up temp files
+    for tmp_dir in tmp_dirs:
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+    #print tmp_files
+    #for tmp in tmp_files:
+    #    os.remove(tmp)            
+    
+
+if __name__=="__main__": __main__()