--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/tophat_parallel.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,325 @@
+
+#!/usr/bin/env python
+
+import optparse, os, shutil, subprocess, sys, tempfile, fileinput, tarfile,random
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def toTar(tarFileName, accepted_hits_outputNames):
+    fileName = os.path.splitext(tarFileName)[0]
+    fileNameBaseName = os.path.basename(fileName)
+    dir = os.path.dirname(tarFileName)    
+    tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
+    currentPath = os.getcwd()
+    os.chdir(dir)
+    for file in accepted_hits_outputNames:
+        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('-o', '--outputTxtFile', dest='outputTxtFile', help='for Differential expression analysis pipeline, new output option gives a txt output containing the list of mapping results.')
+    parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all accepted hits results in a tar file.' )
+    parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' )
+    parser.add_option( '-C', '--color-space', dest='color_space', action='store_true', help='This indicates color-space data' )
+    parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', default='junctions_output.bed', help='Junctions output file; formate is BED.' )
+    parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', default='hits_output_%s.bam' % random.randrange(0, 10000), help='Accepted hits output file; formate is BAM.' )
+    parser.add_option( '', '--own-file', dest='own_file', help='' )
+    parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' )
+    parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \
+                                                                                For, example, for paired end runs with fragments selected at 300bp, \
+                                                                                where each end is 50bp, you should set -r to be 200. There is no default, \
+                                                                                and this parameter is required for paired end runs.')
+    parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' )
+    parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', 
+                        help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' )
+    parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' )
+    parser.add_option( '-i', '--min-intron-length', dest='min_intron_length', 
+                        help='The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.' )
+    parser.add_option( '-I', '--max-intron-length', dest='max_intron_length', 
+                        help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' )
+    parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' )
+    parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' )
+    parser.add_option( '', '--initial-read-mismatches', dest='initial_read_mismatches', help='Number of mismatches allowed in the initial read mapping' )
+    parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' )
+    parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' )
+    parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' )
+    parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.(Not used since version 1.3.0)' )
+    parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' )
+    parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' )
+
+    # Options for supplying own junctions
+    parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \
+                                                                           TopHat will use the exon records in this file to build \
+                                                                           a set of known splice junctions for each gene, and will \
+                                                                           attempt to align reads to these junctions even if they \
+                                                                           would not normally be covered by the initial mapping.')
+    parser.add_option( '-j', '--raw-juncs', dest='raw_juncs', help='Supply TopHat with a list of raw junctions. Junctions are \
+                                                                    specified one per line, in a tab-delimited format. Records \
+                                                                    look like: <chrom> <left> <right> <+/-> left and right are \
+                                                                    zero-based coordinates, and specify the last character of the \
+                                                                    left sequenced to be spliced to the first character of the right \
+                                                                    sequence, inclusive.')
+    parser.add_option( '', '--no-novel-juncs', action="store_true", dest='no_novel_juncs', help="Only look for junctions indicated in the \
+                                                                                            supplied GFF file. (ignored without -G)")
+    parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.")
+    # Types of search.
+    parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.')
+    parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)')
+    parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' )
+    parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.')
+    parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' )
+    parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' )
+    parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' )
+    parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' )
+    parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' )
+    parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' )
+    parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
+    parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
+
+    # Wrapper options.
+    parser.add_option( '-1', '--input1', dest='input1', help='A list of the (forward or single-end) reads files of Sanger FASTQ format, txt format' )
+    #parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
+    #parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
+    parser.add_option( '-2', '--input2', dest='input2', help='The list of reverse reads file in Sanger FASTQ format' )
+    parser.add_option( '', '--single-paired', dest='single_paired', help='' )
+    parser.add_option( '', '--settings', dest='settings', help='' )
+
+    (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp_files = []
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_files.append(tmp)
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='tophat -v', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = open( tmp_stdout.name, 'rb' ).readline().strip()
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Tophat version\n' )
+
+    # Color or base space
+    space = ''
+    if options.color_space:
+        space = '-C'
+
+
+    #reads = options.input1
+    file = open(options.input1,"r")
+    lines = file.readlines()
+    inputFileNames = []
+    accepted_hits_outputNames = []
+    outputName = options.outputTxtFile
+    resDirName = os.path.dirname(outputName) + '/'
+    out = open(outputName, "w")
+    for line in lines:
+        tab = line.split()
+        inputFileNames.append(tab[1])
+        aHitOutName = resDirName + tab[0] + '_' + options.accepted_hits_output_file
+        accepted_hits_outputNames.append(aHitOutName) 
+        out.write(tab[0] + '\t' + aHitOutName + '\n')
+    file.close()
+    out.close()
+    
+    if options.input2:
+        revFile = open(options.input2,"r")
+        lines = revFile.readlines()
+        inputRevFileNames = []
+        for line in lines:
+            revTab = line.split()
+            inputRevFileNames.append(revTab[1])
+        revFile.close()
+
+    
+    # Creat bowtie index if necessary.
+    tmp_index_dirs = []
+    index_paths = []
+    tmp_index_dir = tempfile.mkdtemp()
+    tmp_index_dirs.append(tmp_index_dir)
+    if options.own_file:
+        index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) )
+        index_paths.append(index_path)
+        try:
+            os.link( options.own_file, index_path + '.fa' )
+        except:
+            # Tophat prefers (but doesn't require) fasta file to be in same directory, with .fa extension
+            pass
+        cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file, index_path )
+        try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_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:
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            stop_err( 'Error indexing reference sequence\n' + str( e ) )
+    else:
+        for file in inputFileNames:
+            tmp_index_dir = tempfile.mkdtemp()
+            index_path = tmp_index_dir + '/' + os.path.basename(file).split('.')[0]
+            index_paths.append(index_path)
+            tmp_index_dirs.append(tmp_index_dir)
+
+    
+    
+    # Build tophat command.
+    cmds = []
+    # for inputFileName in inputFileNames:
+    for i in range(len(inputFileNames)):
+        cmd = 'tophat %s %s %s '
+        input_files = inputFileNames[i]
+        if options.input2:
+            input_files += ' ' + inputRevFileNames[i]
+        opts = '-p %s %s' % ( options.num_threads, space )
+        if options.single_paired == 'paired':
+            opts += '-r %s ' % options.mate_inner_dist
+        if options.settings == 'preSet':
+            if options.own_file:
+                cmd = cmd % ( opts, index_paths[0], input_files ) #here add paired end file
+            else:
+                cmd = cmd % ( opts, index_paths[i], input_files ) #here add paired end file
+        else:
+            try:
+                if int( options.min_anchor_length ) >= 3:
+                    opts += '-a %s ' % options.min_anchor_length
+                else:
+                    raise Exception, 'Minimum anchor length must be 3 or greater'
+                opts += '-m %s ' % options.splice_mismatches
+                opts += '-i %s ' % options.min_intron_length
+                opts += '-I %s ' % options.max_intron_length
+                if float( options.junction_filter ) != 0.0:
+                    opts += '-F %s ' % options.junction_filter
+                opts += '-g %s ' % options.max_multihits
+                # Custom junctions options.
+                if options.gene_model_annotations:
+                    opts += '-G %s ' % options.gene_model_annotations
+                if options.raw_juncs:
+                    opts += '-j %s ' % options.raw_juncs
+                if options.no_novel_juncs:
+                    opts += '--no-novel-juncs '
+                if options.library_type:
+                    opts += '--library-type %s ' % options.library_type
+                if options.no_novel_indels:
+                    opts += '--no-novel-indels '
+                else:
+                    if options.max_insertion_length:
+                        opts += '--max-insertion-length %i ' % int( options.max_insertion_length )
+                    if options.max_deletion_length:
+                        opts += '--max-deletion-length %i ' % int( options.max_deletion_length )
+                    # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)
+                    # need to warn user of this fact
+                    #sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
+    
+                # Search type options.
+                if options.coverage_search:
+                    opts += '--coverage-search --min-coverage-intron %s --max-coverage-intron %s ' % ( options.min_coverage_intron, options.max_coverage_intron )
+                else:
+                    opts += '--no-coverage-search '
+                if options.closure_search:
+                    opts += '--closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s '  % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron ) 
+                else:
+                    opts += '--no-closure-search '
+                if options.microexon_search:
+                    opts += '--microexon-search '
+                if options.single_paired == 'paired':
+                    opts += '--mate-std-dev %s ' % options.mate_std_dev
+                if options.initial_read_mismatches:
+                    opts += '--initial-read-mismatches %d ' % int( options.initial_read_mismatches )
+                if options.seg_mismatches:
+                    opts += '--segment-mismatches %d ' % int( options.seg_mismatches )
+                if options.seg_length:
+                    opts += '--segment-length %d ' % int( options.seg_length )
+                if options.min_segment_intron:
+                    opts += '--min-segment-intron %d ' % int( options.min_segment_intron )
+                if options.max_segment_intron:
+                    opts += '--max-segment-intron %d ' % int( options.max_segment_intron )
+                if options.own_file:
+                    cmd = cmd % ( opts, index_paths[0], input_files ) #here to add paired end file
+                else:
+                    cmd = cmd % ( opts, index_paths[i], input_files ) #here to add paired end file
+            except Exception, e:
+                # Clean up temp dirs
+                if os.path.exists( tmp_index_dir ):
+                    shutil.rmtree( tmp_index_dir )
+                stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
+                
+        cmds.append(cmd)
+
+    # Run the command line for each file.
+    for i in range(len(cmds)):
+        try:
+            tmp_out = tempfile.NamedTemporaryFile().name
+            tmp_files.append(tmp_out)
+            tmp_stdout = open( tmp_out, 'wb' )
+            tmp_err = tempfile.NamedTemporaryFile().name
+            tmp_files.append(tmp_err)
+            tmp_stderr = open( tmp_err, 'wb' )
+            proc = subprocess.Popen( args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp_err, '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_stdout.close()
+            tmp_stderr.close()
+            if returncode != 0:
+                raise Exception, stderr
+                
+            # Copy output files from tmp directory to specified files.
+            #shutil.copyfile( os.path.join( "tophat_out", "junctions.bed" ), junctions_outputNames[i] )
+            shutil.copyfile( os.path.join( "tophat_out", "accepted_hits.bam" ), accepted_hits_outputNames[i] )
+            # TODO: look for errors in program output.
+        except Exception, e:
+            stop_err( 'Error in tophat:\n' + str( e ) ) 
+
+    if options.outputTar != None:
+        toTar(options.outputTar, accepted_hits_outputNames)
+
+    
+    # Clean up temp dirs
+    for tmp_index_dir in tmp_index_dirs:
+        if os.path.exists( tmp_index_dir ):
+            shutil.rmtree( tmp_index_dir )
+
+    for tmp in tmp_files:
+        os.remove(tmp)
+
+
+if __name__=="__main__": __main__()