--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tophat_wrapper.py	Mon Jan 27 09:25:27 2014 -0500
@@ -0,0 +1,238 @@
+#!/usr/bin/env python
+
+import optparse, os, shutil, subprocess, sys, tempfile, fileinput
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    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', help='Junctions output file; formate is BED.' )
+    parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', 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( '-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='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( '', '--single-paired', dest='single_paired', help='' )
+    parser.add_option( '', '--settings', dest='settings', help='' )
+
+    (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        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'
+
+    # Creat bowtie index if necessary.
+    tmp_index_dir = tempfile.mkdtemp()
+    if options.own_file:
+        index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) )
+        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:
+        index_path = options.index_path
+
+    # Build tophat command.
+    cmd = 'tophat %s %s %s'
+    reads = options.input1
+    if options.input2:
+        reads += ' ' + options.input2
+    opts = '-p %s %s' % ( options.num_threads, space )
+    if options.single_paired == 'paired':
+        opts += ' -r %s' % options.mate_inner_dist
+    if options.settings == 'preSet':
+        cmd = cmd % ( opts, index_path, reads )
+    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
+            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 )
+            cmd = cmd % ( opts, index_path, reads )
+        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 ) )
+    #print cmd
+
+    # Run
+    try:
+        tmp_out = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp_out, 'wb' )
+        tmp_err = tempfile.NamedTemporaryFile().name
+        tmp_stderr = open( tmp_err, 'wb' )
+        print cmd
+        proc = subprocess.Popen( args=cmd, 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
+            
+        # TODO: look for errors in program output.
+    except Exception, e:
+        stop_err( 'Error in tophat:\n' + str( e ) ) 
+
+    # Clean up temp dirs
+    if os.path.exists( tmp_index_dir ):
+        shutil.rmtree( tmp_index_dir )
+
+if __name__=="__main__": __main__()