/tools/ngs_rna/tophat_wrapper.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 238 lines · 201 code · 15 blank · 22 comment · 54 complexity · a8e837aead14af8a38c01068e04a2c5a MD5 · raw file
- #!/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__()