Provided by: libbio-perl-run-perl_1.7.2-4_all bug


       Bio::Tools::Run::Bowtie - Run wrapper for the Bowtie short-read assembler *BETA*


        # create an index
        $bowtie_build = Bio::Tools::Run::Bowtie->new();
        $index = $bowtie_fac->run( 'reference.fasta', 'index_base' );

        # or with named args...

        $index = $bowtie_fac->run( -ref => 'reference.fasta', -ind => 'index_base' );

        # get the base name of the last index from an index builder
        $index = $bowtie_fac->result;

        # create an assembly
        $bowtie_fac = Bio::Tools::Run::Bowtie->new();
        $bowtie_assy = $bowtie_fac->run( 'reads.fastq', 'index_base' );

        # if IO::Uncompress::Gunzip is available and with named args...
        $bowtie_assy = $bowtie_fac->run( -seq => 'reads.fastq.gz', -ind => 'index_base' );

        # paired-end
        $bowtie_fac = Bio::Tools::Run::Bowtie->new(-command => 'paired',
                                                   -want => 'Bio::Assembly::Scaffold');
        $bowtie_assy = $bowtie_fac->run( 'reads.fastq', 'index_base', 'paired-reads.fastq' );

        # be more strict
        $bowtie_fac->set_parameters( -max_qual_mismatch => 50 );

        # create a Bio::Assembly::Scaffold object
        $bowtie_assy = $bowtie_fac->run( 'reads.fastq', 'index_base', 'paired-reads.fastq'  );

        # print consensus sequences from assembly object
        for $contig ($bowtie_assy->all_contigs) {
           print $contig->get_consensus_sequence->seq,"\n";

        # get the file object of the last assembly
        $io = $bowtie_fac->result( -want => 'Bio::Root::IO' );

        # get a merged SeqFeature::Collection of all hits
        #  - currently only available with SAM format
        $io = $bowtie_fac->result( -want => 'Bio::SeqFeature::Collection' );

        #... or the file name directly
        $filename = $bowtie_fac->result( -want => 'raw' );


       This module provides a wrapper interface for Ben Langmead and Col Trapnell's ultrafast
       memory-efficient short read aligner "bowtie" (see <> for
       manuals and downloads).


       "bowtie" is complex, with many command-line options. This module attempts to provide and
       options comprehensively. You can browse the choices like so:

        $bowtiefac = Bio::Tools::Run::Bowtie->new( -command => 'single' );
        # all bowtie commands
        @all_commands = $bowtiefac->available_parameters('commands');
        @all_commands = $bowtiefac->available_commands; # alias
        # just for single
        @assemble_params = $bowtiefac->available_parameters('params');
        @assemble_switches = $bowtiefac->available_parameters('switches');
        @assemble_all_options = $bowtiefac->available_parameters();

       Reasonably mnemonic names have been assigned to the single-letter command line options.
       These are the names returned by "available_parameters", and can be used in the factory
       constructor like typical BioPerl named parameters.

       As a number of options are mutually exclusive, and the interpretation of intent is based
       on last-pass option reaching bowtie with potentially unpredicted results. This module will
       prevent inconsistent switches and parameters from being passed.

       See <> for details of bowtie options.


       When a command requires filenames, these are provided to the "run" method, not the
       constructor ("new()"). To see the set of files required by a command, use
       "available_parameters('filespec')" or the alias "filespec()":

         $bowtiefac = Bio::Tools::Run::Bowtie->new( -command => 'paired' );
         @filespec = $bowtiefac->filespec;

       This example returns the following array:


       This indicates that ind ("bowtie" index file base name), seq (fasta/fastq),and seq2
       (fasta/fastq) files MUST be specified, and that the out file MAY be specified. Use these
       in the "run" call like so:

        $bowtiefac->run( -ind => 'index_base', -seq => 'seq-a.fq',
                         -seq2 => 'seq-b.fq', -out => 'align.out' );

       Note that named parameters in this form allow you to specify the location of the outfile;
       without named parameters, the outfile is located in a tempdir and does not persist beyond
       the life of the object - with the exception of index creation.

       The object will store the programs STDOUT and STDERR output for you in the "stdout()" and
       "stderr()" attributes:

        handle_map_warning($bowtiefac) if ($bowtiefac->stderr =~ /warning/);


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       is much appreciated.
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       Please direct usage questions or support issues to the mailing list:

       Rather than to the module maintainer directly. Many experienced and reponsive experts will
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       of the problem with code and data examples if at all possible.

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AUTHOR - Dan Kortschak

        Email dan.kortschak


        Mark A. Jensen (maj -at- fortinbras -dot- us)


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = new Bio::Tools::Run::Bowtie();
        Function: Builds a new Bio::Tools::Run::Bowtie object
        Returns : an instance of Bio::Tools::Run::Bowtie
        Args    :

        Title   : run
        Usage   : $assembly = $bowtie_assembler->run($read1_fastq_file,
                  $assembly = $bowtie_assembler->run(%params);
        Function: Run the bowtie assembly pipeline.
        Returns : Assembly results (file, IO object or Assembly object)
        Args    : - fastq file containing single-end reads
                  - name of the base of the bowtie index
                  - [optional] fastq file containing paired-end reads
                  Named params are also available with args:
                  -seq, -seq2, -ind (bowtie index), -ref (fasta reference) and -out
        Note    : gzipped inputs are allowed if IO::Uncompress::Gunzip
                  is available
                  The behaviour for locating indexes follows the definition in
                  the bowtie manual - you may use the environment variable
                  BOWTIE_INDEXES to specify the index path or use an 'indexes'
                  directory under the directory where the bowtie executable
                  is located

        Title   : want
        Usage   : $bowtiefac->want( $class )
        Function: make factory return $class, or raw (scalar) results in file
        Returns : return wanted type
        Args    : [optional] string indicating class or raw of wanted result

        Title   : result
        Usage   : $bowtiefac->result( [-want => $type|$format] )
        Function: return result in wanted format
        Returns : results
        Args    : [optional] hashref of wanted type

        Title   : _determine_format
        Usage   : $bowtiefac->_determine_format
        Function: determine the format of output for current options
        Returns : format of bowtie output
        Args    :

        Title   : _make_bam
        Usage   : $bowtiefac->_make_bam( $file, $sort )
        Function: make a sorted BAM format file from SAM file
        Returns : sorted BAM file name
        Args    : SAM file name and boolean flag to select sorted BAM format

        Title   : _validate_file_input
        Usage   : $bowtiefac->_validate_file_input( -type => $file )
        Function: validate file type for file spec
        Returns : file type if valid type for file spec
        Args    : hash of filespec => file_name

Bio::Tools::Run::AssemblerBase overrides

        Title   : _assembly_format
        Usage   : $bowtiefac->_determine_format
        Function: set the format of output for current options
        Returns : format of bowtie output
        Args    :



        Prepare and check input sequences for bowtie.

        Title   : set_parameters
        Usage   : $bowtiefac->set_parameters(%params);
        Function: sets the parameters listed in the hash or array,
                  maintaining sane options.
        Returns : true on success
        Args    : [optional] hash or array of parameter/values.
        Note    : This will unset conflicts and set required options,
                  but will not prevent non-sane requests in the arguments

        Title   : version
        Usage   : $version = $bowtiefac->version()
        Function: Returns the program version (if available)
        Returns : string representing location and version of the program