NAME

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

SYNOPSIS

        # 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_fac->want('Bio::Assembly::Scaffold');
        $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' );

DESCRIPTION

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

OPTIONS

       "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 <http://bowtie.sourceforge.net/bowtie-manpage.shtml> for details of bowtie options.

FILES

       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:

        ind
        seq
        seq2
        #out

       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/);

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       Rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Dan Kortschak

        Email dan.kortschak adelaide.edu.au

CONTRIBUTORS

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

APPENDIX

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

   new()
        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    :

   run()
        Title   : run
        Usage   : $assembly = $bowtie_assembler->run($read1_fastq_file,
                                                  $index_location,
                                                  $read2_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

   want()
        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

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

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

   _make_bam()
        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

   _validate_file_input()
        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

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

   _check_sequence_input()
        No-op.

   _check_optional_quality_input()
        No-op.

   _prepare_input_sequences()
        Prepare and check input sequences for bowtie.

   set_parameters()
        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

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