Christopher Fields > BioPerl-Run > Bio::Tools::Run::Bowtie

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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
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