Bio::Tools::Run::Bowtie(3pm)				User Contributed Perl Documentation			      Bio::Tools::Run::Bowtie(3pm)

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,"
";
	}

	# 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/ <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 <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

perl v5.12.3							    2011-06-18					      Bio::Tools::Run::Bowtie(3pm)