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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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