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
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
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
Title : _assembly_format
Usage : $bowtiefac->_determine_format
Function: set the format of output for current options
Returns : format of bowtie output
Args :
No-op.
No-op.
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