srf2fastq(1) Staden io_lib srf2fastq(1)NAME
srf2fastq - Converts SRF files to Sanger fastq format
SYNOPSIS
srf2fastq [options] srf_archive ...
DESCRIPTION
srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout.
Note that Illumina also have a fastq format (used in the GERALD directories) which differs slightly in the use of log-odds scores for the
quality values. The format described here is using the traditional Phred style of quality encoding.
OPTIONS -c Outputs calibrated confidence values using the ZTR CNF1 chunk type for a single quality per base. Without this use the original
Illumina _prb.txt files consisting of four quality values per base, stored in the ZTR CNF4 chunks.
-C Masks out sequences tagged as bad quality.
-s root
Generates files on disk with filenames starting root, one file per non-explicit element in the SRF/ZTR region (REGN) chunk. Typi-
cally this results in two files for paired end runs. The filename suffixes come from the names listed in the SRF region chunks.
This option conflicts with the -S parameter.
-S Splits sequences into regions, but sequentially lists each sequence region to stdout instead of splitting to separate files on disk.
This option conflicts with the -s parameter.
-n When using -s the filename suffixes are simply numbered (starting with 1) instead of using the names listed in the SRF region
chunks.
-a Appends region index to the sequence names. Ie generate "name/1" and "name/2" for a paired read.
-e Include any explicit sequence (ZTR region chunk of type 'E') in the sequence output. The explicit sequence is also included in the
quality line too. Currently this is utilised by ABI SOLiD to store the last base of the primer.
-r region list
Reverse complements the sequence and reverses the quality values for all regions in the region list. This is a comma separated list
of integer values enumerating the regions, starting from 1. Note that this option only works when either -s or -S are specified.
EXAMPLES
To extract only the good quality sequences from all srf files in the current directory using calibrated confidence values (if available).
srf2fastq -c -C *.srf > runX.fastq
To extract a paired end run into two separate files with sequences named name/1 and name/2.
srf2fastq -s runX -a -n runX.srf
To extract a paired end run as a single file, alternating forward and reverse sequences, with the second read being reverse complemented.
srf2fastq -S -r 2 runX.srf > runX.fastq
AUTHOR
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
December 10 srf2fastq(1)
Check Out this Related Man Page
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)