Bio::Tools::Run::Bowtie - Run wrapper for the Bowtie short-read assembler *BETA*
Index
Code Index:
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 :
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
# $Id: Bowtie.pm kortsch $
#
# BioPerl module for Bio::Tools::Run::Bowtie
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Dan Kortschak <dan.kortschak@adelaide.edu.au>
#
# Copyright Dan Kortschak and Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# Let the code begin...
package Bio::Tools::Run::Bowtie;
use strict;
our $HAVE_IO_UNCOMPRESS;
BEGIN {
eval 'require IO::Uncompress::Gunzip; $HAVE_IO_UNCOMPRESS = 1';
}
use IPC::Run;
# Object preamble - inherits from Bio::Root::Root
use lib '../../..';
use Bio::Tools::Run::Bowtie::Config;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Run::WrapperBase::CommandExts;
use Bio::Tools::GuessSeqFormat;
use Bio::Tools::Run::Samtools;
use Bio::Seq;
use File::Basename;
use base qw( Bio::Tools::Run::WrapperBase Bio::Tools::Run::AssemblerBase );
## bowtie
our $program_name = '*bowtie';
our $default_cmd = 'single';
our $asm_format; # this is determined dynamically
# Note:
# other globals required by Bio::Tools::Run::AssemblerBase are
# imported from Bio::Tools::Run::Bowtie::Config
our $qual_param = undef;
our $use_dash = 'mixed';
our $join = ' ';
sub new {
my ($class,@args) = @_;
unless (grep /command/, @args) {
push @args, '-command', $default_cmd;
}
#default to SAM output if no other format specified and we are running an alignment
my %args=@args;
if ($args{'-command'} =~ m/(?:single|paired|crossbow)/) {
unless (grep /(?:sam_format|concise|quiet|refout|refidx)/, @args) {
push @args, ('-sam_format', 1);
}
}
my $self = $class->SUPER::new(@args);
foreach (keys %command_executables) {
$self->executables($_, $self->_find_executable($command_executables{$_}));
}
my ($want) = $self->_rearrange([qw(WANT)],@args);
$self->want($want);
$asm_format = $self->_assembly_format;
$self->parameters_changed(1); # set on instantiation, per Bio::ParameterBaseI
return $self;
}
sub run {
my $self = shift;
my ($arg1, $arg2, $arg3); # these are useless names because the different
# programs take very different arguments
my ($index, $seq, $seq2, $ref, $out); # these are the meaningful names that are used
# with named args
if (!(@_ % 2)) {
my %args = @_;
if ((grep /^-\w+/, keys %args) == keys %args) {
($index, $seq, $seq2, $ref, $out) =
$self->_rearrange([qw( IND SEQ SEQ2 REF OUT )], @_);
} elsif (grep /^-\w+/, keys %args) {
$self->throw("Badly formed named args: ".join(' ',@_));
} else {
($arg1, $arg2) = @_;
}
} else {
if (grep /^-\w+/, @_) {
$self->throw("Badly formed named args: ".join(' ',@_));
} else {
($arg1, $arg2, $arg3) = @_;
}
}
# Sanity checks
$self->_check_executable();
my $cmd = $self->command if $self->can('command');
for ($cmd) {
m/(?:single|paired|crossbow)/ && do {
$seq ||= $arg1;
$index ||= $arg2;
$seq2 ||= $arg3;
$seq or $self->throw("Fasta/fastq/raw read(s) file/Bio::Seq required at arg 1/-seq");
$index or $self->throw("Bowtie index base required at arg 2/-index");
# expand gzipped files as nec.
for ($seq, $seq2) {
next unless $_;
if (/\.gz[^.]*$/) {
unless ($HAVE_IO_UNCOMPRESS) {
croak( "IO::Uncompress::Gunzip not available, can't expand '$_'" );
}
my ($tfh, $tf) = $self->io->tempfile;
my $z = IO::Uncompress::Gunzip->new($_);
while (<$z>) { print $tfh $_ }
close $tfh;
$_ = $tf;
}
}
# confirm index files exist
$self->_validate_file_input( -ind => $index ) or
($self->_validate_file_input( -ind => $self->io->catfile(dirname($self->executable),'indexes',$index)) and
$index = $self->io->catfile(dirname($self->executable),'indexes',$index)) or
($self->_validate_file_input( -ind => $self->io->catfile($ENV{BOWTIE_INDEXES},$index)) and
$index = $self->io->catfile($ENV{BOWTIE_INDEXES},$index)) or
$self->throw("Incorrect filetype (expecting bowtie index) or absent file arg 2/-index");
# bowtie prepare the multiple input types
$seq = $self->_prepare_input_sequences($seq);
if ($cmd =~ m/^p/) {
$seq2 && ($seq2 = $self->_prepare_input_sequences($seq2));
} else {
$seq2 && $self->throw("Second sequence input not wanted for command: $cmd");
}
# Assemble
my $format = $self->_assembly_format;
my $suffix = '.'.$format;
if ($out) {
$out .= $suffix;
} else {
my ($bowtieh, $bowtief) = $self->io->tempfile( -dir => $self->tempdir(), -suffix => $suffix );
$bowtieh->close;
$out = $bowtief;
}
my %params = ( -ind => $index, -seq => $seq, -seq2 => $seq2, -out => $out );
map {
delete $params{$_} unless defined $params{$_}
} keys %params;
$self->_run(%params);
$self->{'_result'}->{'index'} = $index;
$self->{'_result'}->{'file_name'} = $out;
$self->{'_result'}->{'format'} = $format;
$self->{'_result'}->{'file'} = Bio::Root::IO->new( -file => $out );
return $self->result;
};
m/build/ && do {
$ref ||= $arg1;
$index ||= $arg2;
$ref or $self->throw("Fasta read(s) file/Bio::Seq required at arg 1/-ref");
$index ||= $self->io->tempdir(CLEANUP => 1).'/index'; # we want a new one each time
$arg3 && $self->throw("Second sequence input not wanted for command: $cmd");
my $format = $self->_assembly_format;
# expand gzipped file as nec.
if ($ref =~ (m/\.gz[^.]*$/)) {
unless ($HAVE_IO_UNCOMPRESS) {
croak( "IO::Uncompress::Gunzip not available, can't expand '$_'" );
}
my ($tfh, $tf) = $self->io->tempfile;
my $z = IO::Uncompress::Gunzip->new($_);
while (<$z>) { print $tfh $_ }
close $tfh;
$ref = $tf;
}
# bowtie prepare the two input types for the first argument
$ref = $self->_prepare_input_sequences($ref);
# Build index
$self->_run( -ref => $ref, -out => $index );
$self->{'_result'}->{'format'} = $format;
$self->{'_result'}->{'file_name'} = $index;
return $index;
};
m/inspect/ && do {
$index ||= $arg1;
$out ||= $arg2;
$index or $self->throw("Bowtie index required at arg 1");
$self->_validate_file_input( -ind => $index ) or
($self->_validate_file_input( -ind => $self->io->catfile(dirname($self->executable),'indexes',$index)) and
$index = $self->io->catfile(dirname($self->executable),'indexes',$index)) or
($self->_validate_file_input( -ind => $self->io->catfile($ENV{BOWTIE_INDEXES},$index)) and
$index = $self->io->catfile($ENV{BOWTIE_INDEXES},$index)) or
$self->throw("'$index' doesn't look like a bowtie index or index component is missing at arg 1/-ind");
$arg3 && $self->throw("Second sequence input not wanted for command: $cmd");
# Inspect index
my $format = $self->_assembly_format;
my $suffix = '.'.$format;
if ($out) {
$out .= $suffix;
} else {
my ($desch, $descf) = $self->io->tempfile( -dir => $self->tempdir(), -suffix => $suffix );
$desch->close;
$out = $descf;
}
$self->_run( -ind => $index, -out => $out );
$self->{'_result'}->{'file_name'} = $out;
$self->{'_result'}->{'format'} = $format;
$self->{'_result'}->{'file'} = Bio::Root::IO->new( -file => $out );
return $self->result;
}
}
}
sub want {
my $self = shift;
return $self->{'_want'} = shift if @_;
return $self->{'_want'};
}
sub result {
my ($self, @args) = @_;
my $want = $self->want ? $self->want : $self->want($self->_rearrange([qw(WANT)],@args));
my $cmd = $self->command if $self->can('command');
my $format = $self->{'_result'}->{'format'};
return $self->{'_result'}->{'format'} if (defined $want && $want eq 'format');
return $self->{'_result'}->{'file_name'} if (!$want || $want eq 'raw' || $cmd eq 'build');
return $self->{'_result'}->{'file'} if ($want =~ m/^Bio::Root::IO/);
for ($cmd) {
m/(?:single|paired|crossbow)/ && do {
my $scaffold;
for ($format) {
m/^bowtie/i && $want =~ m/^Bio::Assembly::Scaffold/ && do {
unless (defined $self->{'_result'}->{'object'} &&
ref($self->{'_result'}->{'object'}) =~ m/^Bio::Assembly::Scaffold/) {
$self->{'_result'}->{'object'} =
$self->_export_results( $self->{'_result'}->{'file_name'},
-index => $self->{'_result'}->{'index'},
-keep_asm => 1 );
}
last;
};
m/^bowtie/i && $want =~ m/^Bio::SeqFeature::Collection/ && do {
$self->warn("Don't know how to create a $want object for $cmd with bowtie format - try SAM format.");
last;
};
m/^sam/i && $want =~ m/^Bio::Assembly::Scaffold/ && do {
unless (defined $self->{'_result'}->{'object'} &&
ref($self->{'_result'}->{'object'}) =~ m/^Bio::Assembly::Scaffold/) {
my $bamf = $self->_make_bam($self->{'_result'}->{'file_name'}, 1);
my $inspector = Bio::Tools::Run::Bowtie->new( -command => 'inspect' );
my $refdb = $inspector->run($self->{'_result'}->{'index'});
$self->{'_result'}->{'object'} =
$self->_export_results($bamf, -refdb => $refdb, -keep_asm => 1 );
}
last;
};
m/^sam/i && $want =~ m/^Bio::SeqFeature::Collection/ && do {
unless (defined $self->{'_result'}->{'object'} &&
ref($self->{'_result'}->{'object'}) =~ m/^Bio::Assembly::Scaffold/) {
my $bamf = $self->_make_bam($self->{'_result'}->{'file_name'}, 0);
my $convert = Bio::Tools::Run::BEDTools->new( -command => 'bam_to_bed' );
my $bedf = $convert->run( -bed => $bamf );
my $merge = Bio::Tools::Run::BEDTools->new( -command => 'merge' );
$merge->run($self->{'_result'}->{'index'});
$self->{'_result'}->{'object'} = $merge->result( -want => $want );
}
last;
};
do {
$self->warn("Don't know how to create a $want object for $cmd.");
return;
}
};
last;
};
m/inspect/ && do {
for ($want) {
m/^Bio::SeqIO/ && $format eq 'fasta' && do {
unless (defined $self->{'_result'}->{'object'} &&
ref($self->{'_result'}->{'object'}) =~ m/^Bio::SeqIO/) {
$self->{'_result'}->{'object'} =
Bio::SeqIO->new(-file => $self->{'_result'}->{'file'},
-format => 'fasta');
}
last;
};
m/^Bio::SeqIO/ && $format ne 'fasta' && do {
$self->warn("Don't know how to create a $want object for names only - try -want => 'Bio::Root::IO'.");
return;
};
do {
$self->warn("Don't know how to create a $want object for $cmd.");
return;
}
}
}
}
return $self->{'_result'}->{'object'};
}
sub _determine_format {
my ($self) = shift;
my $cmd = $self->command if $self->can('command');
for ($cmd) {
m/build/ && do {
return 'ebwt';
};
m/inspect/ && do {
$self->{'_summary'} && return 'text';
return $self->{'_names_only'} ? 'text' : 'fasta';
};
m/(?:single|paired|crossbow)/ && do {
my $format = 'bowtie'; # this is our default position
for (keys %format_lookup) {
$format = $format_lookup{$_} if $self->{'_'.$_};
}
return $format;
}
}
}
sub _make_bam {
my ($self, $file, $sort) = @_;
$self->throw("'$file' does not exist or is not readable")
unless ( -e $file && -r _ );
# make a sorted bam file from a sam file input
my ($bamh, $bamf) = $self->io->tempfile( -dir => $self->tempdir(), -suffix => '.bam' );
$bamh->close;
my $samt = Bio::Tools::Run::Samtools->new( -command => 'view',
-sam_input => 1,
-bam_output => 1 );
$samt->run( -bam => $file, -out => $bamf );
if ($sort) {
my ($srth, $srtf) = $self->io->tempfile( -dir => $self->io->tempdir(CLEANUP=>1), -suffix => '.srt' );
# shared tempdir, so make new - otherwise it is scrubbed during Bio::DB::Sam
$srth->close;
$samt = Bio::Tools::Run::Samtools->new( -command => 'sort' );
$samt->run( -bam => $bamf, -pfx => $srtf);
return $srtf.'.bam';
} else {
return $bamf;
}
}
sub _validate_file_input {
my ($self, @args) = @_;
my (%args);
if (grep (/^-/, @args)) { # named parms
$self->throw("Wrong number of args - requires one named arg") if (@args > 2);
s/^-// for @args;
%args = @args;
} else {
$self->throw("Must provide named filespec");
}
for (keys %args) {
m/^seq|seq2|ref$/ && do {
return unless ( -e $args{$_} && -r _ );
my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$args{$_});
return $guesser->guess if grep {$guesser->guess =~ m/$_/} @{$accepted_types{$_}};
};
m/^ind$/ && do {
return 'ebwt' if
(-e $args{$_}.'.1.ebwt' && -e $args{$_}.'.2.ebwt' && -e $args{$_}.'.3.ebwt' &&
-e $args{$_}.'.4.ebwt' && -e $args{$_}.'.rev.1.ebwt' && -e $args{$_}.'.rev.2.ebwt');
}
}
return;
}
sub _assembly_format {
my $self = shift;
my $format = $self->_determine_format;
return $self->SUPER::_assembly_format($format);
}
sub _check_sequence_input {
return 1;
}
sub _check_optional_quality_input {
return 1;
}
sub _prepare_input_sequences {
my ($self, @args) = @_;
my (%args, $read);
if (grep (/^-/, @args)) { # named parms
$self->throw("Input args not an even number") unless !(@args % 2);
%args = @args;
($read) = @args{qw( -sequence )};
} else {
($read) = @args;
}
# Could use the AssemblerBase routine for this, except that would not permit
# an array of strings
if ($self->inline) { # expect inline data
if (UNIVERSAL::isa($read,'can') && $read->isa("Bio::PrimarySeqI")) { # we have a Bio::*Seq*
$read=$read->seq();
} else { # we have something else
if (ref($read) =~ /ARRAY/i) {
my @ts;
foreach my $seq (@$read) {
if ($seq->isa("Bio::PrimarySeqI")) {
$seq=$seq->seq();
} else {
next if $read=~m/[[^:alpha:]]/;
}
push @ts,$seq;
}
$self->throw("bowtie requires at least one sequence read") unless (@ts);
if (@ts>1) {
$read="'".join(',',@ts)."'";
} else {
($read)=@ts;
}
} else { #must be a string... fail if non-alpha
$self->throw("bowtie requires at least one valid sequence read") if $read=~m/[[^:alpha:]]/;
}
}
} else { # expect file(s) - so test whether it's/they're appropriate
# and make a comma-separated list of filenames
my @ts = (ref($read) =~ /ARRAY/i) ? @$read : ($read);
for my $file (@ts) {
if ( -e $file ) {
my $cmd = $self->command if $self->can('command');
my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$file);
for ($guesser->guess) {
m/^fasta$/ && do {
$cmd =~ m/^b/ && last;
($cmd =~ m/^c/ or $self->fastq or $self->raw) and $self->throw("Fasta reads file '$file' inappropriate");
$self->fasta(1);
last;
};
m/^fastq$/ && do {
($cmd =~ m/^[cb]/ or $self->fasta or $self->raw) and $self->throw("Fastq reads file '$file' inappropriate");
$self->fastq(1);
last;
};
m/^tab$/ && do {
$cmd =~ m/^c/ or $self->throw("Crossbow reads file '$file' inappropriate"); # this is unrecoverable since the object has default program defined
last;
};
m/^raw$/ && do {
($cmd =~ m/^[cb]/ or $self->fasta or $self->fastq) and $self->throw("Raw reads file '$file' inappropriate");
$self->raw(1);
last;
};
do {
$self->throw("File '$file' not a recognised bowtie input filetype");
}
}
} else {
$self->throw("Sequence read file '$file' does not exist");
}
}
if (@ts>1) {
$read="'".join(',',@ts)."'";
} else {
($read)=@ts;
}
}
return $read;
}
sub set_parameters {
my ($self, @args) = @_;
# Mutually exclusive switches/params prevented from being set to
# avoid confusion resulting from setting incompatible switches.
$self->throw("Input args not an even number") if (@args % 2);
my %args = @args;
foreach (keys %args) {
my @added;
my @removed;
s/^-//;
foreach my $conflict (@{$incompat_params{$_}}) {
return if grep /$conflict/, @added;
delete $args{'-'.$conflict};
$args{'-'.$conflict} = undef if $self->{'_'.$conflict};
push @removed, $conflict;
}
foreach my $requirement (@{$corequisite_switches{$_}}) {
return if grep /$requirement/, @removed;
$args{'-'.$requirement}=1 if $args{$_};
push @added, $requirement;
}
}
return $self->SUPER::set_parameters(%args);
}
sub version{
my ($self) = @_;
my $cmd = $self->command if $self->can('command');
defined $cmd or $self->throw("No command defined - cannot determine program executable");
my ($in, $out, $err);
my $dum;
$in = \$dum;
$out = \$self->{'stdout'};
$err = \$self->{'stderr'};
# Get program executable
my $exe = $self->executable;
# Get version switch from switches, translate and dash it
my $version_switch = $param_translation{"$command_prefixes{$cmd}|version"};
$version_switch = $self->_dash_switch( $version_switch );
my @ipc_args = ( $exe, $version_switch );
eval {
IPC::Run::run(\@ipc_args, $in, $out, $err) or
die ("There was a problem running $exe : $!");
};
if ($@) {
$self->throw("$exe call crashed: $@");
}
my @details = split("\n",$self->stdout);
(my $version) = grep /$exe version [[:graph:]]*$/, @details;
$version =~ s/version //;
(my $addressing) = grep /-bit$/, @details;
return $version.' '.$addressing;
}
sub available_commands { shift->available_parameters('commands') };
sub filespec { shift->available_parameters('filespec') };
1;