/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm is in libbio-perl-run-perl 1.7.1-3.
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# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Alignment::Exonerate
=head1 SYNOPSIS
use Bio::Tools::Run::Alignment::Exonerate;
use Bio::SeqIO;
my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
my $query = $qio->next_seq();
my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
my $target = $sio->next_seq();
#exonerate parameters can all be passed via arguments parameter.
#parameters passed are not checked for validity
my $run = Bio::Tools::Run::Alignment::Exonerate->
new(arguments=>'--model est2genome --bestn 10');
my $searchio_obj = $run->run($query,$target);
while(my $result = $searchio->next_result){
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
print $hsp->start."\t".$hsp->end."\n";
}
}
}
=head1 DESCRIPTION
Wrapper for Exonerate alignment program. You can get exonerate at
http://www.ebi.ac.uk/~guy/exonerate/. This wrapper is written without
parameter checking. All parameters are passed via the arugment
parameter that is passed in the constructor. See SYNOPSIS. For
exonerate parameters, run exonerate --help for more details.
=head1 PROGRAM VERSIONS
The tests have been shown to pass with exonorate versions 2.0 - 2.2.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh-at-stanford.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Alignment::Exonerate;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
$PROGRAMNAME @EXONERATE_PARAMS %OK_FIELD);
use strict;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Run::WrapperBase;
use Bio::SearchIO;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase
Bio::Factory::ApplicationFactoryI);
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'exonerate';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{EXONERATEDIR}) if $ENV{EXONERATEDIR};
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 new
Title : new
Usage : my $factory= Bio::Tools::Run::Phrap->new();
Function: creates a new Phrap factory
Returns: Bio::Tools::Run::Phrap
Args :
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) {
$self->executable($value);
next;
}
$self->$attr($value);
}
return $self;
}
=head2 version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
my $exe;
return undef unless $exe = $self->executable;
my $string = `$exe -v` ;
#exonerate from exonerate version 2.0.0\n...
my ($version) = $string =~ /exonerate version ([\d+\.]+)/m;
$version =~ s/\.(\d+)$/$1/;
return $version || undef;
}
=head2 run
Title : run()
Usage : my $feats = $factory->run($seq)
Function: Runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
=cut
sub run {
my ($self,$query,$target) = @_;
my @feats;
my ($file1) = $self->_writeInput($query);
my ($file2) = $self->_writeInput($target);
my $assembly = $self->_run($file1,$file2);
return $assembly;
}
=head2 _input
Title : _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :
=cut
sub _input() {
my ($self,$infile1) = @_;
$self->{'input'} = $infile1 if(defined $infile1);
return $self->{'input'};
}
=head2 _run
Title : _run
Usage : $factory->_run()
Function: Makes a system call and runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args :
=cut
sub _run {
my ($self,$query,$target)= @_;
my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir);
my $param_str = $self->_setparams." ".$self->arguments;
my $str = $self->executable." $param_str $query $target "." > $outfile";
$self->debug( "$str\n");
my $status = system($str);
$self->throw( "Exonerate call ($str) crashed: $? \n") unless $status==0;
my $filehandle;
my $exonerate_obj = Bio::SearchIO->new(-file=>"$outfile",-format=>'exonerate');
close($tfh);
undef $tfh;
unlink $outfile;
return $exonerate_obj;
}
=head2 _writeInput
Title : _writeInput
Usage : $factory->_writeInput($query,$target)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI
=cut
sub _writeInput{
my ($self,$query) = @_;
my ($fh,$infile1);
if (ref($query) =~ /ARRAY/i) {
my @infilearr;
($fh, $infile1) = $self->io->tempfile();
my $temp = Bio::SeqIO->new( -file => ">$infile1",
-format => 'Fasta' );
foreach my $seq1 (@$query) {
unless ($seq1->isa("Bio::PrimarySeqI")) {
return 0;
}
$temp->write_seq($seq1);
push @infilearr, $infile1;
}
}
elsif($query->isa("Bio::PrimarySeqI")) {
($fh, $infile1) = $self->io->tempfile();
my $temp = Bio::SeqIO->new( -file => ">$infile1",
-format => 'Fasta' );
$temp->write_seq($query);
}
else {
$infile1 = $query;
}
return $infile1;
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
=cut
sub _setparams {
my ($self) = @_;
my $param_string = '';
foreach my $attr(@EXONERATE_PARAMS){
next if($attr=~/PROGRAM/);
my $value = $self->$attr();
next unless (defined $value);
my $attr_key = ' -'.(lc $attr);
$param_string .= $attr_key.' '.$value;
}
return $param_string;
}
1;
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