Bio::Tools::Run::Alignment
Exonerate
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Summary
Bio::Tools::Run::Alignment::Exonerate
Package variables
No package variables defined.
Included modules
Bio::Factory::ApplicationFactoryI
Bio::Root::IO
Bio::Root::Root
Bio::SearchIO
Bio::Tools::Run::WrapperBase
Inherit
Bio::Factory::ApplicationFactoryI Bio::Root::Root Bio::Tools::Run::WrapperBase
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";
}
}
}
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.
Methods
Methods description
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None |
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args : |
Title : new
Usage : my $factory= Bio::Tools::Run::Phrap->new();
Function: creates a new Phrap factory
Returns: Bio::Tools::Run::Phrap
Args : |
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none |
Title : run()
Usage : my $feats = $factory->run($seq)
Function: Runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI |
Title : _run
Usage : $factory->_run()
Function: Makes a system call and runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args : |
Title : _writeInput
Usage : $factory->_writeInput($query,$target)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI |
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args : |
Methods code
sub program_name
{ return 'exonerate'; } | sub program_dir
{ return Bio::Root::IO->catfile($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};} | sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ );
if ($attr =~/PROGRAM/i) {
$self->executable($value);
next;
}
$self->$attr($value);
}
return $self;} | sub version
{ my ($self) = @_;
my $exe;
return undef unless $exe = $self->executable;
my $string = `$exe -v` ;
my ($version) = $string =~ /exonerate version ([\d+\.]+)/m;
$version =~ s/\.(\d+)$/$1/;
return $version || undef;} | sub run
{ my ($self,$query,$target) = @_;
my @feats;
my ($file1) = $self->_writeInput($query);
my ($file2) = $self->_writeInput($target);
my $assembly = $self->_run($file1,$file2);
return $assembly;} | sub _input()
{ my ($self,$infile1) = @_;
$self->{'input'} = $infile1 if(defined $infile1);
return $self->{'input'};} | sub _run
{ my ($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 $exonerate_obj;} | sub _writeInput
{ my ($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 $infile1;} | sub _setparams
{ my ($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;} | General documentation
The tests have been shown to pass with exonorate versions 2.0 - 2.2.
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
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.
Email shawnh-at-stanford.edu
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Title : _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :