Raw content of Bio::EnsEMBL::Analysis::Runnable::Blastz
<![CDATA[# Cared for by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright GRL & EBI
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::Blastz
=head1 SYNOPSIS
# To run a blastz job from scratch do the following.
my $query = new Bio::SeqIO(-file => 'somefile.fa',
-format => 'fasta')->next_seq;
my $database = 'multifastafile.fa';
my $blastz = Bio::EnsEMBL::Analysis::Runnable::Blastz->new
('-query' => $query,
'-database' => $database,
'-options' => 'T=2');
$blastz->run();
@featurepairs = $blast->output();
foreach my $fp (@featurepairs) {
print $fp->gffstring . "\n";
}
# Additionally if you have blast runs lying around that need parsing
# you can use the EnsEMBL blastz parser module
# perldoc Bio::EnsEMBL::Analysis::Runnable::Parser::Blastz
=head1 DESCRIPTION
Blastz takes a Bio::Seq (or Bio::PrimarySeq) object and runs blastz with against
the specified multi-FASTA file database. Tthe output is parsed by
Bio::EnsEMBL::Analysis::Runnable::Parser::Blastz and stored as Bio::EnsEMBL::DnaDnaAlignFeature
Other options can be passed to the blast program using the -options method
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Analysis::Runnable::Blastz;
use vars qw(@ISA);
use strict;
# Object preamble
use Bio::EnsEMBL::Analysis::Runnable;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::Analysis::Tools::Blastz;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable);
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($database) = rearrange(['DATABASE'], @args);
$self->database($database) if defined $database;
throw("You must supply a database") if not $self->database;
throw("You must supply a query") if not $self->query;
$self->program("blastz") if not $self->program;
return $self;
}
=head2 run
Title : run
Usage : $obj->run()
Function: Runs blast and BPLite and creates array of feature pairs
Returns : none
Args : none
=cut
sub run{
my ($self, $dir) = @_;
$self->workdir($dir) if($dir);
throw("Can't run ".$self." without a query sequence")
unless($self->query);
$self->write_seq_files();
$self->run_analysis();
$self->delete_files;
return 1;
}
sub run_analysis {
my $self = shift;
my $cmd = $self->program ." ".
$self->query ." ".
$self->database ." ".
$self->options;
my $BlastzParser;
my $blastz_output_pipe = undef;
if($self->results_to_file) {
if (not $self->resultsfile) {
my $resfile = $self->create_filename("blastz", "results");
$self->resultsfile($resfile);
$self->files_to_delete($resfile);
}
$cmd .= " > ". $self->resultsfile;
info("Running blastz...\n$cmd\n");
throw("Error runing blastz cmd\n$cmd\n." .
" Returned error $? BLAST EXIT: '" .
($? >> 8) . "'," ." SIGNAL '" . ($? & 127) .
"', There was " . ($? & 128 ? 'a' : 'no') .
" core dump") unless(system($cmd) == 0);
$BlastzParser = Bio::EnsEMBL::Analysis::Tools::Blastz->
new('-file' => $self->resultsfile);
} else {
info("Running blastz to pipe...\n$cmd\n");
open($blastz_output_pipe, "$cmd |") ||
throw("Error opening Blasts cmd <$cmd>." .
" Returned error $? BLAST EXIT: '" .
($? >> 8) . "'," ." SIGNAL '" . ($? & 127) .
"', There was " . ($? & 128 ? 'a' : 'no') .
" core dump");
$BlastzParser = Bio::EnsEMBL::Analysis::Tools::Blastz->
new('-fh' => $blastz_output_pipe);
}
my @results;
while (defined (my $alignment = $BlastzParser->nextAlignment)) { # nextHSP-like
push @results, $alignment;
}
close($blastz_output_pipe) if(defined($blastz_output_pipe));
$self->output(\@results);
}
#################
# get/set methods
#################
=head2 query
Title : query
Usage : $self->query($seq)
Function: Get/set method for query. If set with a Bio::Seq object it
will get written to the local tmp directory
Returns : filename
Args : Bio::PrimarySeqI, or filename
=cut
sub query {
my ($self, $val) = @_;
if (defined $val) {
if (not ref($val)) {
throw("[$val] : file does not exist\n") unless -e $val;
} elsif (not $val->isa("Bio::PrimarySeqI")) {
throw("[$val] is neither a Bio::Seq not a file");
}
$self->{_query} = $val;
}
return $self->{_query}
}
=head2 database
Title : database
Usage : $self->database($seq)
Function: Get/set method for database. If set with a Bio::Seq object it
will get written to the local tmp directory
Returns : filename
Args : Bio::PrimarySeqI, or filename
=cut
sub database {
my ($self, $val) = @_;
if (defined $val) {
if (not ref($val)) {
throw("[$val] : file does not exist\n") unless -e $val;
} else {
if (ref($val) eq 'ARRAY') {
foreach my $el (@$val) {
throw("All elements of given database array should be Bio::PrimarySeqs")
if not ref($el) or not $el->isa("Bio::PrimarySeq");
}
} elsif (not $val->isa("Bio::PrimarySeq")) {
throw("[$val] is neither a file nor array of Bio::Seq");
} else {
$val = [$val];
}
}
$self->{_database} = $val;
}
return $self->{_database};
}
sub write_seq_files {
my ($self) = @_;
if (ref($self->query)) {
# write the query
my $query_file = $self->create_filename("blastz", "query");
my $seqio = Bio::SeqIO->new(-format => "fasta",
-file => ">$query_file");
$seqio->write_seq($self->query);
$seqio->close;
$self->query($query_file);
$self->files_to_delete($query_file);
}
if (ref($self->database)) {
my $db_file = $self->create_filename("blastz", "database");
my $seqio = Bio::SeqIO->new(-format => "fasta",
-file => ">$db_file");
foreach my $seq (@{$self->database}) {
$seqio->write_seq($seq);
}
$seqio->close;
$self->database($db_file);
$self->files_to_delete($db_file);
}
}
sub results_to_file {
my ($self, $val) = @_;
if (defined $val) {
$self->{_results_to_file} = $val;
}
return $self->{_results_to_file};
}
1;
]]>