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=pod
=head1 LICENSE
Copyright (c) 1999-2012 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <dev@ensembl.org>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=head1 NAME
Bio::EnsEMBL::Pipeline::FASTA::BlastIndexer
=head1 DESCRIPTION
Creates 2bit file of the given GZipped file. The resulting index
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is created under the parameter location I<base_path> in blat/index. The filename
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is prefixed with the port number of the blat server this file should be
run on.
The module also performs filtering of non-reference sequence regions
and can filter the redundant Y chromosome piece for human (as 2bit does
not like repeated sequence region names).
Allowed parameters are:
=over 8
=item file - The file to index
=item program - The location of the faToTwoBit program
=item port_offset - Value to add onto the species_id from the website DB
to name the file correctly
=item base_path - The base of the dumps
=item index - The type of file to index; supported values are empty,
I<dna>, I<dna_sm> or I<dna_rm>. If specified we will look for this
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string in the filename surrounded by '.' e.g. .dna.
=back
The registry should also have a DBAdaptor for the website schema
registered under the species B<multi> and the group B<web> for species_id to
Blat port number.
=cut
package Bio::EnsEMBL::Pipeline::FASTA::BlatIndexer;
use strict;
use warnings;
use base qw/Bio::EnsEMBL::Pipeline::FASTA::Indexer/;
use File::Spec;
use File::stat;
use Bio::EnsEMBL::Utils::IO qw/work_with_file/;
use Bio::EnsEMBL::Utils::Exception qw/throw/;
use Bio::EnsEMBL::Registry;
sub param_defaults {
my ($self) = @_;
return {
program => 'faToTwoBit',
port_offset => 30000,
'index' => 'dna', #or dna_rm and dna_sm
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};
}
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sub fetch_input {
my ($self) = @_;
$self->assert_executable($self->param('program'));
$self->assert_executable('zcat');
$self->assert_executable('gunzip');
return;
}
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sub run {
my ($self) = @_;
if($self->run_indexing()) {
$self->SUPER::run();
}
return;
}
sub run_indexing {
my ($self) = @_;
my $index = $self->param('index');
if($index) {
my $file = $self->param('file');
return (index($file, ".${index}.") > -1) ? 1 : 0;
}
return 1;
}
sub index_file {
my ($self, $file) = @_;
my $target_file = $self->target_file();
my $cmd = sprintf(q{%s %s %s},
$self->param('program'), $file, $target_file);
$self->info('About to run "%s"', $cmd);
my $output = `$cmd 2>&1`;
my $rc = $? >> 8;
throw "Cannot run program '$cmd'. Return code was ${rc}. Program output was $output" if $rc;
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unlink $file or throw "Cannot remove the file '$file' from the filesystem: $!";
#Check the file size. If it's 16 bytes then reject as that is an empty file for 2bit
my $filesize = stat($target_file)->size();
if($filesize <= 16) {
unlink $file;
my $msg = sprintf(
'The file %s produced a 2bit file %d byte(s). Lower than 17 bytes therefore empty 2 bit file',
$file, $filesize
);
$self->throw($msg);
}
return;
}
sub decompress {
my ($self) = @_;
#If we have no non-reference seq regions then use normal decompress
if(! $self->has_non_refs()) {
return $self->SUPER::decompress();
}
#Filter for non-refs
my $source = $self->param('file');
my $target_dir = $self->target_dir();
my ($vol, $dir, $file) = File::Spec->splitpath($source);
$file =~ s/.gz$//;
my $target = File::Spec->catdir($target_dir, $file);
my $allowed_regions = $self->allowed_regions();
$self->info('Decompressing %s to %s', $source, $target);
open my $src_fh, '-|', "zcat $source" or throw "Cannot decompress $source to $target";
work_with_file($target, 'w', sub {
my ($trg_fh) = @_;
my $transfer = 0;
while(my $line = <$src_fh>) {
#HEADER
if(index($line, '>') == 0) {
#regex is looking for NNN:NNN:NNN:1:80:1 i.e. the name
my ($name) = $line =~ />.+\s(.+:.+:.+:\d+:\d+:\d+)/;
$transfer = ($allowed_regions->{$name}) ? 1 : 0;
if($transfer) {
$self->info('%s was an allowed Slice', $name);
}
else {
$self->info('%s will be skipped; not a reference Slice', $name);
}
}
print $trg_fh $line if $transfer;
}
});
close($src_fh);
return $target;
}
sub allowed_regions {
my ($self) = @_;
my $filter_human = 1;
my @slices = grep { $_->is_reference() } @{$self->get_Slices('core', $filter_human)};
my %hash = map { $_->name() => 1 } @slices;
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return \%hash;
}
#Filename like 30061.Homo_sapiens.GRCh37.2bit
sub target_filename {
my ($self) = @_;
my $port = $self->blat_port();
my $name = $self->web_name();
my $assembly = $self->assembly();
return join(q{.}, $port, $name, $assembly, '2bit');
}
sub target_file {
my ($self) = @_;
my $target_dir = $self->target_dir();
my $target_filename = $self->target_filename();
return File::Spec->catfile($target_dir, $target_filename);
return;
}
sub target_dir {
my ($self) = @_;
my $index = $self->param('index');
my $base_dir = ($index eq 'dna') ? 'blat'
: ($index eq 'dna_rm') ? 'blat_rm'
: ($index eq 'dna_sm') ? 'blat_sm'
: q{}
;
if(! $base_dir) {
$self->throw(sprintf('Cannot decode a directory from index type "%s"', $index));
}
return $self->get_dir($base_dir, $self->param('index'));
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}
sub blat_port {
my ($self) = @_;
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor('multi', 'web');
my $id = $dba->dbc()->sql_helper()->execute_single_result(
-SQL => 'select species_id from species where name =?',
-PARAMS => [$self->web_name()]
);
return $id + $self->param('port_offset');
}
sub has_non_refs {
my ($self) = @_;
my $sql = <<'SQL';
select count(*)
from attrib_type at
join seq_region_attrib sra using (attrib_type_id)
join seq_region sr using (seq_region_id)
join coord_system cs using (coord_system_id)
where cs.species_id =?
and at.code =?
SQL
my $dba = $self->get_DBAdaptor();
return $dba->dbc()->sql_helper()->execute_single_result(
-SQL => $sql, -PARAMS => [$dba->species_id(), 'non_ref']);
}
1;