diff variant_effect_predictor/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,160 @@
+=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 <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Pipeline::FASTA::WuBlastIndexer
+
+=head1 DESCRIPTION
+
+Creates WUBlast indexes of the given GZipped file. The resulting index
+is created under the parameter location I<base_path> in blast and then in a
+directory defined by the type of dump. The type of dump also changes the file
+name generated. Genomic dumps have their release number replaced with the
+last repeat masked date. 
+
+Allowed parameters are:
+
+=over 8
+
+=item file - The file to index
+
+=item program - The location of the xdformat program
+
+=item molecule - The type of molecule to index. I<dna> and I<pep> are allowed
+
+=item type - Type of index we are creating. I<genomic> and I<genes> are allowed
+
+=item base_path - The base of the dumps
+
+=item release - Required for correct DB naming
+
+=back
+
+=cut
+
+package Bio::EnsEMBL::Pipeline::FASTA::WuBlastIndexer;
+
+use strict;
+use warnings;
+use base qw/Bio::EnsEMBL::Pipeline::FASTA::Indexer/;
+
+use Bio::EnsEMBL::Utils::Exception qw/throw/;
+use File::Copy qw/copy/;
+use File::Spec;
+use POSIX qw/strftime/;
+
+sub param_defaults {
+  my ($self) = @_;
+  return {
+    program => 'xdformat',
+#    molecule => 'pep', #pep or dna
+#    type => 'genes'    #genes or genomic
+  };
+}
+
+sub fetch_input {
+  my ($self) = @_;
+  my $mol = $self->param('molecule');
+  if($mol ne 'dna' && $mol ne 'pep') {
+    throw "param 'molecule' must be set to 'dna' or 'pep'";
+  }
+  my $type = $self->param('type');
+  if($type ne 'genomic' && $type ne 'genes') {
+    throw "param 'type' must be set to 'genomic' or 'genes'";
+  }
+  $self->assert_executable($self->param('program'));
+  $self->assert_executable('gunzip');
+}
+
+sub write_output {
+  my ($self) = @_;
+  $self->dataflow_output_id({
+    species     => $self->param('species'),
+    type        => $self->param('type'),
+    molecule    => $self->param('molecule'),
+    index_base  => $self->param('index_base')
+  }, 1);
+  return;
+}
+
+sub index_file {
+  my ($self, $file) = @_;
+  my $molecule_arg = ($self->param('molecule') eq 'dna') ? '-n' : '-p' ;
+  my $silence = ($self->debug()) ? 0 : 1;
+  my $target_dir = $self->target_dir();
+  my $target_file = $self->target_file($file);
+  my $db_title = $self->db_title($file);
+  my $date = $self->db_date();
+  
+  my $cmd = sprintf(q{cd %s && %s %s -q%d -I -t %s -d %s -o %s %s }, 
+    $target_dir, $self->param('program'), $molecule_arg, $silence, $db_title, $date, $target_file, $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;
+  unlink $file or throw "Cannot remove the file '$file' from the filesystem: $!";
+  $self->param('index_base', $target_file);
+  return;
+}
+
+sub target_file {
+  my ($self, $file) = @_;
+  my $target_dir = $self->target_dir();
+  my $target_filename = $self->target_filename($file);
+  return File::Spec->catfile($target_dir, $target_filename);
+}
+
+# Produce a dir like /nfs/path/to/blast/genes/XXX && /nfs/path/to/blast/dna/XXX
+sub target_dir {
+  my ($self) = @_;
+  return $self->get_dir('blast', $self->param('type'));
+}
+
+sub db_title {
+  my ($self, $source_file) = @_;
+  my ($vol, $dir, $file) = File::Spec->splitpath($source_file);
+  my $release = $self->param('release');
+  my $title = $file;
+  $title =~ s/$release\.//;
+  return $title;
+}
+
+sub db_date {
+  my ($self) = @_;
+  return strftime('%d-%m-%Y', gmtime());
+}
+
+#Source like Homo_sapiens.GRCh37.68.dna.toplevel.fa
+#Filename like Homo_sapiens.GRCh37.20090401.dna.toplevel.fa
+sub target_filename {
+  my ($self, $source_file) = @_;
+  my ($vol, $dir, $file) = File::Spec->splitpath($source_file);
+  if($self->param('type') eq 'genomic') {
+    my @split = split(/\./, $file);
+    my $rm_date = $self->repeat_mask_date();
+    $split[-4] = $rm_date;
+    return join(q{.}, @split);
+  }
+  return $file;
+}
+
+1;