Bio::EnsEMBL::Compara::Production::GenomicAlignBlock Blat
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Summary
Bio::EnsEMBL::Compara::RunnableDB::Blat
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Runnable::Blat
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner
Synopsis
my $db = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Analysis::RunnableDB::Blat->new (
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$repmask->fetch_input(); #reads from DB
$repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB
Description
This object wraps Bio::EnsEMBL::Analysis::Runnable::Blat to add
functionality to read and write to databases.
The appropriate Bio::EnsEMBL::Analysis object must be passed for
extraction of appropriate parameters. A Bio::EnsEMBL::Analysis::DBSQL::Obj is
required for database access.
Methods
configure_defaults
No description
Code
configure_runnable
No description
Code
Methods description
None available.
Methods code
configure_defaultsdescriptionprevnextTop
sub configure_defaults {
  my $self = shift;
  
  
  # Target type: dna  - DNA sequence
# prot - protein sequence
# dnax - DNA sequence translated in six frames to protein
# The default is dnax
# Query type: dna - DNA sequence
# rna - RNA sequence
# prot - protein sequence
# dnax - DNA sequence translated in six frames to protein
# rnax - DNA sequence translated in three frames to protein
# The default is dnax
#-ooc=/tmp/worker.????/5ooc
#
$self->options('-minScore=30 -t=dnax -q=dnax -mask=lower -qMask=lower'); $self->method_link_type('TRANSLATED_BLAT'); return 0; } ############################################################
}
configure_runnabledescriptionprevnextTop
sub configure_runnable {
  my $self = shift;

  my (@db_chunk) = @{$self->db_DnaFragChunkSet->get_all_DnaFragChunks};

  #
# get the sequences and create the runnable
#
my $qyChunkFile; if($self->query_DnaFragChunkSet->count == 1) { my ($qy_chunk) = @{$self->query_DnaFragChunkSet->get_all_DnaFragChunks}; $qyChunkFile = $self->dumpChunkToWorkdir($qy_chunk); } else { $qyChunkFile = $self->dumpChunkSetToWorkdir($self->query_DnaFragChunkSet); } my @db_chunk_files; #Grouped seq_regions. Fasta files named after the first seq_region in the set
my $db_chunks = $self->db_DnaFragChunkSet->get_all_DnaFragChunks; my $dnafrag = $db_chunks->[0]->dnafrag; my $name = $dnafrag->name . "_" . $db_chunks->[0]->seq_start . "_" . $db_chunks->[0]->seq_end; my $dbChunkFile = "" . $self->dump_loc . "/" . $name . ".fa"; my $program = $self->analysis->program_file; $program = $self->analysis->program unless ($program); $program = 'blat-32' unless($program); if($self->debug) { print("running with analysis '".$self->analysis->logic_name."'\n"); print(" options : ", $self->options, "\n"); print(" program : $program\n"); } $self->delete_fasta_dumps_but_these([$qyChunkFile,$dbChunkFile]); #Do not create ooc files for translated blat analyses
#create 5ooc file by replacing ".fa" with "/ooo5"
#my $oocFile = $dbChunkFile;
#$oocFile =~ s/(.fa)/\/5ooc/;
#my $options = $self->options . " -ooc=$oocFile";
my $options = $self->options; my $runnable = Bio::EnsEMBL::Analysis::Runnable::Blat-> new( -query => $qyChunkFile, -database => $dbChunkFile, -options => $options, -program => $program, -analysis => $self->analysis, ); $self->runnable($runnable); return 1; } 1;
}
General documentation
CONTACTTop
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APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _