Bio::EnsEMBL::Compara::RunnableDB BlastComparaPep
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Summary
Bio::EnsEMBL::Compara::RunnableDB::BlastComparaPep
Package variables
Privates (from "my" definitions)
$g_BlastComparaPep_workdir;
Included modules
Bio::EnsEMBL::Analysis::Runnable
Bio::EnsEMBL::Analysis::Runnable::Blast
Bio::EnsEMBL::Analysis::Tools::BPliteWrapper
Bio::EnsEMBL::Analysis::Tools::FilterBPlite
Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
Bio::EnsEMBL::Hive::Process
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Hive::Process
Synopsis
my $db = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $blast = Bio::EnsEMBL::Compara::RunnableDB::BlastComparaPep->new
(
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$blast->fetch_input(); #reads from DB
$blast->run();
$blast->output();
$blast->write_output(); #writes to DB
Description
This object wraps Bio::EnsEMBL::Analysis::Runnable::Blast 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 databse access.
Methods
dumpPeptidesToFasta
No description
Code
fetch_inputDescriptionCode
global_cleanup
No description
Code
output
No description
Code
runDescriptionCode
runnableDescriptionCode
write_output
No description
Code
Methods description
fetch_inputcode    nextTop
    Title   :   fetch_input
Usage : $self->fetch_input
Function: Fetches input data for repeatmasker from the database
Returns : none
Args : none
runcodeprevnextTop
  Arg[1]     : -none-
Example : $self->run;
Function : Runs the runnable set in fetch_input
Returns : 1 on succesfull completion
Exceptions : dies if runnable throws an unexpected error
runnablecodeprevnextTop
  Arg[1]     : (optional) Bio::EnsEMBL::Analysis::Runnable $runnable
Example : $self->runnable($runnable);
Function : Getter/setter for the runnable
Returns : Bio::EnsEMBL::Analysis::Runnable $runnable
Exceptions : none
Methods code
dumpPeptidesToFastadescriptionprevnextTop
sub dumpPeptidesToFasta {
  my $self = shift;

  my $startTime = time();
  #my $params = eval($self->analysis->parameters); 
my $params = eval($self->analysis->data); my $genomeDB = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($params->{'genome_db_id'}); # create logical path name for fastafile
my $species = $genomeDB->name(); $species =~ s/\s+/_/g; # replace whitespace with '_' characters
#create temp directory to hold fasta databases
$g_BlastComparaPep_workdir = "/tmp/worker.$$/"; mkdir($g_BlastComparaPep_workdir, 0777); my $fastafile = $g_BlastComparaPep_workdir. $species . "_" . $genomeDB->assembly() . ".fasta"; $fastafile =~ s/\/\//\//g; # converts any // in path to /
return $fastafile if(-e $fastafile); print("fastafile = '$fastafile'\n"); # write fasta file to local /tmp/disk
my $subset = $self->{'comparaDBA'}->get_SubsetAdaptor()->fetch_by_dbID($params->{'subset_id'}); $self->{'comparaDBA'}->get_SubsetAdaptor->dumpFastaForSubset($subset, $fastafile); # configure the fasta file for use as a blast database file
my $blastdb = new Bio::EnsEMBL::Analysis::Runnable::BlastDB ( -dbfile => $fastafile, -type => 'PROTEIN'); $blastdb->run; print("registered ". $blastdb->dbname . " for ".$blastdb->dbfile . "\n"); printf("took %d secs to dump database to local disk\n", (time() - $startTime)); return $fastafile; } 1;
}
fetch_inputdescriptionprevnextTop
sub fetch_input {
  my( $self) = @_;

  throw("No input_id") unless defined($self->input_id);

  ## Get the query (corresponds to the member with a member_id = input_id
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc); $self->{'comparaDBA'}->dbc->disconnect_when_inactive(0); my $member_id = $self->input_id; my $member = $self->{'comparaDBA'}->get_MemberAdaptor->fetch_by_dbID($member_id); throw("No member in compara for member_id = $member_id") unless defined($member); if (10 > $member->bioseq->length) { $self->input_job->update_status('DONE'); throw("BLAST : Peptide is too short for BLAST"); } my $query = $member->bioseq(); throw("Unable to make bioseq for member_id = $member_id") unless defined($query); ## Get the db_file (defined in the analysis)
my $dbfile = $self->analysis->db_file; ## Define the filter from the parameters
my ($thr, $thr_type, $options); #my $p = eval($self->analysis->parameters);
my $p = eval($self->analysis->data); if (defined $p->{'-threshold'} && defined $p->{'-threshold_type'}) { $thr = $p->{-threshold}; $thr_type = $p->{-threshold_type}; } else { $thr_type = 'PVALUE'; $thr = 1e-10; } if (defined $p->{'options'}) { $options = $p->{'options'}; } else { $options = ''; } ## Create a parser object. This Bio::EnsEMBL::Analysis::Tools::FilterBPlite
## object wraps the Bio::EnsEMBL::Analysis::Tools::BPliteWrapper which in
## turn wraps the Bio::EnsEMBL::Analysis::Tools::BPlite (a port of Ian
## Korf's BPlite from bioperl 0.7 into ensembl). This parser also filter
## the results according to threshold_type and threshold.
my $regex = '^(\S+)\s*'; if ($p->{'regex'}) { $regex = $p->{'regex'}; } my $parser = Bio::EnsEMBL::Analysis::Tools::FilterBPlite->new( -regex => $regex, -query_type => "pep", -input_type => "pep", -threshold_type => $thr_type, -threshold => $thr, ); ## Create the runnable with the previous parser. The filter is not required
my $runnable = Bio::EnsEMBL::Analysis::Runnable::Blast->new( -query => $query, -database => $dbfile, -program => $self->analysis->program_file, -analysis => $self->analysis, -options => $options, -parser => $parser, -filter => undef, ); $self->runnable($runnable); return 1;
}
global_cleanupdescriptionprevnextTop
sub global_cleanup {
  my $self = shift;
  if($g_BlastComparaPep_workdir) {
    unlink(<$g_BlastComparaPep_workdir/*>);
rmdir($g_BlastComparaPep_workdir); } return 1; } ##########################################
#
# internal methods
#
##########################################
# using the genome_db and longest peptides subset, create a fasta
# file which can be used as a blast database
}
outputdescriptionprevnextTop
sub output {
  my ($self, @args) = @_;

  throw ("Cannot call output without a runnable") if (!defined($self->runnable));

  return $self->runnable->output(@args);
}
rundescriptionprevnextTop
sub run {
  my $self = shift;

  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);

  ## call runnable run method in eval block
eval { $self->runnable->run(); }; ## Catch errors if any
if ($@) { printf(STDERR ref($self->runnable)." threw exception:\n$@$_"); if($@ =~ /"VOID"/) { printf(STDERR "this is OK: member_id=%d doesn't have sufficient structure for a search\n", $self->input_id); } else { die("$@$_"); } } $self->{'comparaDBA'}->dbc->disconnect_when_inactive(0); return 1;
}
runnabledescriptionprevnextTop
sub runnable {
  my $self = shift(@_);

  if (@_) {
    $self->{_runnable} = shift;
  }

  return $self->{_runnable};
}
write_outputdescriptionprevnextTop
sub write_output {
  my( $self) = @_;

  #since the Blast runnable takes in analysis parameters rather than an
#analysis object, it creates new Analysis objects internally
#(a new one for EACH FeaturePair generated)
#which are a shadow of the real analysis object ($self->analysis)
#The returned FeaturePair objects thus need to be reset to the real analysis object
foreach my $feature (@{$self->output}) { if($feature->isa('Bio::EnsEMBL::FeaturePair')) { $feature->analysis($self->analysis); } } $self->{'comparaDBA'}->get_PeptideAlignFeatureAdaptor->store(@{$self->output});
}
General documentation
CONTACTTop
  Contact Jessica Severin on module implemetation/design detail: jessica@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _