Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation PIRSF
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Summary
  Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::PIRSF
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::PIRSF
Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation
Inherit
Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation
Synopsis
  my $seg = Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::PIRSF->
new ( -db => $db,
-input_id => $input_id,
-analysis => $analysis,
);
$seg->fetch_input; # gets sequence from DB
$seg->run;
$seg->write_output; # writes features to to DB
Description
  This object wraps Bio::EnsEMBL::Pipeline::Runnable::Hmmpfam
to add functionality to read and write to databases in
a Pfam-specific way.
Methods
fetch_input
No description
Code
Methods description
None available.
Methods code
fetch_inputdescriptionprevnextTop
sub fetch_input {
  my ($self) = @_;
 
  $self->SUPER::fetch_input;
 
  # PIRSF needs sequence lengths, so we must create one Runnable
# for each input sequence, giving a Bio::PrimarySeq as input
my @query_seqs; if (ref($self->query) and $self->query->isa("Bio::PrimarySeq")) { push @query_seqs, $self->query; } elsif (-e $self->query) { my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => $self->query); while(my $seq = $seqio->next_seq) { push @query_seqs, $seq; } $seqio->close; } else { throw($self->query . " is neither an object ref nor a file name\n"); } foreach my $seq (@query_seqs) { my $run = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::PIRSF-> new(-query => $seq, -analysis => $self->analysis, -database => $self->analysis->db_file, %{$self->parameters_hash} ); $self->runnable($run); }
}
General documentation
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