Bio::EnsEMBL::Pipeline::SeqFetcher Efetch
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Summary
  Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch
Package variables
No package variables defined.
Included modules
Bio::DB::RandomAccessI
Bio::EnsEMBL::Root
Bio::Seq
Inherit
Bio::DB::RandomAccessI Bio::EnsEMBL::Root
Synopsis
    my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch->new(
							      '-executable' => $exe,
							      '-lib'        => $lib,
							     );
    my $seq = $obj->get_Seq_by_acc($acc);
Description
  Object to retrieve sequences as Bio::Seq, using efetch.
Methods
executableDescriptionCode
get_Seq_by_accDescriptionCode
libraryDescriptionCode
new
No description
Code
Methods description
executablecode    nextTop
  Title   : executable
  Usage   : $self->executable('/path/to/executable');
  Function: Get/set for the path to the executable being used by the module. If not set, the executable is looked for in $PATH.
  Returns : string
  Args    : string
get_Seq_by_acccodeprevnextTop
  Title   : get_Seq_by_acc
  Usage   : $self->get_Seq_by_acc($accession);
  Function: Does the sequence retrieval via efetch
  Returns : Bio::Seq
  Args    :
librarycodeprevnextTop
  Title   : library
  Usage   : $self->library('sw');
  Function: Get/set for a library to search in - eg efetch wil not search swall without the prefix sw:
  Returns : string
  Args    : string
Methods code
executabledescriptionprevnextTop
sub executable {
  my ($self, $exe) = @_;
  if ($exe)
    {
      $self->{'_exe'} = $exe;
    }
  return $self->{'_exe'};
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
  my ($self, $acc) = @_;

  if (!defined($acc)) {
    $self->throw("No accession input");
  }  

  my $lib = $self->library;
  if (defined $lib && $lib ne ''){
    $acc = $lib . ":" . $acc;
  }

  my $seqstr;
  my $seq;
  my $efetch = $self->executable;
  
  open(IN,"$efetch -q $acc |") or $self->throw("Error running efetch for acc [$acc]: $efetch");
  $seqstr = <IN>;
  close IN;
  
  if(defined $seqstr && $seqstr ne "no match") {
    chomp($seqstr);
    $seq = new Bio::Seq('-seq'               => $seqstr,
			'-accession_number'  => $acc,
			'-display_id'        => $acc);
  }

  $self->throw("Could not efetch sequence for [$acc]\n") unless defined $seq;
  return $seq;

}

1;
}
librarydescriptionprevnextTop
sub library {
  my ($self, $lib) = @_;
  if ($lib) {
      $self->{'_lib'} = $lib;
    }
  return $self->{'_lib'};
}
newdescriptionprevnextTop
sub new {
  my ($class, @args) = @_;
  my $self = bless {}, $class;

  my ($exe, $lib) = $self->_rearrange([
				       'EXECUTABLE', 
				       'LIBRARY'], @args);

  if (!defined $exe) {
    $exe = 'efetch';
  }
  $self->executable($exe);
  
  
  if (defined $lib) {
    $self->library($lib);
  }  
  return $self; # success - we hope!
}
General documentation
CONTACTTop
Describe contact details here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _