Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch # # Cared for by EnsEMBL <ensembl-dev@ebi.ac.uk> # # Copyright GRL & EBI # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =pod =head1 NAME Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch =head1 SYNOPSIS my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch->new( '-executable' => $exe, '-lib' => $lib, ); my $seq = $obj->get_Seq_by_acc($acc); =head1 DESCRIPTION Object to retrieve sequences as Bio::Seq, using efetch. =head1 CONTACT Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch; use strict; use Bio::EnsEMBL::Root; use Bio::DB::RandomAccessI; use Bio::Seq; use vars qw(@ISA); @ISA = qw(Bio::EnsEMBL::Root Bio::DB::RandomAccessI); 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! } =head2 executable 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 $PATH. Returns : string Args : string =cut sub executable { my ($self, $exe) = @_; if ($exe) { $self->{'_exe'} = $exe; } return $self->{'_exe'}; } =head2 library Title : library Usage : $self->library('sw'); Function: Get/set for a library to search in - eg efetch wil not search swall without the prefix sw: Returns : string Args : string =cut sub library { my ($self, $lib) = @_; if ($lib) { $self->{'_lib'} = $lib; } return $self->{'_lib'}; } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $self->get_Seq_by_acc($accession); Function: Does the sequence retrieval via efetch Returns : Bio::Seq Args : =cut 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;