Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher
<![CDATA[#
#
# Cared for by Val Curwen <vac@sanger.ac.uk>
#
# Copyright Val Curwen
#
# 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
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher->new(
);
$obj->pfetch('/path/to/pfetch');
my $seq = $obj->run_pfetch('z87703');
$obj->getz('/path/to/getz');
my $seq2 = $obj->run_getz('z87703','embl emblnew');
=head1 DESCRIPTION
Object to perform various sequence retrieval functions
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Pipeline::SeqFetcher;
use strict;
use Bio::EnsEMBL::Root;
use Bio::Seq;
use Bio::SeqIO;
use Bio::Index::Fasta;
use Bio::Index::EMBL;
use Bio::Index::SwissPfam;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
=head2 pfetch
Title : pfetch
Usage : $self->pfetch('/usr/local/ensembl/bin/pfetch')
Function: Get/set for pfetch executable
Returns :
Args : path to pfetch executable
=cut
sub pfetch {
my ($self, $pfetch) = @_;
if ($pfetch) {
$self->{'_pfetch'} = $pfetch;
}
return $self->{'_pfetch'};
}
=head2 efetch
Title : efetch
Usage : $self->efetch('/usr/local/ensembl/bin/efetch')
Function: Get/set for efetch executable
Returns :
Args : path to efetch executable
=cut
sub efetch {
my ($self, $efetch) = @_;
if ($efetch) {
$self->{'_efetch'} = $efetch;
}
return $self->{'_efetch'};
}
=head2 getz
Title : getz
Usage : $self->getz('/usr/local/ensembl/bin/getz')
Function: Get/set for getz executable
Returns :
Args : path to getz executable
=cut
sub getz {
my ($self, $getz) = @_;
if ($getz) {
$self->{'_getz'} = $getz;
}
return $self->{'_getz'};
}
=head2 bp_index
Title : bp_index
Usage : $self->bp_index('/usr/local/ensembl/data/bp.inx')
Function: Get/set for a bioperl index
Returns : path to bioperl index
Args : path to bioperl index
=cut
sub bp_index {
my ($self, $inx) = @_;
if ($inx) {
$self->{'_inx'} = $inx;
}
return $self->{'_inx'};
}
=head2 bp_format
Title : bp_format
Usage : $self->bp_format('Fasta')
Function: Get/set for a bioperl index format
Returns : String representing format
Args : String representing format
=cut
sub bp_format {
my ($self, $format) = @_;
if ($format) {
$self->{'_format'} = $format;
}
return $self->{'_format'};
}
=head2 run_pfetch
Title : run_pfetch
Usage : $self->run_pfetch($id)
Function: Retrieves a sequence using pfetch
Returns : Bio::Seq, or undef
Args : id of sequence to be retrieved
=cut
sub run_pfetch {
my ($self,$id) = @_;
if (!defined($id)) {
$self->throw("No id input to run_pfetch");
}
my $seqstr;
my $seq;
my $newid = $self->parse_header($id);
my $pfetch = $self->pfetch;
# if pfetch path not explicitly set, assume it's in $PATH
$pfetch = 'pfetch' unless defined($pfetch);
open(IN,"$pfetch -q $newid |") || $self->throw("Error running pfetch for id [$newid]: $pfetch");
$seqstr = <IN>;
close IN;
chomp($seqstr);
if(defined $seqstr && $seqstr ne "no match") {
$seq = new Bio::Seq('-seq' => $seqstr,
'-id' => $newid);
}
return $seq;
}
=head2 run_efetch
Title : run_efetch
Usage : $self->run_efetch($id)
Function: Retrieves a sequence using efetch
Returns : Bio::Seq, or undef
Args : id of sequence to be retrieved
=cut
sub run_efetch {
my ($self,$id) = @_;
if (!defined($id)) {
$self->throw("No id input to run_efetch");
}
my $seqstr;
my $seq;
my $newid = $self->parse_header($id);
my $efetch = $self->efetch;
# if efetch path not explicitly set, assume it's in $PATH
$efetch = 'efetch' unless defined($efetch);
open(IN,"$efetch -q $newid |") || $self->throw("Error running efetch for id [$newid]: $efetch");
$seqstr = <IN>;
close IN;
# chomp($seqstr);
$seq = new Bio::Seq('-seq' => $seqstr, '-id' => $newid)
unless (!defined $seqstr || $seqstr =~ "not found");
return $seq;
}
=head2 run_getz
Title : run_getz
Usage : $self->run_getz($id,$libs)
Function: Retrieves a sequence using getz from the specified libraries
Returns : Bio::Seq, or undef
Args : id of sequence to be retrieved, string representing libraries to be searched
=cut
sub run_getz {
my ($self,$id,$libs) = @_;
if (!defined($id)) {
$self->throw("No id input to run_getz");
}
if (!defined($libs)) {
$self->throw("No libs input to run_getz");
}
my $seqstr;
my $seq;
my $newid = $self->parse_header($id);
$self->throw("Could not parse id [$id]") unless defined $newid;
my $getz = $self->getz;
# if getz path not explicitly set, assume it's in $PATH
$getz = 'getz' unless defined($getz);
open(IN, "getz -e '[libs={$libs}-ID:$id] | [libs-AccNumber:$id]' |")
|| $self->throw("Error running getz for id [$newid]: $getz");
# hack just for rikens
my $format = 'EMBL';
if($libs eq 'mouseprot') { $format = 'Fasta'; }
my $fh = Bio::SeqIO->new('-fh' => \*IN, "-format"=>$format);
$seq = $fh->next_seq();
close IN;
$self->warn("Problem with getz for [$id]") unless defined $seq;
return $seq;
}
=head2 parse_header
Title : parse_header
Usage : my $newid = $self->parse_header($id);
Function: Parses different sequence headers
Returns : string
Args :string to be parsed
=cut
sub parse_header {
my ($self,$id) = @_;
if (!defined($id)) {
$self->throw("No id input to parse_header");
}
my $newid = $id;
if ($id =~ /\/ug=(\S+)\s+/){
$newid = $1;
}
elsif ($id =~ /^(.*)\|(.*)\|(.*)/) {
if ($2 eq "UG") {
$newid = $3;
}
else {
$newid = $2;
}
$newid =~ s/(.*)\..*/$1/;
}
elsif ($id =~ /^..\:(.*)/) {
$newid = $1;
}
$newid =~ s/ //g;
print STDERR "newid: $newid\n";
return $newid;
}
=head2 run_bp_search
Title : run_bp_search
Usage : $self->run_bp_search($id,$inx,$format)
Function: Retrieves a sequence from the specified Bioperl index
Returns : Bio::Seq, or undef
Args : id of sequence to be retrieved,
string representing path to bioperl index,
string representing index format
=cut
sub run_bp_search {
my ($self,$id,$inx,$format) = @_;
my $seq;
my $index;
if (!defined($id)) {
$self->throw("No id input to run_bp_search");
}
if (!defined($inx)){
$inx = $self->bp_index;
if (!defined($inx)) {
$self->throw("Cannot run_bp_search without an indexfile");
}
}
if (!defined($format)){
$format = $self->bp_format;
if (!defined($format) || ($format ne 'Fasta' &&
$format ne 'EMBL' &&
$format ne 'SwissPfam')) {
$self->throw("Cannot run_bp_search without a valid format: Fasta, EMBL or SwissPfam");
}
}
my $type = 'Bio::Index::' . $format;
eval {
$index = $type->new($inx);
};
if ($@) {
my $tmp = $@; # for some reason, warn empties out $@ ...
$self->warn("Problem opening the index [$inx] - check you have supplied the right format!");
$self->throw ("[$tmp]!");
}
# get the sequence
eval{
$seq = $index->fetch($id); # Returns Bio::Seq object
};
$self->warn("Problem with run_bp_search for [$id]") unless defined $seq;
return $seq;
}
1;
]]>