Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::PrositePattern
<![CDATA[
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::PrositePattern;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
@ISA = qw (Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($confirms) = rearrange(['CONFIRM'], @args);
if (defined $confirms) {
$self->confirm_file($confirms);
}
if (not defined $self->database) {
throw("You must supply a databaser to search");
}
return $self;
}
sub run {
my ($self, @args) = @_;
my $scanning_code =
$self->create_scanning_code_from_patterns($self->database,
$self->confirm_file);
my @fps;
if (-s $self->query) {
my $seqio = Bio::SeqIO->new(-format => 'fasta',
-file => '<'.$self->query);
while(my $seq = $seqio->next_seq) {
push @fps, @{$self->scan_sequence($scanning_code, $seq)};
}
$seqio->close;
} elsif (ref($self->query) and
$self->query->isa("Bio::PrimarySeqI")) {
push @fps, @{$self->scan_sequence($scanning_code, $self->query)};
}
$self->output(\@fps);
}
sub scan_sequence {
my ($self, $code, $seq) = @_;
my (@RESULTS);
my $SEQID = $seq->display_id;
my $SEQ = $seq->seq;
eval($code);
warn($@) if $@;
my @features;
foreach my $res (@RESULTS) {
my $fp = $self->create_protein_feature($res->{start},
$res->{end},
$res->{score},
$res->{seqid},
0, 0,
$res->{acc},
$self->analysis,
0, 0);
push @features, $fp;
}
return \@features;
}
sub create_scanning_code_from_patterns {
my ($self, $pattern_file, $confirm_file) = @_;
my $confirm_hash = {};
if (defined $confirm_file) {
$self->_read_confirm_patterns($confirm_file,
$confirm_hash);
}
my $scan_code = "\n"; # Perl-code to be constructed
open (PAT,"<$pattern_file")
or throw("Cannot open pattern file $pattern_file");
while (<PAT>){
my ($acc,$pattern,$name,$taxonrange) = split(/\s+/);
$taxonrange =~ s/\?//g;
$scan_code .= "while(\$SEQ =~ /$pattern/g){\n";
$scan_code .= " my (\$match,\$start,\$end,\$confirmed) = (\$&,length(\$\`)+1,pos(\$SEQ),0);\n";
$scan_code .= " my \$result = {};\n";
$scan_code .= " \$result->{seqid} = \$SEQID;\n";
$scan_code .= " \$result->{acc} = \"$acc\";\n";
$scan_code .= " \$result->{name} = \"$name\";\n";
$scan_code .= " \$result->{start} = \$start;\n";
$scan_code .= " \$result->{end} = \$end;\n";
$scan_code .= " \$result->{score} = 0;\n";
if (exists($confirm_hash->{$acc})){
foreach my $con_pat (@{$confirm_hash->{$acc}}) {
$scan_code .= " \$result->{score} = 1 if \$match =~ /$con_pat/;\n";
}
}
$scan_code .= " push \@RESULTS, \$result;\n}\n";
}
close (PAT);
#print $scan_code;
return $scan_code;
}
sub _read_confirm_patterns {
my ($self, $confirm_file, $confirms_hash) = @_;
open (PAT,"<$confirm_file")
or throw("Cannot open file of confirms '$confirm_file'");
while (<PAT>){
my ($acc,$pattern)=split(/\s+/);
push @{$confirms_hash->{$acc}}, $pattern;
}
close (PAT);
}
sub confirm_file {
my ($self, $val) = @_;
if (defined $val) {
$self->{_confirm_file} = $val;
}
if (exists $self->{_confirm_file}) {
return $self->{_confirm_file};
} else {
return undef;
}
}
1;
]]>