=head1 NAME
Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation
=head1 SYNOPSIS
# See Bio::Matrix::PSM::IO for detailed documentation on how to use
# PSM parsers
=head1 DESCRIPTION
Parser for mast. This driver unlike meme or transfac for example is
dedicated more to PSM sequence matches
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Stefan Kirov
Email skirov@utk.edu
=head1 APPENDIX
=cut
# Let the code begin...
package Bio::Matrix::PSM::PsmHeader;
use Bio::Matrix::PSM::InstanceSite;
use strict;
use base qw(Bio::Root::Root Bio::Matrix::PSM::PsmHeaderI);
#These define what structures within the
@Bio::Matrix::PSM::PsmHeader::MASTHEADER=qw(html version release seq hid
length instances unstructured);
@Bio::Matrix::PSM::PsmHeader::MEMEHEADER=qw(html version release hid weight length unstructured);
@Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER=qw(unstructured version release);
@Bio::Matrix::PSM::PsmHeader::PSIBLASTHEADER=qw(seq width ic);
@Bio::Matrix::PSM::PsmHeader::ALLHEADER=qw(header release type version html
release weight length id
seq instances unstructured);
=head2 new
Title : new
Usage : my $header= Bio::Matrix::PSM::PsmHeader->new(-seq=>\%seq,
-mid=>\%mid,
-width=>\%width,
-instances=>\%instances,
-header=>\@header,
-type=>'mast');
Function: Creates a new Bio::Matrix::PSM::PsmHeader object
Throws :
Example :
Returns : Bio::Matrix::PSM::PsmHeader object
Args : hash
=cut
sub new {
my ($class,@args)=@_;
my $self = $class->SUPER::new(@args);
return $self;
}
#parse version/release info here from the unstructured array
sub _initialize {
my $self = shift;
my $type=ref($self);
$type=~s/\w+:://g;
$self->{_type} = $type;
my $dat=join(" ",grep(/version|release/i,@{$self->{unstructured}}));
if ($dat && ($dat=~/version\b/i)) {
$self->{version}=substr($dat,$+[0]+1);
$self->{version}=~s/\s.+[^\d\.\:\/]//g;
$self->{version}=~s/^\D//;
}
if ($dat && ($dat=~/release\b/i)) {
my $rel=substr($dat,$+[0]+1);
$rel=~s/[^\d\.\:\/\-]//g;
$rel=~s/^\D//;
if ($rel=~/\d\d:\d\d:\d\d/) { #Reformat if time is available too
my $time=substr($rel,$-[0]+1);
my $dat= substr($rel,0,$-[0]);
$self->{release}="$dat $time";
}
else { $self->{release}=$rel; }
}
return $self;
}
=head2 seq
Title : seq
Usage : my %seq= $header->seq();
Function: Returns the sequence data as a hash, indexed by a sequence ID (motif id or accession number)
In case the input data is a motif it would return the consenus seq for each of them (mast).
Throws :
Example :
Returns : hash
Args :
=cut
sub seq {
my $self = shift;
return () unless ($self->_check('seq'));
return %{$self->{seq}};
}
=head2 hid
Title : hid
Usage : my @hid= $header->hid();
Function: Returns array with the motif ids
Throws :
Example :
Returns : array
Args :
=cut
sub hid {
my $self = shift;
return unless ($self->_check('hid'));
my @header=@{$self->{hid}};
return @header;
}
=head2 length
Title : length
Usage : my %length= $header->length();
Function: Returns the length of the input sequence or motifs as a hash, indexed
by a sequence ID (motif id or accession number)
Throws :
Example :
Returns : hash
Args :
=cut
sub length {
my $self = shift;
return unless ($self->_check('length'));
return $self->{length};
}
=head2 instances
Title : instances
Usage : my %instances= $header->instances();
Function: Returns the info about the input data, contained in the header
Throws :
Example :
Returns : hash
Args :
=cut
sub instances {
my $self = shift;
return unless ($self->_check('instances'));
return %{$self->{instances}};
}
=head2 weight
Title : weight
Usage : my %weights= $header->weight();
Function: Returns the weights of the input sequence as a hash, indexed
by a sequence ID
Throws :
Example :
Returns : hash
Args :
=cut
sub weight {
my $self = shift;
return () unless ($self->_check('weight'));
return %{$self->{weight}};
}
=head2 unstuctured
Title : unstuctured
Usage : my @unstructured= $header->unstuctured();
Function: Returns the unstructured data in the header as an array, one line per
array element, all control symbols are removed with \W
Throws :
Example :
Returns : array
Args :
=cut
sub unstructured {
my $self = shift;
return @{$self->{unstructured}};
}
=head2 version
Title : version
Usage : my $version= $header->version;
Function: Returns the version of the file being parsed if such exists
Throws :
Example :
Returns : string
Args :
=cut
sub version {
my $self = shift;
return $self->{version};
}
=head2 release
Title : release
Usage : my $release= $header->release;
Function: Returns the release of the file being parsed if such exists
Throws :
Example :
Returns : string
Args :
=cut
sub release {
my $self = shift;
return $self->{release};
}
=head2 _check
Title : _check
Usage : if ($self->_check('weights') { #do something} else {return 0;}
Function: Checks if the method called is aplicable to the file format
Throws :
Example :
Returns : boolean
Args : string
=cut
sub _check {
my ($self,$method) = @_;
my $type= $self->{'_type'};
if ($type eq 'meme') {
return 0 unless (grep(/$method/,
@Bio::Matrix::PSM::PsmHeader::MEMEHEADER));
} elsif ($type eq 'mast') {
return 0 unless (grep(/$method/,
@Bio::Matrix::PSM::PsmHeader::MASTHEADER));
} elsif ($type eq 'transfac') {
return 0 unless (grep(/$method/,
@Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER));
} elsif ($type eq 'psiblast') {
return 0 unless (grep(/$method/,
@Bio::Matrix::PSM::PsmHeader::PSIBLASTHEADER));
}
return 1;
}
1;