Raw content of Bio::SearchIO::waba
<![CDATA[# $Id: waba.pm,v 1.8 2002/12/11 22:12:32 jason Exp $
#
# BioPerl module for Bio::SearchIO::waba
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program
alignment output
=head1 SYNOPSIS
# do not use this object directly, rather through Bio::SearchIO
use Bio::SearchIO;
my $in = new Bio::SearchIO(-format => 'waba',
-file => 'output.wab');
while( my $result = $in->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $result->next_hsp ) {
}
}
}
=head1 DESCRIPTION
This parser will process the waba output (NOT the human readable format).
=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
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails 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::SearchIO::waba;
use vars qw(@ISA %MODEMAP %MAPPING @STATES);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::SearchIO;
use POSIX;
BEGIN {
# mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = ('WABAOutput' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
@STATES = qw(Hsp_qseq Hsp_hseq Hsp_stateseq);
%MAPPING =
(
'Hsp_query-from'=> 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_midline' => 'HSP-homology_seq',
'Hsp_stateseq' => 'HSP-hmmstate_seq',
'Hsp_align-len' => 'HSP-hsp_length',
'Hit_id' => 'HIT-name',
'Hit_accession' => 'HIT-accession',
'WABAOutput_program' => 'RESULT-algorithm_name',
'WABAOutput_version' => 'RESULT-algorithm_version',
'WABAOutput_query-def'=> 'RESULT-query_name',
'WABAOutput_query-db' => 'RESULT-query_database',
'WABAOutput_db' => 'RESULT-database_name',
);
}
@ISA = qw(Bio::SearchIO );
=head2 new
Title : new
Usage : my $obj = new Bio::SearchIO::waba();
Function: Builds a new Bio::SearchIO::waba object
Returns : Bio::SearchIO::waba
Args : see Bio::SearchIO
=cut
sub _initialize {
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
$self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::WABAResult'));
$self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::WABAHSP'));
}
=head2 next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result{
my ($self) = @_;
my ($curquery,$curhit);
my $state = -1;
$self->start_document();
my @hit_signifs;
while( defined ($_ = $self->_readline )) {
if( $state == -1 ) {
my ($qid, $qhspid,$qpercent, $junk,
$alnlen,$qdb,$qacc,$qstart,$qend,$qstrand,
$hitdb,$hacc,$hstart,$hend,
$hstrand) =
( /^(\S+)\.(\S+)\s+align\s+ # get the queryid
(\d+(\.\d+)?)\%\s+ # get the percentage
of\s+(\d+)\s+ # get the length of the alignment
(\S+)\s+ # this is the query database
(\S+):(\d+)\-(\d+) # The accession:start-end for query
\s+([\-\+]) # query strand
\s+(\S+)\. # hit db
(\S+):(\d+)\-(\d+) # The accession:start-end for hit
\s+([\-\+])\s*$ # hit strand
/ox );
# Curses. Jim's code is 0 based, the following is to readjust
$hstart++; $hend++; $qstart++; $qend++;
if( ! defined $alnlen ) {
$self->warn("Unable to parse the rest of the WABA alignment info for: $_");
last;
}
$self->{'_reporttype'} = 'WABA'; # hardcoded - only
# one type of WABA AFAIK
if( defined $curquery &&
$curquery ne $qid ) {
$self->end_element({'Name' => 'Hit'});
$self->_pushback($_);
$self->end_element({'Name' => 'WABAOutput'});
return $self->end_document();
}
if( defined $curhit &&
$curhit ne $hacc) {
# slight duplication here -- keep these in SYNC
$self->end_element({'Name' => 'Hit'});
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $hacc});
$self->element({'Name' => 'Hit_accession',
'Data' => $hacc});
} elsif ( ! defined $curquery ) {
$self->start_element({'Name' => 'WABAOutput'});
$self->{'_result_count'}++;
$self->element({'Name' => 'WABAOutput_query-def',
'Data' => $qid });
$self->element({'Name' => 'WABAOutput_program',
'Data' => 'WABA'});
$self->element({'Name' => 'WABAOutput_query-db',
'Data' => $qdb});
$self->element({'Name' => 'WABAOutput_db',
'Data' => $hitdb});
# slight duplication here -- keep these N'SYNC ;-)
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $hacc});
$self->element({'Name' => 'Hit_accession',
'Data' => $hacc});
}
# strand is inferred by start,end values
# in the Result Builder
if( $qstrand eq '-' ) {
($qstart,$qend) = ($qend,$qstart);
}
if( $hstrand eq '-' ) {
($hstart,$hend) = ($hend,$hstart);
}
$self->start_element({'Name' => 'Hsp'});
$self->element({'Name' => 'Hsp_query-from',
'Data' => $qstart});
$self->element({'Name' => 'Hsp_query-to',
'Data' => $qend});
$self->element({'Name' => 'Hsp_hit-from',
'Data' => $hstart});
$self->element({'Name' => 'Hsp_hit-to',
'Data' => $hend});
$self->element({'Name' => 'Hsp_align-len',
'Data' => $alnlen});
$curquery = $qid;
$curhit = $hacc;
$state = 0;
} elsif( ! defined $curquery ) {
$self->warn("skipping because no Hit begin line was recognized\n$_") if( $_ !~ /^\s+$/ );
next;
} else {
chomp;
$self->element({'Name' => $STATES[$state++],
'Data' => $_});
if( $state >= scalar @STATES ) {
$state = -1;
$self->end_element({'Name' => 'Hsp'});
}
}
}
if( defined $curquery ) {
$self->end_element({'Name' => 'Hit'});
$self->end_element({'Name' => 'WABAOutput'});
return $self->end_document();
}
return undef;
}
=head2 start_element
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub start_element{
my ($self,$data) = @_;
# we currently don't care about attributes
my $nm = $data->{'Name'};
if( my $type = $MODEMAP{$nm} ) {
$self->_mode($type);
if( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf("start_%s",lc $type);
$self->_eventHandler->$func($data->{'Attributes'});
}
unshift @{$self->{'_elements'}}, $type;
}
if($nm eq 'WABAOutput') {
$self->{'_values'} = {};
$self->{'_result'}= undef;
$self->{'_mode'} = '';
}
}
=head2 end_element
Title : start_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub end_element {
my ($self,$data) = @_;
my $nm = $data->{'Name'};
my $rc;
# Hsp are sort of weird, in that they end when another
# object begins so have to detect this in end_element for now
if( $nm eq 'Hsp' ) {
foreach ( qw(Hsp_qseq Hsp_midline Hsp_hseq) ) {
$self->element({'Name' => $_,
'Data' => $self->{'_last_hspdata'}->{$_}});
}
$self->{'_last_hspdata'} = {}
}
if( my $type = $MODEMAP{$nm} ) {
if( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf("end_%s",lc $type);
$rc = $self->_eventHandler->$func($self->{'_reporttype'},
$self->{'_values'});
}
shift @{$self->{'_elements'}};
} elsif( $MAPPING{$nm} ) {
if ( ref($MAPPING{$nm}) =~ /hash/i ) {
my $key = (keys %{$MAPPING{$nm}})[0];
$self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
} else {
$self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
}
} else {
$self->warn( "unknown nm $nm ignoring\n");
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( $nm eq 'WABAOutput' );
return $rc;
}
=head2 element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
=cut
sub element{
my ($self,$data) = @_;
$self->start_element($data);
$self->characters($data);
$self->end_element($data);
}
=head2 characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
=cut
sub characters{
my ($self,$data) = @_;
return unless ( defined $data->{'Data'} );
if( $data->{'Data'} =~ /^\s+$/ ) {
return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
}
if( $self->in_element('hsp') &&
$data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
$self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
}
$self->{'_last_data'} = $data->{'Data'};
}
=head2 _mode
Title : _mode
Usage : $obj->_mode($newval)
Function:
Example :
Returns : value of _mode
Args : newvalue (optional)
=cut
sub _mode{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_mode'} = $value;
}
return $self->{'_mode'};
}
=head2 within_element
Title : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
=cut
sub within_element{
my ($self,$name) = @_;
return 0 if ( ! defined $name &&
! defined $self->{'_elements'} ||
scalar @{$self->{'_elements'}} == 0) ;
foreach ( @{$self->{'_elements'}} ) {
if( $_ eq $name ) {
return 1;
}
}
return 0;
}
=head2 in_element
Title : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
=cut
sub in_element{
my ($self,$name) = @_;
return 0 if ! defined $self->{'_elements'}->[0];
return ( $self->{'_elements'}->[0] eq $name)
}
=head2 start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handles a start document event
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= undef;
$self->{'_mode'} = '';
$self->{'_elements'} = [];
}
=head2 end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub end_document{
my ($self,@args) = @_;
return $self->{'_result'};
}
=head2 result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
=cut
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
sub report_count { shift->result_count }
1;
]]>