#
# BioPerl module for Bio::SearchIO::axt
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-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::axt - a parser for axt format reports
=head1 SYNOPSIS
use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-format => 'axt',
-file => 't/data/report.blastz');
while( my $result = $parser->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
}
}
}
=head1 DESCRIPTION
This is a parser and event-generator for AXT format reports. BLASTZ
reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally
in LAV format but are commonly post-processed to AXT format; many precomputed
BLASTZ reports, such as those found in the UCSC Genome
Browser, are in AXT format. This parser will also parse any
AXT format produced from any lav report and directly out of BLAT.
=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/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
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=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::axt;
use vars qw(%MODEMAP %MAPPING @STATES $GAPCHAR);
use strict;
use Bio::Search::Result::ResultFactory;
use Bio::Search::HSP::HSPFactory;
use base qw(Bio::SearchIO);
use POSIX;
BEGIN {
# mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = ('AXTOutput' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
$GAPCHAR = '-';
%MAPPING =
(
'Hsp_score' => 'HSP-score',
'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_positive' => 'HSP-conserved',
'Hsp_identity' => 'HSP-identical',
'Hsp_gaps' => 'HSP-hsp_gaps',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_midline' => 'HSP-homology_seq', # ignoring this for now
'Hsp_align-len' => 'HSP-hsp_length',
'Hit_id' => 'HIT-name',
'AXTOutput_query-def'=> 'RESULT-query_name',
);
}
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::axt->new();
Function: Builds a new Bio::SearchIO::axt object
Returns : an instance of Bio::SearchIO::axt
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
=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) = @_;
local $/ = "\n";
local $_;
my ($curquery,$curhit);
$self->start_document();
my @hit_signifs;
while( defined ($_ = $self->_readline )) {
next if (/^\s+$/);
if( m/^(\d+)\s+ # alignment number - we'll throw this away anyways
(\S+)\s+ # Query name
(\d+)\s+(\d+)\s+ # Query start Query end (always + strand, 0 based)
(\S+)\s+ # Hit name
(\d+)\s+(\d+)\s+ # Hit start Hit end (0 based)
([\-\+])\s+ # Hit strand
([\d\.\-]+)\s+ # Score
/ox ) {
my ($alnnum, $qname,$qstart,$qend, $hname,
$hstart,$hend,$hstrand, $score) = ($1,$2,$3,$4,$5,
$6,$7,$8,$9);
$self->{'_reporttype'} = 'AXT';
# Jim's code is 0 based
# yes, but axt format is one-based, see bug 3145 - cjfields 10-11-10
#$qstart++; $qend++; $hstart++; $hend++;
if( defined $curquery && $curquery ne $qname ) {
$self->end_element({'Name' => 'Hit'});
$self->_pushback($_);
$self->end_element({'Name' => 'AXTOutput'});
return $self->end_document();
}
if( defined $curhit &&
$curhit ne $hname) {
# slight duplication here -- keep these in SYNC
$self->end_element({'Name' => 'Hit'});
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $hname});
} elsif ( ! defined $curquery ) {
$self->start_element({'Name' => 'AXTOutput'});
$self->{'_result_count'}++;
$self->element({'Name' => 'AXTOutput_query-def',
'Data' => $qname });
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $hname});
}
$self->start_element({'Name' => 'Hsp'});
my $queryalign = $self->_readline;
my $hitalign = $self->_readline;
chomp($queryalign);
chomp($hitalign);
my $alnlen = length($queryalign);
my $qgapnum = ( $queryalign =~ s/\Q$GAPCHAR/$GAPCHAR/g);
my $hgapnum = ( $hitalign =~ s/\Q$GAPCHAR/$GAPCHAR/g);
my $totalgaps = ($qgapnum + $hgapnum);
if( $hstrand eq '-' ) { # strand gets inferred by start/end
($hstart,$hend) = ($hend,$hstart);
}
$self->element({'Name' => 'Hsp_score',
'Data' => $score});
$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_gaps',
'Data' => $qgapnum + $hgapnum});
$self->element({'Name' => 'Hsp_querygaps',
'Data' => $qgapnum});
$self->element({'Name' => 'Hsp_hitgaps',
'Data' => $hgapnum});
$self->element({'Name' => 'Hsp_identity',
'Data' => $alnlen - $totalgaps});
$self->element({'Name' => 'Hsp_positive',
'Data' => $alnlen - $totalgaps});
$self->element({'Name' => 'Hsp_qseq',
'Data' => $queryalign});
$self->element({'Name' => 'Hsp_hseq',
'Data' => $hitalign});
$self->end_element({'Name' => 'Hsp'});
$curquery = $qname;
$curhit = $hname;
}
}
# fence post
if( defined $curquery ) {
$self->end_element({'Name' => 'Hit'});
$self->end_element({'Name' => 'AXTOutput'});
return $self->end_document();
}
return;
}
sub _initialize {
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
$self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult'));
$self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::GenericHSP'));
}
=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 'AXTOutput') {
$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( 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 'AXTOutput' );
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;