#
# BioPerl module for Bio::SearchIO::psl
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-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::psl - A parser for PSL output (UCSC)
=head1 SYNOPSIS
use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-file => 'file.psl',
-format => 'psl');
while( my $result = $parser->next_result ) {
}
=head1 DESCRIPTION
This is a SearchIO driver for PSL format.
PSL format is documented here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL
By default it assumes PSL output came from BLAT you can override that
by specifying -program_name =E<gt> 'BLASTZ' when initializing the
SearchIO object.
=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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-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::psl;
use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName);
use strict;
use Bio::Search::HSP::HSPFactory;
use Bio::Search::Hit::HitFactory;
use Bio::Search::Result::ResultFactory;
$DefaultProgramName = 'BLAT';
$DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
# mapping of terms to Bioperl hash keys
%MODEMAP = (
'PSLOutput' => 'result',
'Result' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
%MAPPING = (
'Hsp_bit-score' => 'HSP-bits',
'Hsp_score' => 'HSP-score',
'Hsp_evalue' => 'HSP-evalue',
'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_mismatches' => 'HSP-mismatches',
'Hsp_qgapblocks' => 'HSP-query_gapblocks',
'Hsp_hgapblocks' => 'HSP-hit_gapblocks',
'Hsp_gaps' => 'HSP-hsp_gaps',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hsp_align-len' => 'HSP-hsp_length',
'Hsp_query-frame' => 'HSP-query_frame',
'Hsp_hit-frame' => 'HSP-hit_frame',
'Hit_id' => 'HIT-name',
'Hit_len' => 'HIT-length',
'Hit_accession' => 'HIT-accession',
'Hit_def' => 'HIT-description',
'Hit_signif' => 'HIT-significance',
'Hit_score' => 'HIT-score',
'Hit_bits' => 'HIT-bits',
'PSLOutput_program' => 'RESULT-algorithm_name',
'PSLOutput_version' => 'RESULT-algorithm_version',
'PSLOutput_query-def' => 'RESULT-query_name',
'PSLOutput_query-len' => 'RESULT-query_length',
'PSLOutput_query-acc' => 'RESULT-query_accession',
'PSLOutput_querydesc' => 'RESULT-query_description',
'PSLOutput_db' => 'RESULT-database_name',
'PSLOutput_db-len' => 'RESULT-database_entries',
'PSLOutput_db-let' => 'RESULT-database_letters',
);
use base qw(Bio::SearchIO);
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::psl->new();
Function: Builds a new Bio::SearchIO::psl object
Returns : an instance of Bio::SearchIO::psl
Args :
=cut
sub _initialize {
my ( $self, @args ) = @_;
$self->SUPER::_initialize(@args);
my ($pname) = $self->_rearrange( [qw(PROGRAM_NAME)], @args );
$self->program_name( $pname || $DefaultProgramName );
$self->_eventHandler->register_factory(
'result',
Bio::Search::Result::ResultFactory->new(
-type => 'Bio::Search::Result::GenericResult'
)
);
$self->_eventHandler->register_factory(
'hit',
Bio::Search::Hit::HitFactory->new(
-type => 'Bio::Search::Hit::GenericHit'
)
);
$self->_eventHandler->register_factory(
'hsp',
Bio::Search::HSP::HSPFactory->new(
-type => 'Bio::Search::HSP::PSLHSP'
)
);
}
=head2 next_result
Title : next_result
Usage : my $result = $parser->next_result
Function: Parse the next result from the data stream
Returns : L<Bio::Search::Result::ResultI> or undef if no more results
Args : none
=cut
sub next_result {
my ($self) = @_;
my ( $lastquery, $lasthit );
local $/ = "\n";
local $_;
# skip over any header lines
while( defined($_ = $self->_readline) and ! /^\d+\s+\d+\s+/ ) {}
$self->_pushback($_);
# now start the main parsing loop
while ( defined( $_ = $self->_readline ) ) {
my (
$matches, $mismatches, $rep_matches, $n_count,
$q_num_insert, $q_base_insert, $t_num_insert, $t_base_insert,
$strand, $q_name, $q_length, $q_start,
$q_end, $t_name, $t_length, $t_start,
$t_end, $block_count, $block_sizes, $q_starts,
$t_starts
) = split;
$q_length > 0 or $self->throw("parse error, invalid query length '$q_length'");
my $score = sprintf( "%.2f", 100 * ( $matches + $mismatches + $rep_matches ) / $q_length );
# this is overall percent identity...
my $match_total = $matches + $mismatches + $rep_matches;
$match_total > 0
or $self->throw("parse error, matches + mismatches + rep_matches must be > 0!");
my $percent_id = sprintf("%.2f", 100 * ( $matches + $rep_matches ) / $match_total );
# Remember Jim's code is 0 based
if ( defined $lastquery
&& $lastquery ne $q_name )
{
$self->end_element( { 'Name' => 'Hit' } );
$self->end_element( { 'Name' => 'PSLOutput' } );
$self->_pushback($_);
return $self->end_document;
}
elsif ( !defined $lastquery ) {
$self->{'_result_count'}++;
$self->start_element( { 'Name' => 'PSLOutput' } );
$self->element(
{
'Name' => 'PSLOutput_program',
'Data' => $self->program_name
}
);
$self->element(
{
'Name' => 'PSLOutput_query-def',
'Data' => $q_name
}
);
$self->element(
{
'Name' => 'PSLOutput_query-len',
'Data' => $q_length
}
);
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
'Name' => 'Hit_id',
'Data' => $t_name
}
);
$self->element(
{
'Name' => 'Hit_len',
'Data' => $t_length
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => $score
}
);
}
elsif ( $lasthit ne $t_name ) {
$self->end_element( { 'Name' => 'Hit' } );
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
'Name' => 'Hit_id',
'Data' => $t_name
}
);
$self->element(
{
'Name' => 'Hit_len',
'Data' => $t_length
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => $score
}
);
}
my $identical = $matches + $rep_matches;
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
{
'Name' => 'Hsp_score',
'Data' => $score
}
);
$self->element(
{
'Name' => 'Hsp_identity',
'Data' => $identical
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => $identical
}
);
$self->element(
{
'Name' => 'Hsp_mismatches',
'Data' => $mismatches
}
);
$self->element(
{
'Name' => 'Hsp_gaps',
'Data' => $q_base_insert + $t_base_insert
}
);
# query gaps are the number of target inserts and vice-versa
$self->element(
{
'Name' => 'Hsp_querygaps',
'Data' => $t_base_insert
}
);
$self->element(
{
'Name' => 'Hsp_hitgaps',
'Data' => $q_base_insert
}
);
if ( $strand eq '+' ) {
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => $q_start + 1
}
);
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => $q_end
}
);
}
else {
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => $q_start + 1
}
);
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => $q_end
}
);
}
my $hsplen =
($q_base_insert +
$t_base_insert +
abs( $t_end - $t_start ) +
abs( $q_end - $q_start ))/2;
$self->element(
{
'Name' => 'Hsp_hit-from',
'Data' => $t_start + 1
}
);
$self->element(
{
'Name' => 'Hsp_hit-to',
'Data' => $t_end
}
);
$self->element(
{
'Name' => 'Hsp_align-len',
'Data' => $hsplen
}
);
# cleanup trailing commas in some output
$block_sizes =~ s/\,$//;
$q_starts =~ s/\,$//;
$t_starts =~ s/\,$//;
my @blocksizes = split( /,/, $block_sizes ); # block sizes
my @qstarts = split( /,/, $q_starts ); # starting position of each block
# in query
my @tstarts = split( /,/, $t_starts ); # starting position of each block
# in target
my ( @qgapblocks, @hgapblocks );
for ( my $i = 0 ; $i < $block_count ; $i++ ) {
if ( $strand eq '+' ) {
push @qgapblocks, [ $qstarts[$i] + 1, $blocksizes[$i] ];
}
else {
push @qgapblocks, [ $q_length - $qstarts[$i], $blocksizes[$i] ];
}
push @hgapblocks, [ $tstarts[$i] + 1, $blocksizes[$i] ];
}
$self->element(
{
'Name' => 'Hsp_qgapblocks',
'Data' => \@qgapblocks
}
);
$self->element(
{
'Name' => 'Hsp_hgapblocks',
'Data' => \@hgapblocks
}
);
$self->end_element( { 'Name' => 'Hsp' } );
$lastquery = $q_name;
$lasthit = $t_name;
}
if ( defined $lasthit || defined $lastquery ) {
$self->end_element( { 'Name' => 'Hit' } );
$self->end_element( { 'Name' => 'Result' } );
return $self->end_document;
}
}
=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 = 'start_'.lc $type;
$self->_eventHandler->$func( $data->{'Attributes'} );
}
unshift @{ $self->{'_elements'} }, $type;
}
if ( $nm eq 'PSLOutput' ) {
$self->{'_values'} = {};
$self->{'_result'} = undef;
$self->{'_mode'} = '';
}
}
=head2 end_element
Title : end_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : return value from the associated end_$type event handler
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 = 'end_'.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 {
$self->warn(
__PACKAGE__ . "::end_element: unknown nm '$nm', ignoring\n" );
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc
if ( defined $nm
&& defined $MODEMAP{$nm}
&& $MODEMAP{$nm} eq 'result' );
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 }
=head2 program_name
Title : program_name
Usage : $obj->program_name($newval)
Function: Get/Set the program name
Returns : value of program_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub program_name {
my $self = shift;
$self->{'program_name'} = shift if @_;
return $self->{'program_name'} || $DefaultProgramName;
}
1;