#
# BioPerl module for Bio::SearchIO::sim4
#
# 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::sim4 - parser for Sim4 alignments
=head1 SYNOPSIS
# do not use this module directly, it is a driver for SearchIO
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-file => 'results.sim4',
-format => 'sim4');
while ( my $result = $searchio->next_result ) {
while ( my $hit = $result->next_hit ) {
while ( my $hsp = $hit->next_hsp ) {
# ...
}
}
}
=head1 DESCRIPTION
This is a driver for the SearchIO system for parsing Sim4.
http://globin.cse.psu.edu/html/docs/sim4.html
Cannot parse LAV or 'exon file' formats (A=2 or A=5)
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 CONTRIBUTORS
Luc Gauthier (lgauthie@hotmail.com)
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SearchIO::sim4;
use strict;
use vars qw($DEFAULTFORMAT %ALIGN_TYPES
%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
use POSIX;
use Bio::SearchIO::SearchResultEventBuilder;
use base qw(Bio::SearchIO);
$DEFAULTFORMAT = 'SIM4';
$DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
%ALIGN_TYPES = (
0 => 'Ruler',
1 => 'Query',
2 => 'Mid',
3 => 'Sbjct'
);
%MODEMAP = (
'Sim4Output' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
%MAPPING = (
'Hsp_query-from'=> 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_qlength' => 'HSP-query_length',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_hlength' => 'HSP-hit_length',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_midline' => 'HSP-homology_seq',
'Hsp_score' => 'HSP-score',
'Hsp_align-len' => 'HSP-hsp_length',
'Hsp_identity' => 'HSP-identical',
'Hit_id' => 'HIT-name',
'Hit_desc' => 'HIT-description',
'Hit_len' => 'HIT-length',
'Sim4Output_program' => 'RESULT-algorithm_name',
'Sim4Output_query-def' => 'RESULT-query_name',
'Sim4Output_query-desc'=> 'RESULT-query_description',
'Sim4Output_query-len' => 'RESULT-query_length',
);
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::sim4->new();
Function: Builds a new Bio::SearchIO::sim4 object
Returns : an instance of Bio::SearchIO::sim4
Args :
=cut
=head2 next_result
Title : next_result
Usage : my $result = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result {
my ($self) = @_;
local $/ = "\n";
local $_;
# Declare/adjust needed variables
$self->{'_last_data'} = '';
my ($seentop, $qfull, @hsps, %alignment, $format);
my $hit_direction = 1;
# Start document and main element
$self->start_document();
$self->start_element({'Name' => 'Sim4Output'});
my $lastquery = '';
# Read output report until EOF
while( defined($_ = $self->_readline) ) {
# Skip empty lines, chomp filled ones
next if( /^\s+$/); chomp;
# Make sure sim4 output format is not 2 or 5
if (!$seentop) {
if ( /^\#:lav/ ) { $format = 2; }
elsif ( /^<|>/ ) { $format = 5; }
$self->throw("Bio::SearchIO::sim4 module cannot parse 'type $format' outputs.") if $format;
}
# This line indicates the start of a new hit
if( /^seq1\s*=\s*(\S+),\s+(\d+)/ ) {
my ($nm,$desc) = ($1,$2);
# First hit? Adjust some parameters if so
if ( ! $seentop ) {
$self->element( {'Name' => 'Sim4Output_query-def',
'Data' => $nm} );
$self->element( {'Name' => 'Sim4Output_query-len',
'Data' => $desc} );
$seentop = 1;
} elsif( $nm ne $lastquery ) {
$self->_pushback($_);
last;
}
$lastquery = $nm;
# A previous HSP may need to be ended
$self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
# A previous hit exists? End it and reset needed variables
if ( $self->in_element('hit') ) {
foreach (@hsps) {
$self->start_element({'Name' => 'Hsp'});
while (my ($name, $data) = each %$_) {
$self->{'_currentHSP'}{$name} = $data;
}
$self->end_element({'Name' => 'Hsp'});
$self->{'_currentHSP'} = {};
}
$format = 0 if @hsps;
@hsps = ();
%alignment = ();
$qfull = 0;
$hit_direction = 1;
$self->end_element({'Name' => 'Hit'});
}
# This line describes the current hit... so let's start it
} elsif( /^seq2\s*=\s*(\S+)\s+\(>?(\S+)\s*\),\s*(\d+)/ ) {
$self->start_element({'Name' => 'Hit'});
$self->element( {'Name' => 'Hit_id', 'Data' => $2} );
$self->element( {'Name' => 'Hit_desc', 'Data' => $1} );
$self->element( {'Name' => 'Hit_len', 'Data' => $3} );
# This line may give additional details about query or subject
} elsif( /^>(\S+)\s*(.*)?/ ) {
# Previous line was query details... this time subject details
if( $qfull ) {
$format = 4 if !$format;
$self->element({'Name' => 'Hit_desc', 'Data' => $2});
# First line of this type is always query details for a given hit
} else {
$self->element({'Name' => 'Sim4Output_query-desc', 'Data' => $2});
$qfull = 1;
}
# This line indicates that subject is on reverse strand
} elsif( /^\(complement\)/ ) {
$hit_direction = -1;
# This line describes the current HSP... so add it to @hsps array
} elsif( /^\(?(\d+)\-(\d+)\)?\s+\(?(\d+)\-(\d+)\)?\s+(\d+)/ ) {
my ($qs,$qe,$hs,$he,$pid) = ($1,$2,$3,$4,$5);
push @hsps, {
'Hsp_query-from' => $qs,
'Hsp_query-to' => $qe,
'Hsp_hit-from' => $hit_direction >= 0 ? $hs : $he,
'Hsp_hit-to' => $hit_direction >= 0 ? $he : $hs,
'Hsp_identity' => 0, #can't determine correctly from raw pct
'Hsp_qlength' => abs($qe - $qs) + 1,
'Hsp_hlength' => abs($he - $hs) + 1,
'Hsp_align-len' => abs($qe - $qs) + 1,
};
# This line indicates the start of an alignment block
} elsif( /^\s+(\d+)\s/ ) {
# Store the current alignment block in a hash
for( my $i = 0; defined($_) && $i < 4; $i++ ) {
my ($start, $string) = /^\s+(\d*)\s(.*)/;
$alignment{$ALIGN_TYPES{$i}} = { start => $start, string => $i != 2
? $string
: (' ' x (length($alignment{$ALIGN_TYPES{$i-1}}{string}) - length($string))) . $string
};
$_ = $self->_readline();
}
# 'Ruler' line indicates the start of a new HSP
if ($alignment{Ruler}{start} == 0) {
$format = @hsps ? 3 : 1 if !$format;
# A previous HSP may need to be ended
$self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
# Start the new HSP and fill the '_currentHSP' property with available details
$self->start_element({'Name' => 'Hsp'});
$self->{'_currentHSP'} = @hsps ? shift @hsps : {
'Hsp_query-from' => $alignment{Query}{start},
'Hsp_hit-from' => $alignment{Sbjct}{start},
}
}
# Midline indicates a boundary between two HSPs
if ( $alignment{Mid}{string} =~ /<|>/g ) {
my ($hsp_start, $hsp_end);
# Are we currently in an open HSP?
if ( $self->in_element('hsp') ) {
# Find end pos, adjust 'gaps', 'seq' and 'midline' properties... then close HSP
$hsp_end = (pos $alignment{Mid}{string}) - 1;
$self->{'_currentHSP'}{'Hsp_querygaps'} +=
($self->{'_currentHSP'}{'Hsp_qseq'} .= substr($alignment{Query}{string}, 0, $hsp_end)) =~ s/ /-/g;
$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
($self->{'_currentHSP'}{'Hsp_hseq'} .= substr($alignment{Sbjct}{string}, 0, $hsp_end)) =~ s/ /-/g;
($self->{'_currentHSP'}{'Hsp_midline'} .= substr($alignment{Mid}{string}, 0, $hsp_end)) =~ s/-/ /g;
$self->end_element({'Name' => 'Hsp'});
# Does a new HSP start in the current alignment block?
if ( $alignment{Mid}{string} =~ /\|/g ) {
# Find start pos, start new HSP and fill it with available details
$hsp_start = (pos $alignment{Mid}{string}) - 1;
$self->start_element({'Name' => 'Hsp'});
$self->{'_currentHSP'} = @hsps ? shift @hsps : {};
$self->{'_currentHSP'}{'Hsp_querygaps'} +=
($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g;
$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g;
($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g;
}
}
# No HSP is currently open...
else {
# Find start pos, start new HSP and fill it with available
# details then skip to next alignment block
$hsp_start = index($alignment{Mid}{string}, '|');
$self->start_element({'Name' => 'Hsp'});
$self->{'_currentHSP'} = @hsps ? shift @hsps : {
'Hsp_query-from' => $alignment{Query}{start},
};
$self->{'_currentHSP'}{'Hsp_querygaps'} +=
($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g;
$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g;
($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g;
next;
}
}
# Current alignment block does not contain HSPs boundary
else {
# Start a new HSP if none is currently open
# (Happens if last boundary finished at the very end of previous block)
if ( !$self->in_element('hsp') ) {
$self->start_element({'Name' => 'Hsp'});
$self->{'_currentHSP'} = @hsps ? shift @hsps : {
'Hsp_query-from' => $alignment{Query}{start},
'Hsp_hit-from' => $alignment{Sbjct}{start},
}
}
# Adjust details of the current HSP
$self->{'_currentHSP'}{'Hsp_query-from'} ||=
$alignment{Query}{start} -
length($self->{'_currentHSP'}{'Hsp_qseq'} || '');
$self->{'_currentHSP'}{'Hsp_hit-from'} ||=
$alignment{Sbjct}{start} -
length($self->{'_currentHSP'}{'Hsp_hseq'} || '');
$self->{'_currentHSP'}{'Hsp_querygaps'} +=
($self->{'_currentHSP'}{'Hsp_qseq'} .=
$alignment{Query}{string}) =~ s/ /-/g;
$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
($self->{'_currentHSP'}{'Hsp_hseq'} .=
$alignment{Sbjct}{string}) =~ s/ /-/g;
($self->{'_currentHSP'}{'Hsp_midline'} .=
$alignment{Mid}{string}) =~ s/-/ /g;
}
}
}
# We are done reading the sim4 report, end everything and return
if( $seentop ) {
# end HSP if needed
$self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
# end Hit if needed
if ( $self->in_element('hit') ) {
foreach (@hsps) {
$self->start_element({'Name' => 'Hsp'});
while (my ($name, $data) = each %$_) {
$self->{'_currentHSP'}{$name} = $data;
}
$self->end_element({'Name' => 'Hsp'});
}
$self->end_element({'Name' => 'Hit'});
}
# adjust result's algorithm name, end output and return
$self->element({'Name' => 'Sim4Output_program',
'Data' => $DEFAULTFORMAT . ' (A=' . (defined $format ? $format : '?') . ')'});
$self->end_element({'Name' => 'Sim4Output'});
return $self->end_document();
}
return;
}
=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'};
my $type = $MODEMAP{$nm};
if( $type ) {
if( $self->_will_handle($type) ) {
my $func = sprintf("start_%s",lc $type);
$self->_eventHandler->$func($data->{'Attributes'});
}
unshift @{$self->{'_elements'}}, $type;
if($type eq 'result') {
$self->{'_values'} = {};
$self->{'_result'}= undef;
}
}
}
=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 $type = $MODEMAP{$nm};
my $rc;
if( $nm eq 'Hsp' ) {
$self->{'_currentHSP'}{'Hsp_midline'} ||= '';
$self->{'_currentHSP'}{'Hsp_query-to'} ||=
$self->{'_currentHSP'}{'Hsp_query-from'} + length($self->{'_currentHSP'}{'Hsp_qseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_querygaps'};
$self->{'_currentHSP'}{'Hsp_hit-to'} ||=
$self->{'_currentHSP'}{'Hsp_hit-from'} + length($self->{'_currentHSP'}{'Hsp_hseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_hitgaps'};
$self->{'_currentHSP'}{'Hsp_identity'} ||=
($self->{'_currentHSP'}{'Hsp_midline'} =~ tr/\|//);
$self->{'_currentHSP'}{'Hsp_qlength'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1;
$self->{'_currentHSP'}{'Hsp_hlength'} ||= abs($self->{'_currentHSP'}{'Hsp_hit-to'} - $self->{'_currentHSP'}{'Hsp_hit-from'}) + 1;
$self->{'_currentHSP'}{'Hsp_align-len'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1;
$self->{'_currentHSP'}{'Hsp_score'} ||= int(100 * ($self->{'_currentHSP'}{'Hsp_identity'} / $self->{'_currentHSP'}{'Hsp_align-len'}));
foreach (keys %{$self->{'_currentHSP'}}) {
$self->element({'Name' => $_, 'Data' => delete ${$self->{'_currentHSP'}}{$_}});
}
}
if( $type = $MODEMAP{$nm} ) {
if( $self->_will_handle($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->debug( "unknown nm $nm, ignoring\n");
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( defined $type && $type 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'} && $data->{'Data'} !~ /^\s+$/ );
if( $self->in_element('hsp') &&
$data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
$self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
}
$self->{'_last_data'} = $data->{'Data'};
}
=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 : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= undef;
$self->{'_elements'} = [];
$self->{'_reporttype'} = $DEFAULTFORMAT;
}
=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 $self->{'_result'};
}
sub write_result {
my ($self, $blast, @args) = @_;
if( not defined($self->writer) ) {
$self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS");
$self->writer( $DEFAULT_WRITER_CLASS->new() );
}
$self->SUPER::write_result( $blast, @args );
}
sub result_count {
return 1; # can a sim4 report contain more than one result?
}
sub report_count { shift->result_count }
=head2 _will_handle
Title : _will_handle
Usage : Private method. For internal use only.
if( $self->_will_handle($type) ) { ... }
Function: Provides an optimized way to check whether or not an element of a
given type is to be handled.
Returns : Reference to EventHandler object if the element type is to be handled.
undef if the element type is not to be handled.
Args : string containing type of element.
Optimizations:
1. Using the cached pointer to the EventHandler to minimize repeated lookups.
2. Caching the will_handle status for each type that is encountered
so that it only need be checked by calling handler->will_handle($type) once.
This does not lead to a major savings by itself (only 5-10%).
In combination with other optimizations, or for large parse jobs, the
savings good be significant.
To test against the unoptimized version, remove the parentheses from
around the third term in the ternary " ? : " operator and add two
calls to $self-E<gt>_eventHandler().
=cut
sub _will_handle {
my ($self,$type) = @_;
my $handler = $self->{'_handler_cache'} ||= $self->_eventHandler;
my $will_handle = defined($self->{'_will_handle_cache'}->{$type})
? $self->{'_will_handle_cache'}->{$type}
: ($self->{'_will_handle_cache'}->{$type} =
$handler->will_handle($type));
return $will_handle ? $handler : undef;
}
1;