#
# BioPerl module for Bio::SearchIO::megablast
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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::megablast - a driver module for Bio::SearchIO to parse
megablast reports (format 0)
=head1 SYNOPSIS
# do not use this module directly
use Bio::SearchIO;
# for default format output from megablast
my $in = Bio::SearchIO->new(-file => 'file.mbl',
-format => 'megablast',
-report_format => 0);
while( my $r = $in->next_result ) {
while( my $hit = $r->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
}
}
}
=head1 DESCRIPTION
Beware!
Because of the way megablast report format 0 is coded, realize that score
means # gap characters + # mismatches for a HSP.
The docs from NCBI regarding FORMAT 0
# 0: Produce one-line output for each alignment, in the form
#
# 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score
#
# Here subject(query)-id is a gi number, an accession or some other type of
# identifier found in the FASTA definition line of the respective sequence.
#
# + or - corresponds to same or different strand alignment.
#
# Score for non-affine gapping parameters means the total number of
# differences (mismatches + gap characters). For affine case it is the
# actual (raw) score of the alignment.
FORMAT 1 parsing has not been implemented
FORMAT 2 parsing should work with the SearchIO 'blast' parser
=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.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::megablast;
use strict;
use vars qw(%MAPPING %MODEMAP $DEFAULT_BLAST_WRITER_CLASS);
use base qw(Bio::SearchIO);
BEGIN {
# mapping of MegaBlast terms to Bioperl hash keys
%MODEMAP = ('MegaBlastOutput' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
# This should really be done more intelligently, like with
# XSLT
%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',
'Hit_score' => 'HIT-score',
'Hsp_score' => 'HSP-score',
'Hsp_identity' => 'HSP-identical',
'Hsp_positive' => 'HSP-conserved',
'Hit_id' => 'HIT-name',
'MegaBlastOutput_program' => 'RESULT-algorithm_name',
'MegaBlastOutput_query-def'=> 'RESULT-query_name',
);
$DEFAULT_BLAST_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
}
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::blast->new();
Function: Builds a new Bio::SearchIO::blast object
Returns : Bio::SearchIO::blast
Args : -fh/-file => filehandle/filename to BLAST file
-format => 'blast'
=cut
sub _initialize {
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($fmt) = $self->_rearrange([qw(REPORT_FORMAT)], @args);
$self->throw("Must provide a value for -report_format when initializing a megablast parser") unless defined $fmt ;
$self->report_format($fmt);
return 1;
}
=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 $fmt = $self->report_format;
my ($lastquery,$lasthit);
while( defined($_ = $self->_readline) ) {
if( $fmt == 0 ) {
if( /^\'(\S+)\'\=\=\'(\+|\-)(\S+)\'\s+
\((\d+)\s+(\d+)\s+(\d+)\s+(\d+)\)\s+
(\d+)/ox )
{
my ($hit,$strand,$query,
$h_start,$q_start,$h_end,$q_end,
$score) = ($1,$2,$3,$4,$5,$6,$7,$8);
if( ! defined $lastquery ) {
$self->start_element({'Name' => 'MegaBlastOutput'});
$self->element({'Name' => 'MegaBlastOutput_program',
'Data' => 'MEGABLAST'});
$self->element({'Name' => 'MegaBlastOutput_query-def',
'Data' => $query});
} elsif( $lastquery ne $query ) {
$self->_pushback($_);
$self->end_element({'Name' => 'Hit'}) if( defined $lasthit);
$self->end_element({ 'Name' => 'MegaBlastOutput'});
$lasthit = undef;
$lastquery = undef;
return $self->end_document();
}
if( ! defined $lasthit || $lasthit ne $hit ) {
$self->end_element({'Name' => 'Hit'}) if( defined $lasthit);
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $hit});
}
$self->start_element({'Name' => 'Hsp'});
$self->element({'Name' => 'Hsp_score',
'Data' => $score});
# flip flop start/end if strand is < 0
# since strandedness is inferred from the query
# because of the way it is coded all queries will
# be on the forward strand and hits will be either
# +/-
# also the NCBI docs state:
# 0: Produce one-line output for each alignment, in the form
#
# 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score
#
# Here subject(query)-id is a gi number, an accession or some other type of
# identifier found in the FASTA definition line of the respective sequence.
#
# + or - corresponds to same or different strand alignment.
#
# Score for non-affine gapping parameters means the total number of
# differences (mismatches + gap characters). For affine case it is the
# actual (raw) score of the alignment.
# and yet when rev strand hits are made I see
# (MBL 2.2.4)
# 'Contig634'=='-503384' (1 7941 321 7620) 19
# so the query is on the rev strand and the
# subject is on the fwd strand
# so I am flip-flopping everything when I see a '-'
if( $strand eq '-' ) {
($h_start,$h_end) = ( $h_end,$h_start);
($q_start,$q_end) = ( $q_end,$q_start);
}
$self->element({'Name' => 'Hsp_hit-from',
'Data' => $h_start});
$self->element({'Name' => 'Hsp_hit-to',
'Data' => $h_end});
$self->element({'Name' => 'Hsp_query-from',
'Data' => $q_start});
$self->element({'Name' => 'Hsp_query-to',
'Data' => $q_end});
# might not be quite right -- need to know length of the HSP
my $numid = (abs($q_end - $q_start) - $score);
$self->element({'Name' => 'Hsp_identity',
'Data' => $numid});
$self->element({'Name' => 'Hsp_positive',
'Data' => $numid});
$self->end_element({'Name' => 'Hsp'});
$lasthit = $hit;
$lastquery = $query;
} else {
$self->debug("Unknown line in fmt0 parsing: $_");
}
}
}
if( defined $lastquery && $fmt == 0 ) {
$self->end_element({'Name' => 'Hit'}) if( defined $lasthit);
$self->end_element({ 'Name' => 'MegaBlastOutput'});
return $self->end_document();
}
return 0;
}
=head2 report_format
Title : report_format
Usage : $obj->report_format($newval)
Function: Get/Set the report_format value
Returns : value of report_format (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub report_format{
my $self = shift;
return $self->{'_report_format'} = shift if @_;
return $self->{'_report_format'};
}
=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 do not 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 'MegaBlastOutput') {
$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;
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 'MegaBlastOutput' );
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'};
$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;