#
# BioPerl module for Bio::Search::HSP::BlastPullHSP
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps
=head1 SYNOPSIS
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.blast');
while (my $result = $in->next_result) {
while (my $hit = $result->next_hit) {
print $hit->name, "\n";
print $hit->score, "\n";
print $hit->significance, "\n";
while (my $hsp = $hit->next_hsp) {
# process HSPI objects
}
}
}
=head1 DESCRIPTION
This object implements a parser for BlastN hsp output.
=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 - Sendu Bala
Email bix@sendu.me.uk
=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::Search::HSP::BlastPullHSP;
use strict;
use base qw(Bio::Search::HSP::PullHSPI);
=head2 new
Title : new
Usage : my $obj = Bio::Search::HSP::BlastNHSP->new();
Function: Builds a new Bio::Search::HSP::BlastNHSP object.
Returns : Bio::Search::HSP::BlastNHSP
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
hsp, and $start and $end define the tell() position within the
filehandle that the hsp data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_setup(@args);
my $fields = $self->_fields;
foreach my $field (qw( header alignment query_strand hit_strand )) {
$fields->{$field} = undef;
}
$self->_dependencies( { ( score => 'header',
bits => 'header',
evalue => 'header',
total_gaps => 'header',
query_strand => 'header',
hit_strand => 'header',
alignment => 'header',
query_string => 'alignment',
hit_string => 'alignment',
homology_string => 'alignment',
query_start => 'alignment',
query_end => 'alignment',
hit_start => 'alignment',
hit_end => 'alignment',
hit_identical_inds => 'seq_inds',
hit_conserved_inds => 'seq_inds',
hit_nomatch_inds => 'seq_inds',
hit_gap_inds => 'seq_inds',
query_identical_inds => 'seq_inds',
query_conserved_inds => 'seq_inds',
query_nomatch_inds => 'seq_inds',
query_gap_inds => 'seq_inds' ) } );
return $self;
}
#
# PullParserI discovery methods so we can answer all HitI questions
#
sub _discover_header {
my $self = shift;
$self->_chunk_seek(0);
my $header = $self->_get_chunk_by_end("\nQuery");
$self->{_after_header} = $self->_chunk_tell;
($self->_fields->{bits}, $self->_fields->{score}, $self->_fields->{evalue},
$self->_fields->{total_gaps}, $self->_fields->{query_strand}, $self->_fields->{hit_strand})
= $header =~ /^\s*(\S+) bits \((\d+)\),\s+Expect = (\S+)(?:\s+.+Gaps = (\d+))?(?:.+Strand\s*=\s*(\w+)\s*\/\s*(\w+))?/sm;
if ($self->_fields->{query_strand}) {
# protein blasts don't have strand
for my $strand_type ('query_strand', 'hit_strand') {
$self->_fields->{$strand_type} = $self->_fields->{$strand_type} eq 'Plus' ? 1 : -1;
}
}
else {
$self->_fields->{query_strand} = 0;
$self->_fields->{hit_strand} = 0;
}
if ($self->_fields->{evalue} =~ /^e/) {
$self->_fields->{evalue} = '1'.$self->_fields->{evalue};
}
# query_gaps isn't always given
$self->_fields->{total_gaps} = '[unset]' unless $self->_fields->{total_gaps};
$self->_fields->{header} = 1;
}
sub _discover_alignment {
my $self = shift;
$self->_chunk_seek($self->{_after_header});
# work out various basic fields for the hsp
# (quicker to do this all at once instead of each method working on
# alignment itself)
my ($query_string, $hit_string, $homology_string, $q_start, $h_start, $q_end, $h_end);
while (my $strip = $self->_get_chunk_by_end("\nQuery") || $self->_get_chunk_by_nol(4)) {
$strip =~ /\s+(\d+)\s+(\S+)\s+(\d+)\s+(\S.+)\nSbjct:?\s+(\d+)\s+(\S+)\s+(\d+)/gm || last;
my $q1 = $1;
$query_string .= $2;
my $q2 = $3;
my $hom = $4;
my $h1 = $5;
$hit_string .= $6;
my $h2 = $7;
$hom = ' 'x(length($6) - length($hom)).$hom;
$homology_string .= $hom;
for my $q ($q1, $q2) {
if (! defined $q_start || $q < $q_start) {
$q_start = $q;
}
if (! defined $q_end || $q > $q_end) {
$q_end = $q;
}
}
for my $h ($h1, $h2) {
if (! defined $h_start || $h < $h_start) {
$h_start = $h;
}
if (! defined $h_end || $h > $h_end) {
$h_end = $h;
}
}
}
$self->_fields->{query_string} = $query_string;
$self->_fields->{hit_string} = $hit_string;
$self->_fields->{homology_string} = $homology_string;
$self->_fields->{query_start} = $q_start;
$self->_fields->{query_end} = $q_end;
$self->_fields->{hit_start} = $h_start;
$self->_fields->{hit_end} = $h_end;
($self->{_query_gaps}) = $query_string =~ tr/-//;
($self->{_hit_gaps}) = $hit_string =~ tr/-//;
($self->{_total_gaps}) = $self->{_query_gaps} + $self->{_hit_gaps};
$self->_fields->{alignment} = 1; # stop this method being called again
}
# seq_inds related methods, all just need seq_inds field to have been gotten
sub _discover_seq_inds {
my $self = shift;
my ($seqString, $qseq, $sseq) = ( $self->get_field('homology_string'),
$self->get_field('query_string'),
$self->get_field('hit_string') );
# (code largely lifted from GenericHSP)
# Using hashes to avoid saving duplicate residue numbers.
my %identicalList_query = ();
my %identicalList_sbjct = ();
my %conservedList_query = ();
my %conservedList_sbjct = ();
my @gapList_query = ();
my @gapList_sbjct = ();
my %nomatchList_query = ();
my %nomatchList_sbjct = ();
my $resCount_query = $self->get_field('query_end');
my $resCount_sbjct = $self->get_field('hit_end');
my ($mchar, $schar, $qchar);
while ($mchar = chop($seqString) ) {
($qchar, $schar) = (chop($qseq), chop($sseq));
if ($mchar eq '+' || $mchar eq '.' || $mchar eq ':') {
$conservedList_query{ $resCount_query } = 1;
$conservedList_sbjct{ $resCount_sbjct } = 1;
}
elsif ($mchar eq ' ') {
$nomatchList_query{ $resCount_query } = 1;
$nomatchList_sbjct{ $resCount_sbjct } = 1;
}
else {
$identicalList_query{ $resCount_query } = 1;
$identicalList_sbjct{ $resCount_sbjct } = 1;
}
if ($qchar eq '-') {
push(@gapList_query, $resCount_query);
}
else {
$resCount_query -= 1;
}
if ($schar eq '-') {
push(@gapList_sbjct, $resCount_sbjct);
}
else {
$resCount_sbjct -= 1;
}
}
my $fields = $self->_fields;
$fields->{hit_identical_inds} = [ sort { $a <=> $b } keys %identicalList_sbjct ];
$fields->{hit_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_sbjct ];
$fields->{hit_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_sbjct ];
$fields->{hit_gap_inds} = [ reverse @gapList_sbjct ];
$fields->{query_identical_inds} = [ sort { $a <=> $b } keys %identicalList_query ];
$fields->{query_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_query ];
$fields->{query_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_query ];
$fields->{query_gap_inds} = [ reverse @gapList_query ];
$fields->{seq_inds} = 1;
}
=head2 query
Title : query
Usage : my $query = $hsp->query
Function: Returns a SeqFeature representing the query in the HSP
Returns : L<Bio::SeqFeature::Similarity>
Args : none
=cut
sub query {
my $self = shift;
unless ($self->{_created_query}) {
$self->SUPER::query( new Bio::SeqFeature::Similarity
('-primary' => $self->primary_tag,
'-start' => $self->get_field('query_start'),
'-end' => $self->get_field('query_end'),
'-expect' => $self->get_field('evalue'),
'-score' => $self->get_field('score'),
'-strand' => $self->get_field('query_strand'),
'-seq_id' => $self->get_field('query_name'),
'-seqlength'=> $self->get_field('query_length'),
'-source' => $self->get_field('algorithm'),
'-seqdesc' => $self->get_field('query_description'),
'-frame' => 0 # not known?
) );
$self->{_created_query} = 1;
}
return $self->SUPER::query(@_);
}
=head2 hit
Title : hit
Usage : my $hit = $hsp->hit
Function: Returns a SeqFeature representing the hit in the HSP
Returns : L<Bio::SeqFeature::Similarity>
Args : [optional] new value to set
=cut
sub hit {
my $self = shift;
unless ($self->{_created_hit}) {
$self->SUPER::hit( new Bio::SeqFeature::Similarity
('-primary' => $self->primary_tag,
'-start' => $self->get_field('hit_start'),
'-end' => $self->get_field('hit_end'),
'-expect' => $self->get_field('evalue'),
'-score' => $self->get_field('score'),
'-strand' => $self->get_field('hit_strand'),
'-seq_id' => $self->get_field('name'),
'-seqlength'=> $self->get_field('length'),
'-source' => $self->get_field('algorithm'),
'-seqdesc' => $self->get_field('description'),
'-frame' => 0 # not known?
) );
$self->{_created_hit} = 1;
}
return $self->SUPER::hit(@_);
}
=head2 gaps
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gap characters in the query, hit, or total alignment.
Returns : Integer, number of gap characters or 0 if none
Args : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
=cut
sub gaps {
my ($self, $type) = @_;
$type = lc $type if defined $type;
$type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/);
$type = 'hit' if $type =~ /sbjct|subject/;
if ($type eq 'total') {
my $answer = $self->get_field('total_gaps');
return $answer unless $answer eq '[unset]';
}
$self->get_field('alignment'); # make sure gaps have been calculated
return $self->{'_'.$type.'_gaps'};
}
=head2 strand
Title : strand
Usage : $hsp->strand('query')
Function: Retrieves the strand for the HSP component requested
Returns : +1 or -1 (0 if unknown)
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
'query' to retrieve the query strand (default)
'list' or 'array' to retrieve both query and hit together
=cut
sub strand {
my $self = shift;
my $val = shift;
$val = 'query' unless defined $val;
$val =~ s/^\s+//;
if ($val =~ /^q/i) {
return $self->get_field('query_strand');
}
elsif ($val =~ /^hi|^s/i) {
return $self->get_field('hit_strand');
}
elsif ($val =~ /^list|array/i) {
return ($self->get_field('query_strand'), $self->get_field('hit_strand'));
}
else {
$self->warn("unrecognized component '$val' requested\n");
}
return 0;
}
=head2 start
Title : start
Usage : $hsp->start('query')
Function: Retrieves the start for the HSP component requested
Returns : integer, or list of two integers (query start and subject start) in
list context
Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
'query' to retrieve the query start (default)
=cut
sub start {
my $self = shift;
my $val = shift;
$val = (wantarray ? 'list' : 'query') unless defined $val;
$val =~ s/^\s+//;
if ($val =~ /^q/i) {
return $self->get_field('query_start');
}
elsif ($val =~ /^(hi|s)/i) {
return $self->get_field('hit_start');
}
elsif ($val =~ /^list|array/i) {
return ($self->get_field('query_start'), $self->get_field('hit_start') );
}
else {
$self->warn("unrecognized component '$val' requested\n");
}
return 0;
}
=head2 end
Title : end
Usage : $hsp->end('query')
Function: Retrieves the end for the HSP component requested
Returns : integer, or list of two integers (query end and subject end) in
list context
Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
'query' to retrieve the query end (default)
=cut
sub end {
my $self = shift;
my $val = shift;
$val = (wantarray ? 'list' : 'query') unless defined $val;
$val =~ s/^\s+//;
if ($val =~ /^q/i) {
return $self->get_field('query_end');
}
elsif ($val =~ /^(hi|s)/i) {
return $self->get_field('hit_end');
}
elsif ($val =~ /^list|array/i) {
return ($self->get_field('query_end'), $self->get_field('hit_end'));
}
else {
$self->warn("unrecognized end component '$val' requested\n");
}
return 0;
}
=head2 pvalue
Title : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP
Returns : undef (Hmmpfam reports do not have p-values)
Args : none
=cut
sub pvalue { }
1;