#
# BioPerl module for Bio::Search::Result::BlastPullResult
#
# 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::Result::BlastPullResult - A parser and result object for BLASTN
results
=head1 SYNOPSIS
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
-file => 'result.blast');
while (my $result = $in->next_result) {
print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
}
=head1 DESCRIPTION
This object implements a parser for NCBI BLASTN result 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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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::Result::BlastPullResult;
use strict;
use Bio::Search::Hit::BlastPullHit;
use base qw(Bio::Root::Root Bio::Search::Result::PullResultI);
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::Result::hmmpfam->new();
Function: Builds a new Bio::SearchIO::Result::hmmpfam object
Returns : Bio::SearchIO::Result::hmmpfam
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
-parameters => hash ref of search parameters (key => value), optional
-statistics => hash ref of search statistics (key => value), optional
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
result, and $start and $end define the tell() position within the
filehandle that the result data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_setup(@args);
foreach my $field (qw( header hit_table hsp_table alignments next_model
models query_length stats_and_params)) {
$self->_fields->{$field} = undef;
}
$self->_dependencies( { ( query_name => 'header',
query_accession => 'header',
query_description => 'header',
query_length => 'header',
hit_table => 'header',
num_hits => 'hit_table',
no_hits_found => 'hit_table' ) } );
return $self;
}
#
# PullParserI discovery methods so we can answer all ResultI questions
#
sub _discover_header {
my $self = shift;
$self->_chunk_seek(0);
my $header = $self->_get_chunk_by_end("Value\n");
if (!$header) {
$header = $self->_get_chunk_by_end("***** No hits found ******\n");
$self->{_no_hits_found} = 1;
}
$self->throw("Invalid header returned") unless $header;
$self->{_after_header} = $self->_chunk_tell;
($self->_fields->{query_name}) = $header =~ /^\s*(\S+)/;
$self->_fields->{query_accession} = '';
$self->_fields->{query_description} = '';
if ($header =~ /^Length=(\d+)/m) {
$self->_fields->{query_length} = $1;
}
elsif ($header =~ /\((\d+) letters\)/) {
# older form?
$self->_fields->{query_length} = $1;
if ($header =~ /^\s*\(\d+ letters/) {
# there wasn't a query sequence name
$self->_fields->{query_name} = '';
}
}
$self->_fields->{header} = 1;
}
sub _discover_hit_table {
my $self = shift;
$self->_chunk_seek($self->{_after_header});
my $table = $self->_get_chunk_by_end("\n>");
if (!$table && !$self->{_no_hits_found}) {
# no alignments, presumably; hit table comprises the remainder of this
# result
while (my $line = $self->_get_chunk_by_nol(1)) {
$table .= $line;
}
}
$table ||= '';
$self->{_after_hit_table} = $self->_chunk_tell;
my $evalue_cutoff = $self->get_field('evalue_cutoff');
undef $evalue_cutoff if $evalue_cutoff eq '[unset]';
my $score_cutoff = $self->get_field('score_cutoff');
undef $score_cutoff if $score_cutoff eq '[unset]';
my @table;
my $no_hit = 1;
while ($table =~ /^(\S+)\s+(\S.*?)?\s+(\S+)\s+([\de]\S*)\s*\n/gm) {
$no_hit = 0;
my ($name, $desc, $score, $evalue) = ($1, $2, $3, $4);
$desc ||= '';
if ($evalue =~ /^e/) {
$evalue = '1'.$evalue;
}
next if ($evalue_cutoff && $evalue > $evalue_cutoff);
next if ($score_cutoff && $score < $score_cutoff);
push(@table, [$name, $desc, $score, $evalue]);
}
$self->_fields->{hit_table} = \@table;
$self->{_next_hit_index} = @table > 0 ? 0 : -1;
$self->_fields->{no_hits_found} = $no_hit;
$self->_fields->{num_hits} = @table;
}
sub _discover_next_hit {
my $self = shift;
my $hit_table = $self->get_field('hit_table');
return if $self->{_next_hit_index} == -1;
my $hit_row = ${$hit_table}[$self->{_next_hit_index}];
$self->_chunk_seek($self->{_end_of_previous_hit} || $self->{_after_hit_table});
my ($start, $end) = $self->_find_chunk_by_end("\n>");
unless ($end) {
$start = $self->{_end_of_previous_hit} || $self->{_after_hit_table};
$end = $self->_chunk_true_end;
}
else {
$end += $self->_chunk_true_start;
}
$start += $self->_chunk_true_start;
$self->{_end_of_previous_hit} = $end - $self->_chunk_true_start;
#*** needs to inherit piped_behaviour, and we need to deal with _sequential
# ourselves
$self->_fields->{next_hit} = Bio::Search::Hit::BlastPullHit->new(-parent => $self,
-chunk => [$self->chunk, $start, $end],
-hit_data => $hit_row);
$self->{_next_hit_index}++;
if ($self->{_next_hit_index} > $#{$hit_table}) {
$self->{_next_hit_index} = -1;
}
}
sub _discover_stats_and_params {
my $self = shift;
$self->_chunk_seek(0);
my ($start, $end) = $self->_find_chunk_by_end("\n Database: ");
$self->_chunk_seek($end);
my $gapped = 0;
while ($self->_get_chunk_by_nol(1)) {
if (/Number of letters in database:\s+(\S+)/) {
my $stat = $1;
$stat =~ s/,//g;
$self->add_statistic('dbletters', $stat);
}
elsif (/Number of sequences in database:\s+(\S+)/) {
my $stat = $1;
$stat =~ s/,//g;
$self->add_statistic('dbentries', $stat);
}
elsif (/^Lambda/) {
my $line = $self->_get_chunk_by_nol(1);
$line =~ /\s+(\S+)\s+(\S+)\s+(\S+)/;
$self->add_statistic($gapped ? 'lambda_gapped' : 'lambda', $1);
$self->add_statistic($gapped ? 'kappa_gapped' : 'kappa', $2);
$self->add_statistic($gapped ? 'entropy_gapped' : 'entropy', $3);
$gapped = 1;
}
elsif (/^Matrix: (.+)\n/) {
$self->add_parameter('matrix', $1);
}
elsif (/^Gap Penalties: Existence: (\d+), Extension: (\d+)/) {
$self->add_parameter('gapopen', $1);
$self->add_parameter('gapext', $2);
}
elsif (/^Number of Hits to DB: (\d+)/) {
$self->add_statistic('Hits_to_DB', $1);
}
elsif (/^Number of extensions: (\d+)/) {
$self->add_statistic('num_extensions', $1);
}
elsif (/^Number of successful extensions: (\d+)/) {
$self->add_statistic('num_successful_extensions', $1);
}
elsif (/^Number of sequences better than (\S+):/) {
$self->add_parameter('expect', $1);
}
elsif (/^[Ll]ength of query: (\d+)/) {
$self->add_statistic('querylength', $1);
}
elsif (/^[Ee]ffective HSP length: (\d+)/) {
$self->add_statistic('effective_hsplength', $1);
}
elsif (/^[Ee]ffective length of database: (\d+)/) {
$self->add_statistic('effectivedblength', $1);
}
elsif (/^[Ee]ffective search space: (\d+)/) {
$self->add_statistic('effectivespace', $1);
}
elsif (/^[Ee]ffective search space used: (\d+)/) {
$self->add_statistic('effectivespaceused', $1);
}
elsif (/^([TAXS]\d?): (\d+)(?: \((\S+))?/) {
$self->add_statistic($1, $2);
$self->add_statistic($1.'_bits', $3) if $3;
}
}
$self->_fields->{stats_and_params} = 1;
}
=head2 next_hit
Title : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
=cut
sub next_hit {
my $self = shift;
my $hit = $self->get_field('next_hit');
undef $self->_fields->{next_hit};
return $hit;
}
=head2 hits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the HitI objects contained within this Result
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
See Also: L<Bio::Search::Hit::HitI>
=cut
sub hits {
my $self = shift;
my $old = $self->{_next_hit_index} || 0;
$self->rewind;
my @hits;
while (defined(my $hit = $self->next_hit)) {
push(@hits, $hit);
}
$self->{_next_hit_index} = @hits > 0 ? $old : -1;
return @hits;
}
=head2 sort_hits
Title : sort_hits
Usage : $result->sort_hits('<score')
Function : Sorts the hits so that they come out in the desired order when
hits() or next_hit() is called.
Returns : n/a
Args : A coderef for the sort function. See the documentation on the Perl
sort() function for guidelines on writing sort functions.
By default the sort order is ascending significance value (ie.
most significant hits first).
*** example
=cut
sub sort_hits {
my ($self, $code_ref) = @_;
$self->throw("Not implemented yet");
}
=head2 rewind
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iterator to the beginning, so that
next_hit() will subsequently return the first hit and so on.
Returns : n/a
Args : none
=cut
sub rewind {
my $self = shift;
unless ($self->_fields->{hit_table}) {
$self->get_field('hit_table');
}
$self->{_next_hit_index} = @{$self->_fields->{hit_table}} > 0 ? 0 : -1;
}
=head2 get_statistic
Title : get_statistic
Usage : my $gap_ext = $result->get_statistic('kappa')
Function: Returns the value for a specific statistic available
from this result
Returns : string
Args : name of statistic (string)
=cut
sub get_statistic {
my $self = shift;
$self->get_field('stats_and_params');
return $self->SUPER::get_statistic(@_);
}
=head2 get_parameter
Title : get_parameter
Usage : my $gap_ext = $result->get_parameter('gapext')
Function: Returns the value for a specific parameter used
when running this result
Returns : string
Args : name of parameter (string)
=cut
sub get_parameter {
my $self = shift;
$self->get_field('stats_and_params');
return $self->SUPER::get_parameter(@_);
}
1;