Bio::Search::HSP HmmpfamHSP
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Summary
Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
Package variables
No package variables defined.
Inherit
Bio::Search::HSP::PullHSPI
Synopsis
    # generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
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 } } }
Description
This object implements a parser for hmmpfam hsp output, a program in the HMMER
package.
Methods
newDescriptionCode
_discover_alignment
No description
Code
_discover_seq_inds
No description
Code
queryDescriptionCode
hitDescriptionCode
gapsDescriptionCode
pvalueDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::HSP::HmmpfamHSP->new();
Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
Returns : Bio::Search::HSP::HmmpfamHSP
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
-hsp_data => array ref with [rank query_start query_end hit_start
hit_end score evalue]
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)
querycodeprevnextTop
 Title   : query
Usage : my $query = $hsp->query
Function: Returns a SeqFeature representing the query in the HSP
Returns : Bio::SeqFeature::Similarity
Args : none
hitcodeprevnextTop
 Title   : hit
Usage : my $hit = $hsp->hit
Function: Returns a SeqFeature representing the hit in the HSP
Returns : Bio::SeqFeature::Similarity
Args : [optional] new value to set
gapscodeprevnextTop
 Title    : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gaps in the query, hit, or total alignment.
Returns : Integer, number of gaps 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'
pvaluecodeprevnextTop
 Title   : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP
Returns : undef (Hmmpfam reports do not have p-values)
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
	my $self = $class->SUPER::new(@args);
	
	$self->_setup(@args);
	
	my $fields = $self->_fields;
	foreach my $field (qw( alignment )) {
		$fields->{$field} = undef;
	}
	
	my $hsp_data = $self->_raw_hsp_data;
	if ($hsp_data && ref($hsp_data) eq 'ARRAY') {
		my @hsp_data = @{$hsp_data}; # don't alter the reference
foreach my $field (qw(rank query_start query_end hit_start hit_end score evalue)) { $fields->{$field} = shift(@hsp_data); } } $self->_dependencies( { ( query_string => 'alignment', hit_string => 'alignment', homology_string => '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
#
}
_discover_alignmentdescriptionprevnextTop
sub _discover_alignment {
    my $self = shift;
    my $alignments_hash = $self->get_field('alignments');
	
    my $identifier = $self->get_field('name').'~~~~'.$self->get_field('rank');
	
    while (! defined $alignments_hash->{$identifier}) {
		last unless $self->parent->parent->_next_alignment;
    }
    my $alignment = $alignments_hash->{$identifier};
	
    if ($alignment) {
		# work out query, hit and homology strings, and some stats
# (quicker to do this all at once instead of each method working on
# $alignment string itself)
my ($query_string, $hit_string, $homology_string); while ($alignment =~ /\s+(\S+)\n\s+(\S.+)\n\s+\S+\s+\d+\s+(\S+)\s+\d/gm) { my $hi = $1; my $ho = $2; $query_string .= $3; $hi =~ s/\*\-\>//; $ho = ' 'x(length($hi) - length($ho)).$ho; $hi =~ s/\<\-\*//; $hit_string .= $hi; $homology_string .= $ho; } $self->_fields->{query_string} = $query_string; $self->_fields->{hit_string} = $hit_string; $homology_string =~ s/ $//; $self->_fields->{homology_string} = $homology_string; ($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
}
_discover_seq_indsdescriptionprevnextTop
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;
}
querydescriptionprevnextTop
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'   => 1,
                   '-seq_id'   => $self->get_field('query_name'),
                   #'-seqlength'=> $self->get_field('query_length'),  (not known)
'-source' => $self->get_field('algorithm'), '-seqdesc' => $self->get_field('query_description') ) ); $self->{_created_query} = 1; } return $self->SUPER::query(@_);
}
hitdescriptionprevnextTop
sub hit {
    my $self = shift;
    unless ($self->{_created_hit}) {
		# the full length isn't always known (given in the report), but don't
# warn about the missing info all the time
my $verbose = $self->parent->parent->parent->verbose; $self->parent->parent->parent->verbose(-1); my $seq_length = $self->get_field('length'); $self->parent->parent->parent->verbose($verbose); $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' => 1, '-seq_id' => $self->get_field('name'), $seq_length ? ('-seqlength' => $seq_length) : (), '-source' => $self->get_field('algorithm'), '-seqdesc' => $self->get_field('description') ) ); $self->{_created_hit} = 1; } return $self->SUPER::hit(@_);
}
gapsdescriptionprevnextTop
sub gaps {
    my ($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/;
    
    $self->get_field('alignment'); # make sure gaps have been calculated
return $self->{'_'.$type.'_gaps'};
}
pvaluedescriptionprevnextTop
sub pvalue {
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _