File Coverage

Bio/Search/HSP/FastaHSP.pm

Criterion	Covered	Total	%
statement	48	50	96.0
branch	16	24	66.6
condition	4	12	33.3
subroutine	6	6	100.0
pod	4	4	100.0
total	78	96	81.2

#
# BioPerl module for Bio::Search::HSP::FastaHSP
#
# Please direct questions and support issues to
#
# Cared for by Jason Stajich
#
# 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::Search::HSP::FastaHSP - HSP object for FASTA specific data

=head1 SYNOPSIS

  # get a FastaHSP from a SearchIO stream
  my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');

  while( my $r = $in->next_result) {
      while( my $hit = $r->next_result ) {
           while( my $hsp = $hit->next_hsp ) {
              print "smith-waterman score (if available): ",
                    $hsp->sw_score(),"\n";
           }
      }
  }

=head1 DESCRIPTION

Describe the object here

=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.

  [e-mail]                  - 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

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.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::Search::HSP::FastaHSP;
use strict;


use base qw(Bio::Search::HSP::GenericHSP);

=head2 new

 Title   : new
 Usage   : my $obj = Bio::Search::HSP::FastaHSP->new();
 Function: Builds a new Bio::Search::HSP::FastaHSP object
 Returns : Bio::Search::HSP::FastaHSP
 Args    : -swscore => smith-waterman score

=cut

sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  my ($swscore, $evalue2) = $self->_rearrange([qw(SWSCORE EVALUE2)], @args);

  defined $swscore && $self->sw_score($swscore);

  defined $evalue2 && $self->evalue2($evalue2);

  return $self;
}


=head2 sw_score

 Title   : sw_score
 Usage   : $obj->sw_score($newval)
 Function: Get/Set Smith-Waterman score
 Returns : value of sw_score
 Args    : newvalue (optional)


=cut

sub sw_score{
    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_sw_score'} ) {
	$value = 0 unless defined $value; # default value
	$self->{'_sw_score'} = $value;
    }
    return $self->{'_sw_score'};
}

=head2 evalue2

 Title   : evalue2
 Usage   : $obj->evalue2($newval)
 Function: Get/Set E2() expectation value
 Returns : value of evalue2
 Args    : newvalue (optional)


=cut

sub evalue2{
    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_evalue2'} ) {
	$value = 0 unless defined $value; # default value
	$self->{'_evalue2'} = $value;
    }
    return $self->{'_evalue2'};
}


sub get_aln {
    my ($self) = @_;
    require Bio::LocatableSeq;
    require Bio::SimpleAlign;
    my $aln = Bio::SimpleAlign->new();
    my $hs = $self->hit_string();
    my $qs = $self->query_string();

    # fasta reports some extra 'regional' sequence information
    # we need to clear out first
    # this seemed a bit insane to me at first, but it appears to
    # work --jason

    # modified to deal with LocatableSeq's end point verification and to deal
    # with frameshifts (which shift the end points in translated sequences).

    # we infer the end of the regional sequence where the first
    # non space is in the homology string
    # then we use the HSP->length to tell us how far to read
    # to cut off the end of the sequence

    my ($start, $rest) = (0, 0);
    if( $self->homology_string() =~ /^(\s+)?(.*?)\s*$/ ) {
      ($start, $rest) = ($1 ? CORE::length($1) : 0, CORE::length($2));
    }
    $self->debug("hs seq is '$hs'\n");
    $self->debug("qs seq is '$qs'\n");

    $hs = substr($hs, $start,$rest);
    $qs = substr($qs, $start,$rest);

    my $seqonly = $qs;
    $seqonly =~ s/\s+//g;
    my ($q_nm,$s_nm) = ($self->query->seq_id(),
			$self->hit->seq_id());
    unless( defined $q_nm && CORE::length ($q_nm) ) {
	$q_nm = 'query';
    }
    unless( defined $s_nm && CORE::length ($s_nm) ) {
	$s_nm = 'hit';
    }
    $self->_calculate_seq_positions;
    my $query = Bio::LocatableSeq->new('-seq'   => $seqonly,
				      '-id'    => $q_nm,
				      '-start' => $self->query->start,
				      '-end'   => $self->query->end,
                      '-frameshifts' => (exists $self->{seqinds}{_frameshiftRes_query}) ?
                            $self->{seqinds}{_frameshiftRes_query} : undef,
                      '-mapping' => [1, $self->{_query_mapping}],
                      -verbose => $self->verbose
				      );
    $seqonly = $hs;
    $seqonly =~ s/\s+//g;
    my $hit =  Bio::LocatableSeq->new('-seq'    => $seqonly,
				      '-id'    => $s_nm,
				      '-start' => $self->hit->start,
				      '-end'   => $self->hit->end,
                      '-frameshifts' => exists $self->{seqinds}{_frameshiftRes_sbjct} ?
                            $self->{seqinds}{_frameshiftRes_sbjct} : undef,
                      '-mapping' => [1, $self->{_hit_mapping}],
                      -verbose => $self->verbose
				      );
    $aln->add_seq($query);
    $aln->add_seq($hit);
    return $aln;
}


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