Bio::Search::HSP FastaHSP
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Summary
Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data
Package variables
No package variables defined.
Inherit
Bio::Search::HSP::GenericHSP
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"; } } }
Description
Describe the object here
Methods
newDescriptionCode
sw_scoreDescriptionCode
evalue2DescriptionCode
get_aln
No description
Code
Methods description
newcode    nextTop
 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
sw_scorecodeprevnextTop
 Title   : sw_score
Usage : $obj->sw_score($newval)
Function: Get/Set Smith-Waterman score
Returns : value of sw_score
Args : newvalue (optional)
evalue2codeprevnextTop
 Title   : evalue2
Usage : $obj->evalue2($newval)
Function: Get/Set E2() expectation value
Returns : value of evalue2
Args : newvalue (optional)
Methods code
newdescriptionprevnextTop
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 $self;
}
sw_scoredescriptionprevnextTop
sub sw_score {
    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_sw_score'} ) {
	$value = 0 unless defined $value; # default value
$self->{'_sw_score'} = $value; } return $self->{'_sw_score'};
}
evalue2descriptionprevnextTop
sub evalue2 {
    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_evalue2'} ) {
	$value = 0 unless defined $value; # default value
$self->{'_evalue2'} = $value; } return $self->{'_evalue2'};
}
get_alndescriptionprevnextTop
sub get_aln {
    my ($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; } 1;
}
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 - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _