Hsp

High-scoring Segment Pair Object

Introduction

The HSP object provides access by name to the fields of a BLAST result. Unlike a standard object, the similarity object is stored as a list reference, not a hash reference. The HSP fields are pulled from the appropriate places in the list.

A blast takes a sequence called the query and matches it against a database. When describing the data in an HSP, we will refer repeatedly to the query sequence and the database sequence. Often, the query and database sequences will be given by peg IDs. In some cases, however, they will be contig IDs. In both cases, the match is represented by an alignment between portions of the sequences. Gap characters may be required to get the alignments to match, and the number of gaps is part of the data in the HSP.

new

my $hsp = Hsp->new(  @data );
my $hsp = Hsp->new( \@data );

Create an HSP object from an array of fields.

data

An array of data in fields:

 0   qid        query sequence id
 1   qdef       query sequence comment
 2   qlen       total query sequence length
 3   sid        subject sequence id
 4   sdef       subject sequence comment
 5   slen       total subject sequence length
 6   scr        match score
 7   e_val      match e-value (probability match is a coincidence)
 8   p_n        the p-number
 9   p_val      the Poisson value
10   n_mat      match length
11   n_id       identity count
12   n_pos      positive count
13   n_gap      gap count
14   dir        frame direction or shift
15   q1         start position of match in the query sequence
16   q2         end position of match in the query sequence
17   qseq       query alignment sequence
18   s1         start position of match in the subject sequence
19   s2         end position of match in the subject sequence
20   sseq       subject alignment sequence

RETURN

Returns an HSP object that allows the values to be accessed by name.

qid

my $qid = $hsp->qid

Return the query sequence id.

qdef

my $qdef = $hsp->qdef

Return the query sequence comment.

qlen

my $qlen = $hsp->qlen

Return the total query sequence length.

sid

my $sid = $hsp->sid

Return the subject sequence id.

sdef

my $sdef = $hsp->sdef

Return the subject sequence comment.

slen

my $slen = $hsp->slen

Return the total subject sequence length.

scr

my $scr = $hsp->scr

Return the match score.

e_val

my $e_val = $hsp->e_val

Return the match e-value (probability match is a coincidence).

p_n

my $p_n = $hsp->p_n

Return the the p-number.

p_val

my $p_val = $hsp->p_val

Return the the Poisson value.

n_mat

my $n_mat = $hsp->n_mat

Return the match length.

n_id

my $n_id = $hsp->n_id

Return the identity count.

pct

my $pct = $hsp->pct;

Return the percent identity.

n_pos

my $n_pos = $hsp->n_pos

Return the positive count.

n_gap

my $n_gap = $hsp->n_gap

Return the gap count.

dir

my $dir = $hsp->dir

Return the frame direction or shift.

q1

my $q1 = $hsp->q1

Return the start position of match in the query sequence.

q2

my $q2 = $hsp->q2

Return the end position of match in the query sequence.

qseq

my $qseq = $hsp->qseq

Return the query alignment sequence.

s1

my $s1 = $hsp->s1

Return the start position of match in the subject sequence.

s2

my $s2 = $hsp->s2

Return the end position of match in the subject sequence.

sseq

my $sseq = $hsp->sseq

Return the subject alignment sequence.

sloc

my $sloc = $hsp->sloc;

Return the match region of the subject sequence as a BasicLocation object.

qloc

my $qloc = $hsp->qloc;

Return the match region of the query sequence as a BasicLocation object.