Sim

Similarity Object

Introduction

The similarity object provides access by name to the fields of a similarity list. Unlike a standard object, the similarity object is stored as a list reference, not a hash reference. The similarity 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 a similarity, 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 similarity.

new

my $sim = Sim->new(  @data );
my $sim = Sim->new( \@data );

Create a similarity object from an array of fields.

  • data

An array of data in fields:

 0   id1        query sequence id
 1   id2        subject sequence id
 2   iden       percentage sequence identity
 3   ali_ln     alignment length
 4   mismatches  number of mismatch
 5   gaps       number of gaps
 6   b1         query seq match start
 7   e1         query seq match end
 8   b2         subject seq match start
 9   e2         subject seq match end
10   psc        match e-value
11   bsc        bit score
12   ln1        query sequence length
13   ln2        subject sequence length
14   tool       tool used to produce similarities

The following fields may vary by tool:

15   loc1       query seq locations string (b1-e1,b2-e2,b3-e3)
16   loc2       subject seq locations string (b1-e1,b2-e2,b3-e3)
17   dist       tree distance
  • RETURN

Returns a similarity object that allows the values to be accessed by name.

new_from_hsp

my $sim = Sim->new_from_hsp(  @hsp );
my $sim = Sim->new_from_hsp( \@hsp );
my $sim = Sim->new_from_hsp( \@hsp, $tool );

Create a similarity object from a gjoparseblast hsp.

  • hsp

An array of data on a blast hsp as returned by gjoparseblast::blast_hsp_list() or gjoparseblast::next_blast_hsp().

  • RETURN

Returns a similarity object that allows the values to be accessed by name.

as_string

my $simString = "$sim";

or

my $simString = $sim->as_string;

Return the similarity as a descriptive string, consisting of the query peg, the similar peg, and the match score.

new_from_line

my $sim = Sim->new_from_line($line);

Create a similarity object from a blast output line. The line is presumed to have the complete list of similarity values in it, tab-separated.

  • line

Input line, containing the similarity values in it delimited by tabs. A line terminator may be present at the end.

  • RETURN

Returns a similarity object that allows the values to be accessed by name.

validate

my $okFlag = $sim->validate();

Return TRUE if the similarity values are valid, else FALSE.

as_line

my $line = $sim->as_line;

Return the similarity as an output line. This is exactly the reverse of /new_from_line.

id1

my $id = $sim->id1;

Return the ID of the query sequence that was blasted against the database.

id2

my $id = $sim->id2;

Return the ID of the sequence in the database that matched the query sequence.

iden

my $percent = $sim->iden;

Return the percentage identity between the query and database sequences.

ali_ln

my $chars = $sim->ali_ln;

Return the length (in characters) of the alignment between the two similar sequences.

mismatches

my $count = $sim->mismatches;

Return the number of alignment positions that do not match.

gaps

my $count = $sim->gaps;

Return the number of gaps required to align the sequences.

b1

my $beginOffset = $sim->b1;

Return the position in the query sequence at which the alignment begins.

e1

my $endOffset = $sim->e1;

Return the position in the query sequence at which the alignment ends.

b2

my $beginOffset = $sim->b2;

Position in the database sequence at which the alignment begins.

e2

my $endOffset = $sim->e2;

Return the position in the database sequence at which the alignment ends.

psc

my $score = $sim->psc;

Return the similarity score as a floating-point number. The score is the computed probability that the similarity is a result of random chance. A score of 0 indicates a perfect match. A higher score indicates a less-perfect match. Values of 1e-10 or less are considered good matches.

bsc

my $score = $sim->bsc;

Return the bit score for this similarity. The bit score is an estimate of the search space required to find the similarity by chance. A higher bit score indicates a better match.

bsc

my $score = $sim->bit_score;

Return the bit score for this similarity. The bit score is an estimate of the search space required to find the similarity by chance. A higher bit score indicates a better match.

nbsc

my $score = $sim->nbsc;

Return the normalized bit score for this similarity. This is the bit score divided by the length of the matching sequence regions. It is a better summary of the overall sequence similarity than is the percentage identity. Typically identical sequences have a value close to 2, and it goes down to 0 as the similarity decreases (values less than 0 are possible, but are never significant and hence are never reported in a local similarity search).

ln1

my $length = $sim->ln1;

Return the number of characters in the query sequence.

ln2

my $length = $sim->ln2;

Return the length of the database sequence.

tool

my $name = $sim->tool;

Return the name of the tool used to find this similarity.

usage

my $pod_as_text = Module::usage;
my $pod_as_text = Module->usage;
my $pod_as_text = Package->usage;
my $pod_as_text = $object->usage;

Returns the module’s pod documentation as text.