Bio::FastParsers::Blast::Table::Hsp(3)

NAME
Bio::FastParsers::Blast::Table::Hsp - Internal class for tabular BLAST parser

VERSION
version 0.221230

SYNOPSIS
    # see Bio::FastParsers::Blast::Table

DESCRIPTION
This class implements a single line of a tabular BLAST report. Such a line does not correspond to a hit but to a High-Scoring-Pair (HSP). All its methods are accessors. Beyond the standard fields found in the BLAST tabular output (e.g., "hit_id", "evalue"), additional methods are available for easier handling of reverse strand coordinates (e.g., "query_start", "hit_strand").

METHODS

  query_id
Returns the id of the query sequence.

This method does not accept any arguments.

  hit_id
Returns the id of the hit (or subject) sequence.

This method does not accept any arguments.

  percent_identity
Returns the identity (in percents) of the HSP.

This method does not accept any arguments.

  hsp_length
Returns the length (in nt or aa) of the HSP.

This method does not accept any arguments.

  mismatches
Returns the number of mismatches of the HSP.

This method does not accept any arguments.

  gaps
Returns the number of gaps (or gap openings) of the HSP.

This method does not accept any arguments.

  query_from
Returns the HSP start in query coordinates. The value of "query_from" is higher than the value of "query_to" on reverse strands.

This method does not accept any arguments.

  query_to
Returns the HSP end in query coordinates. The value of "query_to" is lower than the value of "query_from" on reverse strands.

This method does not accept any arguments.

  hit_from
Returns the HSP start in hit (or subject) coordinates. The value of "hit_from" is higher than the value of "hit_to" on reverse strands.

This method does not accept any arguments.

  hit_to
Returns the HSP end in hit (or subject) coordinates. The value of "hit_to" is lower than the value of "hit_from" on reverse strands.

This method does not accept any arguments.

  evalue
Returns the E-value (or expect) of the HSP.

This method does not accept any arguments.

  bit_score
Returns the score (in bits) of the HSP.

This method does not accept any arguments.

  query_strand
Returns the strand (+1/-1) of the query in the HSP.

This method does not accept any arguments.

  hit_strand
Returns the strand (+1/-1) of the hit in the HSP.

This method does not accept any arguments.

  query_start
Returns the HSP start in query coordinates. The value of "query_start" is guaranteed to be lower than the value of "query_end".

This method does not accept any arguments.

  query_end
Returns the HSP end in query coordinates. The value of "query_end" is guaranteed to be higher than the value of "query_start".

This method does not accept any arguments.

  hit_start
Returns the HSP start in hit (or subject) coordinates. The value of "hit_start" is guaranteed to be lower than the value of "hit_end".

This method does not accept any arguments.

  hit_end
Returns the HSP end in hit (or subject) coordinates. The value of "hit_end" is guaranteed to be higher than the value of "hit_start".

This method does not accept any arguments.

ALIASES

  expect
Alias for "evalue" method. For API consistency.

AUTHOR
Denis BAURAIN <denis.baurain@uliege.be>

COPYRIGHT AND LICENSE
This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.