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Bio-FastParsers-0.221230
River stage one • 7 direct dependents • 8 total dependents
1 ++
/ Bio::FastParsers::Blast::Table::Hsp

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.