NAME

Bio::FastParsers::Hmmer::Table - Front-end class for tabular HMMER parser

VERSION

version 0.221230

SYNOPSIS

use aliased 'Bio::FastParsers::Hmmer::Table';

# open and parse HMMER report in tabular format
my $infile = 'test/hmmer.tblout';
my $report = Table->new( file => $infile );

# loop through hits
while (my $hit = $hit->next_hit) {
    my ($target_name, $evalue) = ($hit->target_name, $hit->evalue);
    # ...
}

DESCRIPTION

# TODO

ATTRIBUTES

file

Path to HMMER report file in tabular format (--tblout) to be parsed

METHODS

next_hit

Shifts the first Hit of the report off and returns it, shortening the report by 1 and moving everything down. If there are no more Hits in the report, returns undef.

# $report is a Bio::FastParsers::Hmmer::Table
while (my $hit = $report->next_hit) {
    # process $hit
    # ...
}

This method does not accept any arguments.

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Arnaud DI FRANCO <arnaud.difranco@gmail.com>

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.