NAME

Bio::MUST::Apps::Debrief42::TaxReport - Front-end class for tabular tax-report parser

VERSION

version 0.213470

SYNOPSIS

use aliased 'Bio::MUST::Apps::Debrief42::TaxReport';

# open and parse FortyTwo tax-report in tabular format
my $infile = 'test/uL4.tax-report';
my $report = TaxReport->new( file => $infile );

# loop through lines
while (my $new_seq = $report->next_line) {
    my ($seq_id, $contam) = ($new_seq->hit_id, $new_seq->contam_org);
    # ...
}

DESCRIPTION

# TODO

ATTRIBUTES

file

Path to FortyTwo tax-report file in tabular format to be parsed

METHODS

next_seq

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

# $report is a Bio::MUST::Apps::Debrief42::TaxReport
while (my $new_seq = $report->next_seq) {
    # process $new_seq
    # ...
}

This method does not accept any arguments.

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Mick VAN VLIERBERGHE <mvanvlierberghe@doct.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.