# BioPerl module for Bio::Community::IO::Driver::generic
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Copyright Florent Angly <florent.angly@gmail.com>
#
# You may distribute this module under the same terms as perl itself
=head1 NAME
Bio::Community::IO::Driver::generic - Driver to read and write files in a generic tab-delimited site-by-species table format
=head1 SYNOPSIS
my $in = Bio::Community::IO->new( -file => 'gaas_communities.txt', -format => 'generic' );
# See Bio::Community::IO for more information
=head1 DESCRIPTION
This Bio::Community::IO::Driver::generic driver reads and writes files in a generic
format. Multiple communities can be written in a file to generate a site-by-
species table (OTU table), in which the entries are tab-delimited. Example:
Species site A site B
species 1 321 94
species 2 0 58
species 3 47 26
For each Bio::Community::Member $member generated from a generic site-by-species
file, $member->desc() contains the content of the species field. Since the
generic format does not specify a member ID, one is automatically generated
and can be retrieved using $member->id().
=head1 CONSTRUCTOR
See L<Bio::Community::IO>.
=head1 AUTHOR
Florent Angly L<florent.angly@gmail.com>
=head1 SUPPORT AND BUGS
User feedback is an integral part of the evolution of this and other Bioperl
modules. Please direct usage questions or support issues to the mailing list,
L<bioperl-l@bioperl.org>, rather than to the module maintainer directly. Many
experienced and reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem with code and
data examples if at all possible.
If you have found a bug, please report it on the BioPerl bug tracking system
to help us keep track the bugs and their resolution:
=head1 COPYRIGHT
Copyright 2011,2012,2013 by the BioPerl Team L<bioperl-l@bioperl.org>
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
use Moose;
'Bio::Community::Role::Table';
our $multiple_communities = 1; # format supports several communities per file
our $explicit_ids = 0; # IDs are not explicitly recorded
#### sorting only effective for first community???
our $default_sort_members = 0; # unsorted
our $default_abundance_type = 'count'; # absolute count (positive integer)
our $default_missing_string = 0; # empty members get a '0'
has '_line' => (
is => 'rw',
isa => 'PositiveInt',
required => 0,
init_arg => undef,
default => 1,
lazy => 1,
);
has '_col' => (
is => 'rw',
isa => 'PositiveInt',
required => 0,
init_arg => undef,
default => 1,
lazy => 1,
);
has '_members' => (
is => 'rw',
isa => 'ArrayRef', # ArrayRef[Bio::Community::Member] but keep it lean
required => 0,
init_arg => undef,
default => sub { [] },
lazy => 1,
predicate => '_has_members',
);
has '_id2line' => (
is => 'rw',
isa => 'HashRef', # HashRef[String] but keep it lean
required => 0,
init_arg => undef,
default => sub { {} },
lazy => 1,
);
method _generate_members () {
# Make members from the first column
my @members;
my $col = 1;
for my $line (2 .. $self->_get_max_line) {
my $value = $self->_get_value($line, $col);
my $member = Bio::Community::Member->new( -desc => $value );
$self->_attach_taxon($member, $value, 1);
$self->_attach_weights($member);
push @members, $member;
}
$self->_members(\@members);
}
method next_member () {
my ($member, $count);
my $line = $self->_line;
while ( $line++ ) {
# Get the abundance of the member (undef if out-of-bounds)
$count = $self->_get_value($line, $self->_col);
# No more members for this community.
last if not defined $count;
# Skip members with no abundance
next if not $count; # e.g. ''
next if $count == 0; # e.g. 0.0
# Get the member itself
$member = $self->_members->[$line - 2];
$self->_line($line);
last;
}
return $member, $count;
}
method _next_community_init () {
# Go to start of next column and return name of new community.
my $col = $self->_col + 1;
my $line = 1;
my $name = $self->_get_value($line, $col);
$self->_col( $col );
$self->_line( $line );
return $name;
}
method _next_community_finish () {
return 1;
}
method _next_metacommunity_init () {
$self->_generate_members();
my $name = ''; # no provision for metacommunity name in this format
return $name;
}
method _next_metacommunity_finish () {
return 1;
}
method write_member (Bio::Community::Member $member, Count $count) {
my $id = $member->id;
my $line = $self->_id2line->{$id};
if (not defined $line) {
# This member has not been written previously for another community
$line = $self->_get_max_line + 1;
$self->_set_value( $line, 1, $member->desc );
$self->_id2line->{$id} = $line;
}
$self->_set_value($line, $self->_col, $count);
$self->_line( $line + 1 );
return 1;
}
method _write_community_init (Bio::Community $community) {
# Write header for that community
my $col = $self->_col + 1;
my $line = 1;
$self->_set_value($line, $col, $community->name);
$self->_line( $line + 1);
$self->_col( $col );
return 1;
}
method _write_headers () {
$self->_set_value(1, 1, 'Species');
}
method _write_community_finish (Bio::Community $community) {
return 1;
}
method _write_metacommunity_init (Bio::Community::Meta $meta) {
$self->_write_headers; # write first column header
return 1;
}
method _write_metacommunity_finish (Bio::Community::Meta $meta) {
return 1;
}
__PACKAGE__->meta->make_immutable;
1;