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#! perl
use strict;
use warnings;
use Test::More;
use lib '.';
use t::TestUtils;
use Grinder;
my ($factory, $nof_reads, $read, %sources);
# Specified genome abundance for a single shotgun library
ok $factory = Grinder->new(
-reference_file => data('shotgun_database_extended.fa'),
-abundance_file => data('abundances.txt') ,
-length_bias => 0 ,
-random_seed => 1910567890 ,
-total_reads => 1000 ,
), 'Genome abundance for a single shotgun libraries';
while ( $read = $factory->next_read ) {
my $source = $read->reference->id;
if (not exists $sources{$source}) {
$sources{$source} = 1;
} else {
$sources{$source}++;
}
};
ok exists $sources{'seq1'};
ok exists $sources{'seq2'};
ok not exists $sources{'seq3'};
ok exists $sources{'seq4'};
ok exists $sources{'seq5'};
# These tests are quite sensitive to the seed used. Ideal average answer should
# be 250 here
between_ok( $sources{'seq1'}, 230, 280 );
between_ok( $sources{'seq2'}, 230, 280 );
between_ok( $sources{'seq4'}, 230, 280 );
between_ok( $sources{'seq5'}, 230, 280 );
is $factory->next_lib, undef;
%sources = ();
# Specified genome abundance for a single amplicon library
ok $factory = Grinder->new(
-abundance_file => data('abundances2.txt') ,
-reference_file => data('amplicon_database.fa') ,
-forward_reverse => data('forward_reverse_primers.fa'),
-copy_bias => 0 ,
-unidirectional => 1 ,
-read_dist => 48 ,
-random_seed => 1910567890 ,
-total_reads => 1000 ,
), 'Genome abundance for a single amplicon libraries';
while ( $read = $factory->next_read ) {
my $source = $read->reference->id;
# Strip amplicon sources of the 'amplicon' part
$source =~ s/_amplicon.*$//;
if (not exists $sources{$source}) {
$sources{$source} = 1;
} else {
$sources{$source}++;
}
};
ok exists $sources{'seq1'};
ok exists $sources{'seq2'};
ok exists $sources{'seq3'};
# These tests are quite sensitive to the seed used. Ideal average answer should
# be 600, 300 and 100 here
between_ok( $sources{'seq1'}, 570, 630 );
between_ok( $sources{'seq2'}, 270, 330 );
between_ok( $sources{'seq3'}, 70 , 130 );
is $factory->next_lib, undef;
%sources = ();
# Specified genome abundance for multiple shotgun libraries
ok $factory = Grinder->new(
-reference_file => data('shotgun_database_extended.fa'),
-abundance_file => data('abundances_multiple.txt') ,
-length_bias => 0 ,
-random_seed => 1232567890 ,
-total_reads => 1000 ,
), 'Genome abundance for multiple shotgun libraries';
ok $factory->next_lib;
$nof_reads = 0;
while ( $read = $factory->next_read ) { $nof_reads++ };
is $nof_reads, 1000;
ok $factory->next_lib;
ok $factory->next_lib;
while ( $read = $factory->next_read ) {
my $source = $read->reference->id;
if (not exists $sources{$source}) {
$sources{$source} = 1;
} else {
$sources{$source}++;
}
};
ok not exists $sources{'seq1'};
ok not exists $sources{'seq2'};
ok exists $sources{'seq3'};
ok not exists $sources{'seq4'};
ok not exists $sources{'seq5'};
is $sources{'seq3'}, 1000;
is $factory->next_lib, undef;
done_testing();
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