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|
#! perl
use strict;
use warnings;
use Test::More;
use lib '.';
use t::TestUtils;
use Grinder;
my ($factory, $nof_reads, $read);
# Tracking read information in the read description
ok $factory = Grinder->new(
-reference_file => data('shotgun_database_extended.fa'),
-total_reads => 10 ,
-unidirectional => 0 ,
-desc_track => 1 ,
), 'Bidirectional shotgun tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=.*position=(complement\()?\d+\.\.\d+(\))?/;
}
ok $factory = Grinder->new(
-reference_file => data('shotgun_database_extended.fa'),
-total_reads => 10 ,
-unidirectional => 1 ,
-desc_track => 1 ,
), 'Forward shotgun tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=.*position=\d+\.\.\d+/;
}
ok $factory = Grinder->new(
-reference_file => data('shotgun_database_extended.fa'),
-total_reads => 10 ,
-unidirectional => -1 ,
-desc_track => 1 ,
), 'Reverse shotgun tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=.*position=complement\(\d+\.\.\d+\)/;
}
ok $factory = Grinder->new(
-reference_file => data('amplicon_database.fa'),
-forward_reverse => data('forward_primer.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-total_reads => 10 ,
-desc_track => 1 ,
), 'Amplicon tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=\S+.*amplicon=\d+\.\.\d+.*position=.*/;
}
ok $factory = Grinder->new(
-reference_file => data('revcom_amplicon_database.fa'),
-forward_reverse => data('forward_primer.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-total_reads => 10 ,
-desc_track => 1 ,
), 'Reverse-complemented amplicon tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=\S+.*amplicon=complement\(\d+\.\.\d+\).*position=.*/;
}
ok $factory = Grinder->new(
-reference_file => data('amplicon_database.fa'),
-forward_reverse => data('forward_primer.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-total_reads => 10 ,
-desc_track => 1 ,
-chimera_perc => 100 ,
-chimera_dist => (1) ,
-chimera_kmer => 0 ,
), 'Bimeric amplicon tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=\S+,\S+.*amplicon=\d+\.\.\d+,\d+\.\.\d+.*position=.*/;
}
ok $factory = Grinder->new(
-reference_file => data('amplicon_database.fa'),
-forward_reverse => data('forward_primer.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-total_reads => 10 ,
-desc_track => 1 ,
-chimera_perc => 100 ,
-chimera_dist => (0, 1) ,
-chimera_kmer => 10 ,
), 'Trimeric amplicon tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=\S+(,\S+){2}.*amplicon=\d+\.\.\d+(,\d+\.\.\d+){2}.*position=.*/;
}
ok $factory = Grinder->new(
-reference_file => data('shotgun_database.fa'),
-total_reads => 10 ,
-desc_track => 0 ,
), 'No tracking';
ok $read = $factory->next_read;
while ($factory->next_read) {
is $read->desc, undef;
}
ok $factory = Grinder->new(
-reference_file => data('shotgun_database.fa'),
-total_reads => 10 ,
), 'Tracking default';
ok $read = $factory->next_read;
while ($factory->next_read) {
like $read->desc, qr/reference=.*position=.*(complement\()?\d+\.\.\d+(\))?/;
}
done_testing();
|
