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|
#! perl
use strict;
use warnings;
use Test::More;
use lib '.';
use t::TestUtils;
use Grinder;
my ($factory, $read, $nof_reads, %got_amplicons, %expected_amplicons);
# Template with several matching amplicons and forward primer only
ok $factory = Grinder->new(
-reference_file => data('multiple_amplicon_database.fa'),
-forward_reverse => data('forward_primer.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-read_dist => 100 ,
-total_reads => 100 ,
), 'Forward primer only';
$nof_reads = 0;
while ( $read = $factory->next_read ) {
$nof_reads++;
$got_amplicons{$read->seq} = undef;
ok_read_forward_only($read, 1, $nof_reads);
};
is $nof_reads, 100;
%expected_amplicons = (
'AAACTTAAAGGAATTGRCGGttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttGTACACACCGCCCGT' => undef,
'AAACTUAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGTccccc' => undef,
'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaggggggggaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGTggggg' => undef,
);
is_deeply( \%got_amplicons, \%expected_amplicons );
undef %got_amplicons;
# Template with several matching amplicons and forward and reverse primers
ok $factory = Grinder->new(
-reference_file => data('multiple_amplicon_database.fa'),
-forward_reverse => data('forward_reverse_primers.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-read_dist => 100 ,
-total_reads => 100 ,
), 'Forward and reverse primers';
$nof_reads = 0;
while ( $read = $factory->next_read ) {
$nof_reads++;
$got_amplicons{$read->seq} = undef;
ok_read_forward_reverse($read, 1, $nof_reads);
};
is $nof_reads, 100;
%expected_amplicons = (
'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT' => undef,
'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaggggggggaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT' => undef,
'AAACTTAAAGGAATTGRCGGttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttGTACACACCGCCCGT' => undef,
'AAACTUAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT' => undef,
);
is_deeply( \%got_amplicons, \%expected_amplicons );
undef %got_amplicons;
# Template with several nested amplicons and forward and reverse primers
ok $factory = Grinder->new(
-reference_file => data('nested_amplicon_database.fa'),
-forward_reverse => data('forward_reverse_primers.fa') ,
-length_bias => 0 ,
-unidirectional => 1 ,
-read_dist => 100 ,
-total_reads => 100 ,
), 'Forward and reverse primers, nested amplicons';
$nof_reads = 0;
while ( $read = $factory->next_read ) {
$nof_reads++;
$got_amplicons{$read->seq} = undef;
ok_read_forward_reverse($read, 1, $nof_reads);
};
is $nof_reads, 100;
%expected_amplicons = (
'AAACTUAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT' => undef,
'AAACTTAAAGGAATTGRCGGttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttGTACACACCGCCCGT' => undef,
'AAACTTAAAGGAATTGACGGggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggGTACACACCGCCCGT' => undef,
);
is_deeply( \%got_amplicons, \%expected_amplicons );
undef %got_amplicons;
done_testing();
sub ok_read_forward_reverse {
my ($read, $req_strand, $nof_reads) = @_;
isa_ok $read, 'Bio::Seq::SimulatedRead';
like $read->reference->id, qr/^seq\d+$/;
my $strand = $read->strand;
if (not defined $req_strand) {
$req_strand = $strand;
} else {
is $strand, $req_strand;
}
my $readseq = $read->seq;
is $read->id, $nof_reads;
is $read->length, 95;
}
sub ok_read_forward_only {
my ($read, $req_strand, $nof_reads) = @_;
isa_ok $read, 'Bio::Seq::SimulatedRead';
like $read->reference->id, qr/^seq\d+$/;
my $strand = $read->strand;
if (not defined $req_strand) {
$req_strand = $strand;
} else {
is $strand, $req_strand;
}
my $readseq = $read->seq;
is $read->id, $nof_reads;
my $readlength = $read->length;
ok ( ($readlength == 95) or ($readlength == 100) );
}
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