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t/cap3.t  view on Meta::CPAN

'CGCGGCCGCTTTTTTTTTTTTTGAGCAAATCGAGCACACTGTGGATGGGGAAGGCACTAC
GGCGACCAAAGTGTGTGGATCCTTGGCATCCAGAGGGGGGTCAGCCCTGACACCGCGGGC
TGAGGGCAGTGATGTTGCCACCTGAGGAGCCTGCCAGCTCCTCTGCCACCTCTAGCACAG
AAGCACCTCACACAGGCGGCAAACATGGCAAACAGGGGATGGCGGGCAGGGTCAGGTCAC
TCTACGCTGCGGGTGAGACGATAACTGGCACGGAGAGCCGATGCCGAACACAGATGCGGA
GCAGCCGAATGGATCCGGTGCTTCGCAATTGACGCGAGGGCAGCCGTGCGTGCGGCCCTA
CCCAAGGCGTTGCGAGAGCGGCCGC',
'TATTGAACCATCGCCCGGCGTTGTGCTGCGCGTTATTCCGTGTCCCGCCTCCTGACCGTG
ACCTGCTTGACTGGCTTCCGATCCCCTTTACCATTGCGGCACAGAAAAGGATTGCGATTC
AAAAAAAAAAAAAA',
'CCGCTGACCCCCCGGCCCCACTGGGGCCTGCCCTGCTTGGGCGACGTGGAGGGCCTGCCA
CCTAACCACCATCATCTGTATTTCCCCTTCTGCGGGCATCATACCCCATGTCACCCATCC
CGGCCTTTCCTGCTGACAATCAGCTGACCTCCTCGGGAACATGGATGTCCAGTCTCAACT
GAGGCCAGTTAATGAGAGGCCTGCTCCCACACCACTCCCACCCGGATCGCCAAACACAAA
CACAAACACAGAACTCATACGTACACACCACGCACTACGCATTTGCACGTGCACCCCGCA
CCTCCCCTATTATTCGTT',
);

my @exp_contig_seq_ids = (
    [
    'gi|125991078',
    'gi|109775518',
    ],
    [
    'gi|125991053',
    'gi|109784559',
    ],
    [
    'gi|125991021',
    'gi|125991020',
    'gi|125989076',
    ],
    [
    'gi|125991014',
    'gi|109780664',
    ],
    [
    'gi|125991007',
    'gi|109778688',
    'gi|109773906',
    ]
);

my $cap = $class->new( seqs => file('test', 'seqs4cap3.fasta') );

is_deeply [ $cap->all_contig_names ], \@exp_contig_names,
            'got expected names for all contigs';
is_deeply [ map { $_->full_id } $cap->all_singlets ], \@exp_singlet_ids,
            'got expected SeqIds from singlets';

is_deeply [ map { $_->seq } $cap->all_contigs ],
          [ map { $_->seq } @exp_contig_seqs ],
            'got expected Seqs for all contigs';
is_deeply [ map { $_->seq } $cap->all_singlets ],
          [ map { $_->seq } @exp_singlet_seqs ],
            'got expected Seqs for all singlets';

for my $i (1..5) {
    is_deeply [ map { $_->full_id } @{ $cap->seq_ids_for('Contig' . $i) } ],
            $exp_contig_seq_ids[$i-1],
            "got expected SeqIds for fragments of Contig $i";
}

is_deeply [ map { [ map { $_->full_id } @{$_} ] } $cap->all_contig_seq_ids ],
            \@exp_contig_seq_ids,
            'got expected SeqIds for all contig fragments';

done_testing;