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# -*-Perl-*- Test Harness script for Bioperl
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 351,
-requires_module => 'IO::Scalar');
use_ok('Bio::Tools::CodonTable');
use_ok('Bio::SeqIO::table');
}
my @names = qw(A6
A6r
A6ps1
A6ps2
CaMK2d
CaMKK2
AMPKa1
AMPKa2
MARK3
MARK2);
my @accs = qw(SK001
SK512
SK752
SK766
SK703
SK482
SK032
SK033
SK096
SK120);
my @num_anns = (5, 5, 5, 5, 6, 7, 7, 7, 7, 7);
my @psg = (0, 0, 1, 1, 0, 0, 0, 0, 0, 0);
my @rs = (0, 0, 0, 0, 1, 1, 1, 1, 1, 1);
ok my $seqin = Bio::SeqIO->new(-file => test_input_file("test.tsv"),
-format => 'table',
-species => "Homo sapiens",
-delim => "\t",
-header => 1,
-display_id => 1,
-accession_number => 2,
-seq => 7,
-annotation => 1,
-trim => 1);
run_tests([@names],[@accs],[@num_anns],[@psg],[@rs]);
$seqin->close();
ok $seqin = Bio::SeqIO->new(-file => test_input_file("test.tsv"),
-format => 'table',
-species => "Homo sapiens",
-delim => "\t",
-header => 1,
-display_id => 1,
-accession_number => 2,
-seq => 7,
-colnames => "[Family,Subfamily,Pseudogene?,Protein,Novelty]",
-trim => 1);
run_tests([@names],[@accs],[4,4,4,4,4,5,5,5,5,5],[@psg],[@rs]);
$seqin->close();
ok $seqin = Bio::SeqIO->new(-file => test_input_file("test.tsv"),
-format => 'table',
-species => "Homo sapiens",
-delim => "\t",
-header => 1,
-display_id => 1,
-accession_number => 2,
-seq => 7,
-annotation => "[4,5,6,8,10]",
-trim => 1);
run_tests([@names],[@accs],[4,4,4,4,4,5,5,5,5,5],[@psg],[@rs]);
# Tests to check that 'description' is read from 'table' format
ok $seqin = Bio::SeqIO->new(
-file => test_input_file("test-1.tab"),
-format => 'table',
-header => 1,
-display_id => 1,
-accession_number => 1,
-seq => 3,
-desc => 2
);
ok($seqin);
my $seq = $seqin->next_seq;
ok($seq);
is( $seq->desc, 'd1');
is( $seq->display_id, 'n1');
is( $seq->seq, 'aaaa');
$seq = $seqin->next_seq;
ok($seq);
is( $seq->desc, 'd2');
is( $seq->display_id, 'n2');
is( $seq->seq, 'tttt');
$seqin->close();
# Tests to check that we can _not_ write to 'table' format
ok $seqin = Bio::SeqIO->new(
-file => test_input_file("test-1.tab.gb"),
-format => 'genbank'
);
ok($seqin);
$seq = $seqin->next_seq;
ok($seq);
my $tmpfile = test_output_file();
my $seqout = Bio::SeqIO->new( -format => 'table', -file => ">$tmpfile" );
# dies_ok not available
# dies_ok { $seqout->write_seq($seq) } "write_seq() not implemented";
sub run_tests {
my ($names_,$accs_,$num_anns_,$psg_,$rs_) = @_;
my @names = @$names_;
my @accs = @$accs_;
my @num_anns = @$num_anns_;
my @psg = @$psg_;
my @rs = @$rs_;
my $n = 0;
my $translator = Bio::Tools::CodonTable->new(-id => 1);
while (my $seq = $seqin->next_seq()) {
$n++;
is ($seq->display_id, shift(@names));
is ($seq->accession_number, shift(@accs));
ok ($seq->species);
is ($seq->species->binomial, "Homo sapiens");
my @anns = $seq->annotation->get_Annotations();
is (scalar(@anns), shift(@num_anns));
@anns = grep { $_->value eq "Y";
} $seq->annotation->get_Annotations("Pseudogene?");
is (scalar(@anns), shift(@psg));
# check sequences and that they translate to what we expect
if (($n >= 5) && ($seq->display_id ne "MARK3")) {
my $dna = $seq->seq;
my $protein = "";
my $frame = 0;
while ($frame <= 2) {
my $inframe = substr($dna,$frame);
# translate to protein
my $protseq = $translator->translate($inframe);
# chop off everything after the stop and before the first Met
while ($protseq =~ /(M[^\*]+)/g) {
$protein = $1 if length($1) > length($protein);
}
$frame++;
}
# retrieve expected result from annotation and compare
my ($protann) = $seq->annotation->get_Annotations("Protein");
ok (defined $protann);
is ($protein, $protann->value);
}
@anns = grep { $_->value eq "Known - Refseq";
} $seq->annotation->get_Annotations("Novelty");
is (scalar(@anns), shift(@rs));
@anns = $seq->annotation->get_Annotations("Subfamily");
is (scalar(@anns), ($n <= 5) ? 0 : 1);
@anns = $seq->annotation->get_Annotations("Family");
is (scalar(@anns), 1);
is (substr($anns[0]->value,0,4), ($n <= 4) ? "A6" : "CAMK");
}
is ($n, 10);
}
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