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# -*-Perl-*- Test Harness script for Bioperl
# $Id: CUTG.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 37,
-requires_modules => [qw(IO::String LWP::UserAgent)]);
use_ok('Bio::DB::CUTG');
use_ok('Bio::CodonUsage::Table');
use_ok('Bio::CodonUsage::IO');
use_ok('Bio::SeqIO');
use_ok('Bio::Tools::SeqStats');
}
my $outfile = test_output_file();
my $verbose = test_debug();
# try reading from file
ok my $io = Bio::CodonUsage::IO->new
(-file=> test_input_file('MmCT'));
ok my $cut2 = $io->next_data();
is int($cut2->aa_frequency('LEU')), 10;
# write
ok $io = Bio::CodonUsage::IO->new(-file => ">$outfile");
$io->write_data($cut2);
ok -e $outfile;
# can we read what we've written?
ok $io = Bio::CodonUsage::IO->new(-file => "$outfile");
ok $cut2 = $io->next_data();
is int($cut2->aa_frequency('LEU')), 10;
# now try making a user defined CUT from a sequence
ok my $seqobj = Bio::SeqIO->new (-file =>test_input_file('HUMBETGLOA.fa'),
-format => 'fasta')->next_seq;
is $seqobj->subseq(10,20), 'TTGACACCACT';
ok my $codcont_Ref = Bio::Tools::SeqStats->count_codons($seqobj);
is $codcont_Ref->{'TGA'}, 16;
ok my $cut = Bio::CodonUsage::Table->new(-data=>$codcont_Ref);
is $cut->codon_rel_frequency('CTG'), 0.18;
is $cut->codon_abs_frequency('CTG'), 2.6;
is $cut->codon_count('CTG'), 26;
is $cut->get_coding_gc(1), "39.70";
ok my $ref = $cut->probable_codons(20);
# requiring Internet access, set env BIOPERLDEBUG to 1 to run
SKIP: {
test_skip(-tests => 14, -requires_networking => 1);
ok my $tool = Bio::WebAgent->new(-verbose => $verbose);
ok $tool->sleep;
is $tool->delay(1), 1;
ok $tool->sleep;
# get CUT from web
ok my $db = Bio::DB::CUTG->new();
$db->verbose($verbose ? $verbose : -1);
my $cdtable;
eval {$cdtable = $db->get_request(-sp =>'Pan troglodytes');};
skip "Server/network problems? Skipping those tests\n$@", 5 if $@;
# tests for Table.pm, the answers seem to change with time, so not specific
cmp_ok($cdtable->cds_count(), '>', 10);
cmp_ok(int($cdtable->aa_frequency('LEU')), '>', 1);
ok $cdtable->get_coding_gc('all');
cmp_ok($cdtable->codon_rel_frequency('ttc'), '<', 1);
## now lets enter a non-existent species ans check handling..
## should default to human...
my $db2 = Bio::DB::CUTG->new();
$db2->verbose($verbose ? $verbose : -1);
eval {$cut2 = $db2->get_request(-sp =>'Wookie magnus');};
skip "Server/network problems? Skipping those tests\n$@", 1 if $@;
is $cut2->species(), 'Homo sapiens';
$db = Bio::DB::CUTG->new();
$db->verbose($verbose ? $verbose : -1);
eval {$cdtable = $db->get_request(-sp =>'Homo sapiens');};
skip "Server/network problems? Skipping those tests\n$@", 4 if $@;
# tests for Table.pm, the answers seem to change with time, so not specific
cmp_ok($cdtable->cds_count(), '>', 10);
cmp_ok(int($cdtable->aa_frequency('LEU')), '>', 1);
ok $cdtable->get_coding_gc('all');
cmp_ok($cdtable->codon_rel_frequency('ttc'), '<', 1);
}
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