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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: DBCUTG.t,v 1.8 2003/12/18 03:03:26 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG $ERROR);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
$ERROR = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 22;
plan tests => $NUMTESTS;
eval {
require IO::String;
require LWP::UserAgent;
};
if( $@ ) {
warn("IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests");
$ERROR = 1;
}
}
END {
foreach ( $Test::ntest..$NUMTESTS) {
skip('unable to run all of the tests depending on web access',1);
}
}
exit 0 if $ERROR == 1;
use Data::Dumper;
require Bio::DB::CUTG;
require Bio::CodonUsage::Table;
require Bio::CodonUsage::IO;
require Bio::SeqIO;
require Bio::Tools::SeqStats;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
if( $DEBUG ) {
ok $tool->sleep;
ok $tool->delay(1), 1;
ok $tool->sleep;
#get CUT from web
ok my $db = Bio::DB::CUTG->new();
my $cdtable = $db->get_request(-sp =>'Pan troglodytes');
exit unless $cdtable;
#tests for Table.pm
ok $cdtable->cds_count(), 401;
ok int($cdtable->aa_frequency('LEU')), 9;
ok $cdtable->get_coding_gc('all');
ok $cdtable->codon_rel_frequency('ttc'), "0.68";
#now try reading from file
ok my $io = Bio::CodonUsage::IO->new
(-file=> Bio::Root::IO->catfile("t", "data", "MmCT"));
ok my $cut2 = $io->next_data();
ok int($cut2->aa_frequency('LEU')), 10;
#now try making a user defined CUT from a sequence
ok my $seqobj = Bio::SeqIO->new (-file=>
Bio::Root::IO->catfile("t", "data",
"HUMBETGLOA.fa"),
-format => 'fasta')->next_seq;
ok $seqobj->subseq(10,20), 'TTGACACCACT';
ok my $codcont_Ref = Bio::Tools::SeqStats->count_codons($seqobj);
ok $codcont_Ref->{'TGA'}, 16;
ok my $cut = Bio::CodonUsage::Table->new(-data=>$codcont_Ref);
ok $cut->codon_rel_frequency('CTG'), 0.18;
ok $cut->codon_abs_frequency('CTG'), 2.6;
ok $cut->codon_count('CTG'), 26;
ok $cut->get_coding_gc(1), "39.70";
} else {
for ( $Test::ntest..$NUMTESTS) {
skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
}
}
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