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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: EMBOSS.t,v 1.6.2.3 2002/03/18 14:31:09 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;
BEGIN {
use vars qw($NTESTS);
# 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; };
if( $@ ) {
use lib 't';
}
use Test;
$NTESTS = 18;
plan tests => $NTESTS }
use Bio::Factory::EMBOSS;
use Bio::Root::IO;
use Bio::SeqIO;
use Bio::AlignIO;
my $compseqoutfile = 'dna1.4.compseq';
my $wateroutfile = 'cysprot.water';
my $consoutfile = 'cysprot.cons';
END {
foreach ( $Test::ntest..$NTESTS ) {
skip("EMBOSS not installed locally",1);
}
unlink($compseqoutfile);
unlink($wateroutfile);
unlink($consoutfile);
}
my $verbose = $ENV{'BIOPERLDEBUG'} || -1;
ok(1);
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my $factory = new Bio::Factory::EMBOSS(-verbose => $verbose);
ok($factory);
my $compseqapp = $factory->program('compseq');
if( ! $compseqapp ) {
# no EMBOSS installed
exit();
}
ok($compseqapp);
my %input = ( '-word' => 4,
'-sequence' => Bio::Root::IO->catfile('t',
'data',
'dna1.fa'),
'-outfile' => $compseqoutfile);
$compseqapp->run(\%input);
ok(-e $compseqoutfile);
#if( open(IN, $compseqoutfile) ) {
# while(<IN>) { print }
#}
my $water = $factory->program('water');
ok ($water);
# testing in-memory use of
my $in = new Bio::SeqIO(-format => 'fasta',
-file => Bio::Root::IO->catfile('t',
'data',
'cysprot1a.fa'));
my $seq = $in->next_seq();
ok($seq);
my @amino;
$in = new Bio::SeqIO(-format => 'fasta',
-file => Bio::Root::IO->catfile('t',
'data',
'amino.fa'));
while( my $s = $in->next_seq) {
push @amino, $s;
}
$water->run({ '-sequencea' => $seq,
'-seqall' => \@amino,
'-gapopen' => '10.0',
'-gapextend' => '0.5',
'-outfile' => $wateroutfile});
ok(-e $wateroutfile);
my $alnin = new Bio::AlignIO(-format => 'emboss',
-file => $wateroutfile);
ok( $alnin);
my $aln = $alnin->next_aln;
ok($aln);
ok($aln->length, 43);
ok($aln->overall_percentage_identity, 100);
ok($aln->average_percentage_identity, 100);
my ($first) = $aln->each_seq();
ok($first->seq(), 'SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE');
$aln = $alnin->next_aln;
ok($aln);
ok($aln->length, 339);
ok(sprintf("%.2f",$aln->overall_percentage_identity), 33.04);
ok(sprintf("%.2f",$aln->average_percentage_identity), 40.58);
my $cons = $factory->program('cons');
$cons->verbose(0);
$in = new Bio::AlignIO(-format => 'msf',
-file => Bio::Root::IO->catfile('t',
'data',
'cysprot.msf'));
my $aln2 = $in->next_aln;
$cons->run({ '-msf' => $aln2,
'-outseq'=> $consoutfile});
ok(-e $consoutfile);
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