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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: phd.t,v 1.6 2001/10/14 21:46:23 jason Exp $
#
use strict;
use vars qw($DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'};
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; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 5;
}
END {
unlink qw(write_phd.phd);
}
print("Checking if the Bio::SeqIO::phd module could be used, even though it shouldn't be directly use'd...\n") if ( $DEBUG);
# test 1
use Bio::SeqIO::phd;
ok(1);
print("Checking to see if SeqWithQuality objects can be created from a file...\n") if ($DEBUG);
my $in_phd = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
"phredfile.phd"),
'-format' => 'phd',
'-verbose' => $DEBUG || 0);
ok(1);
my @phreds;
print("I saw these in qualfile.qual:\n") if($DEBUG);
my $phd = $in_phd->next_seq();
print("Checking to see if this is the right reference...\n") if( $DEBUG);
ok(ref($phd) eq "Bio::Seq::SeqWithQuality");
my $position = 6;
if( $DEBUG ) {
print("What is the base at position $position (using subseq)?\n");
print($phd->subseq($position,$position)."\n");
print("What is the base at position $position (using baseat)?\n");
print($phd->baseat($position)."\n");
print("What is the quality at $position? (using subqual)\n");
}
my @qualsretr = @{$phd->subqual($position,$position)};
if( $DEBUG ) {
print($qualsretr[0]."\n");
print("What is the quality at $position? (using qualat)\n");
print($phd->qualat($position)."\n");
}
print("OK. Now testing write_phd...\n") if($DEBUG);
my $out_phd = Bio::SeqIO->new(-file => ">write_phd.phd",
'-format' => 'phd');
print("Did it return the right reference?\n") if($DEBUG);
ok(ref($out_phd) eq "Bio::SeqIO::phd");
$out_phd->write_seq( -SeqWithQuality => $phd,
-CHROMAT_FILE => $phd->id(),
-ABI_THUMBPRINT => "",
-PHRED_VERSION => "",
-CALL_METHOD => "",
-QUALITY_LEVELS => "",
-TIME => "",
-TRACE_ARRAY_MIN_INDEX => "",
-TRACE_ARRAY_MAX_INDEX => "",
-CHEM => "",
-DYE => ""
);
ok( -e "write_phd.phd");
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