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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: WABA.t,v 1.3 2002/09/16 22:13:31 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'
my $error;
use strict;
use lib '.';
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( $@ ) {
use lib 't';
}
use vars qw($NTESTS);
$NTESTS = 62;
$error = 0;
use Test;
plan tests => $NTESTS;
}
if( $error == 1 ) {
exit(0);
}
use Bio::SearchIO;
use Bio::Root::IO;
my $wabain = new Bio::SearchIO(-format => 'waba',
-file => Bio::Root::IO->catfile('t','data',
'test.waba'));
# These won't look the same as the WABA file because Jim's code is 0 based
# while we (bioperl) are 1 based.
my @results = (
[ 'U57623', 'pair1_hs.fa', 'pair1_mm.fa',
[ 'U02884', 3,
[qw(3833 34 2972 1 243 3688 1 40.9)],
[qw(4211 3022 6914 1 3705 6848 1 43.7)],
[qw(2218 7004 9171 1 6892 8712 1 50.3)],
],
],
[ 'X57152', 'pair9_hs.fa', 'pair9_mm.fa',
[ 'X80685', 1,
[qw(7572 4 5845 1 632 7368 1 46.8)],
],
]
);
while( my $wabar = $wabain->next_result ) {
my @r = @{shift @results};
ok($wabar->query_name, shift @r);
ok($wabar->query_database, shift @r);
ok($wabar->database_name, shift @r);
while( my $wabah = $wabar->next_hit ) {
my (@h) = @{shift @r};
ok( $wabah->name, shift @h);
ok( $wabah->hsps(), shift @h);
while( my $wabahsp = $wabah->next_hsp ) {
my ( @hsp) = @{shift @h};
ok($wabahsp->length('total'), shift @hsp);
ok($wabahsp->query->start, shift @hsp);
ok($wabahsp->query->end, shift @hsp);
ok($wabahsp->strand('query'), shift @hsp);
ok($wabahsp->start('hit'), shift @hsp);
ok($wabahsp->end('subject'), shift @hsp);
ok($wabahsp->subject->strand, shift @hsp);
ok(length($wabahsp->query_string), $wabahsp->length('total'));
ok(length($wabahsp->hit_string), $wabahsp->length('total'));
ok(length($wabahsp->hmmstate_string), $wabahsp->length('total'));
my $hs = $wabahsp->hit_string;
ok($wabahsp->gaps('hit'), $hs =~ tr/\-//);
my $qs = $wabahsp->query_string;
ok($wabahsp->gaps('query'), $qs =~ tr/\-//);
ok(sprintf("%.1f",$wabahsp->percent_identity),shift @hsp);
}
}
}
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