# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 132);
use_ok('Bio::Seq::Meta');
use_ok('Bio::Seq::Meta::Array');
use_ok('Bio::SeqIO');
use_ok('Bio::AlignIO');
use_ok('Bio::Seq::Quality');
}
my $DEBUG = test_debug();
ok my $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA");
is $seq->is_flush, 1;
is $seq->revcom->seq, 'TCGATCG-AT';
is $seq->meta, "";
ok $seq->force_flush(1);
is $seq->meta, " ";
$seq->seq("AT-CGATCGATT");
is $seq->meta, " ";
ok not $seq->force_flush(0);
ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA");
is $seq->is_flush, 1;
is $seq->revcom->seq, 'TCGATCG-AT';
is $seq->meta_text, "";
ok $seq->force_flush(1);
$seq->seq("AT-CGATCGATT");
is $seq->meta_text, "0 0 0 0 0 0 0 0 0 0 0 0";
ok not $seq->force_flush(0);
ok $seq = Bio::Seq::Quality->new( -seq => "AT-CGATCGA");
is $seq->meta_text, "";
ok $seq->force_flush(1);
is $seq->meta_text, "0 0 0 0 0 0 0 0 0 0";
$seq->seq("AT-CGATCGATT");
is $seq->meta_text, "0 0 0 0 0 0 0 0 0 0 0 0";
ok not $seq->force_flush(0);
ok $seq = Bio::Seq::Meta->new
( -seq => "",
-meta => "",
-alphabet => 'dna',
-id => 'myid'
);
# create a sequence object
ok $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA",
-id => 'test',
-verbose => 2,
-force_flush => 1
);
is $seq->meta, " ";
is $seq->meta_length, 10;
# Create some random meta values, but gap in the wrong place
my $metastring = "a-abb bb ";
$seq->meta($metastring);
$seq->verbose(1);
# create some random meta values, but not for the last residue
$metastring = "aa-bb bb";
ok $seq->meta($metastring), $metastring. " ";
# truncate the sequence by assignment
$seq->force_flush(1);
$seq->seq('AT-CGA');
$seq->alphabet('dna');
is $seq->meta, 'aa-bb ';
is $seq->start, 1;
is $seq->end, 5;
$seq->force_flush(0);
# truncate the sequence with trunc()
is $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
is $seq->start, 2;
is $seq->end, 5;
is $seq->seq, 'AT-CG';
is $seq->meta, 'aa-bb';
is $seq->strand, -1;
# revcom
ok $seq = $seq->revcom;
is $seq->seq, 'CG-AT';
is $seq->meta, 'bb-aa';
is $seq->strand, 1;
# submeta
is $seq->subseq(2,4), 'G-A';
is $seq->submeta(2,4), 'b-a';
is $seq->submeta(2,undef, 'c-c'), 'c-ca';
is $seq->submeta(2,4), 'c-c';
is $seq->meta, 'bc-ca';
is $seq->meta(''), ' ';
is $seq->submeta(2,undef, 'c-c'), 'c-c ';
is $seq->meta, ' c-c ';
# add named meta annotations
my $first = '11-22';
is $seq->named_meta('first', $first), $first;
is $seq->named_meta('first'), $first;
my $second = '[[-]]';
ok $seq->named_meta('second', $second);
# undefined range arguments
is $seq->named_submeta('second', 3, 4), '-]';
is $seq->named_submeta('second', 3), '-]]';
is $seq->named_submeta('second'), '[[-]]';
my @names = $seq->meta_names;
is @names, 3;
is $names[0], 'DEFAULT';
#
# IO tests
#
sub diff {
my ($infile, $outfile) = @_;
my ($in, $out);
open my $FH_IN, '<', $infile or die "Could not read file '$infile': $!\n";
$in .= $_ while (<$FH_IN>);
close $FH_IN;
open my $FH_OUT, '<', $outfile or die "Could not read file '$outfile': $!\n";
$out .= $_ while (<$FH_OUT>);
close $FH_OUT;
print "|$in||$out|\n" if $DEBUG;
is $in, $out;
}
# SeqIO
my $str = Bio::SeqIO->new
( '-file'=> test_input_file('test.metafasta'),
'-format' => 'metafasta');
ok $seq = $str->next_seq;
my $outfile = test_output_file();
my $strout = Bio::SeqIO->new
('-file'=> ">". $outfile,
'-format' => 'metafasta');
ok $strout->write_seq($seq);
diff (test_input_file('test.metafasta'),
$outfile
);
# AlignIO
$str = Bio::AlignIO->new
( '-file'=> test_input_file('testaln.metafasta'),
'-format' => 'metafasta');
ok my $aln = $str->next_aln;
$outfile = test_output_file();
$strout = Bio::AlignIO->new
('-file'=> ">". $outfile,
'-format' => 'metafasta');
ok $strout->write_aln($aln);
diff (test_input_file('testaln.metafasta'),
$outfile
);
#
##
### tests for Meta::Array
##
#
ok $seq = Bio::Seq::Meta::Array->new
( -seq => "",
-meta => "",
-alphabet => 'dna',
-id => 'myid'
);
# create a sequence object
ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA",
-id => 'test',
-force_flush => 1,
-verbose => 2
);
is $seq->is_flush, 1;
#is $seq->meta_text, " ";
is $seq->meta_text, '0 0 0 0 0 0 0 0 0 0';
# create some random meta values, but not for the last residue
$metastring = "a a - b b 0 b b 0";
is join (' ', @{$seq->meta($metastring)}), $metastring. ' 0';
is $seq->meta_text, $metastring. ' 0';
# truncate the sequence by assignment
$seq->seq('AT-CGA');
$seq->alphabet('dna');
is $seq->meta_text, 'a a - b b 0';
# truncate the sequence with trunc()
is $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
is $seq->seq, 'AT-CG';
is $seq->meta_text, 'a a - b b';
is $seq->strand, -1;
#is $seq->length, 5;
#is $seq->meta_length, 6;
#ok $seq->force_flush(1);
#is $seq->meta_length, 5;
# revcom
ok $seq = $seq->revcom;
is $seq->seq, 'CG-AT';
is $seq->meta_text, 'b b - a a';
is $seq->strand, 1;
# submeta
is $seq->subseq(2,4), 'G-A';
is $seq->submeta_text(2,4), 'b - a';
is $seq->submeta_text(2,undef, 'c - c'), 'c - c';
is $seq->submeta_text(2,4), 'c - c';
is $seq->meta_text, 'b c - c a';
is $seq->meta_text(''), '0 0 0 0 0';
is $seq->submeta_text(2,undef, 'c - c'), 'c - c';
is $seq->meta_text, '0 c - c 0';
# add named meta annotations
$first = '1 10 - 222 23';
is $seq->named_meta_text('first', $first), $first;
is $seq->named_meta_text('first'), $first;
$second = '[ [ - ] ]';
ok $seq->named_meta_text('second', $second);
# undefined range arguments
is $seq->named_submeta_text('second', 3, 4), '- ]';
is $seq->named_submeta_text('second', 3), '- ] ]';
is $seq->named_submeta_text('second'), '[ [ - ] ]';
@names = $seq->meta_names;
is @names, 3;
is $names[0], 'DEFAULT';
#
# testing the forcing of flushed meta values
#
ok $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA",
-id => 'test',
-verbose => 2
);
is $seq->submeta(4, 6, '456'), '456';
is $seq->meta_length, 6;
is $seq->length, 10;
is $seq->meta, " 456";
ok $seq->force_flush(1);
is $seq->meta, " 456 ";
ok $seq->seq('aaatttc');
is $seq->meta, " 456 ";
ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA",
-id => 'test',
-verbose => 2
);
is join (' ', @{$seq->submeta(4, 6, '4 5 6')}), '4 5 6';
is $seq->meta_length, 6;
is $seq->length, 10;
is $seq->meta_text, "0 0 0 4 5 6";
ok $seq->force_flush(1);
is $seq->meta_text, "0 0 0 4 5 6 0 0 0 0";
ok $seq->seq('aaatttc');
is $seq->meta_text, "0 0 0 4 5 6 0";
is $seq->meta_length, 7;
ok $seq = Bio::Seq::Quality->new( -seq => "AT-CGATCGA",
-id => 'test',
-verbose => 2
);
is join (' ', @{$seq->submeta(4, 6, '4 5 6')}), '4 5 6';
is $seq->meta_length, 6;
is $seq->length, 10;
is $seq->meta_text, "0 0 0 4 5 6";
ok $seq->force_flush(1);
is $seq->meta_text, "0 0 0 4 5 6 0 0 0 0";
ok $seq->seq('aaatttc');
is $seq->meta_text, "0 0 0 4 5 6 0";
is $seq->meta_length, 7;
is $seq->trace_length, 7;
#is $seq->quality_length, 7;
is $seq->is_flush, 1;
is $seq->trace_is_flush, 1;
is $seq->quality_is_flush, 1;
# quality: trace_lengths, trace_is_flush, quality_is_flush