# -*-Perl-*- Test Harness script for Bioperl
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin( -tests => 47 );
use_ok( 'Bio::Align::Utilities',
qw( aa_to_dna_aln bootstrap_replicates cat dna_to_aa_aln ) );
use_ok('Bio::AlignIO');
use_ok('Bio::SeqIO');
}
my $in = Bio::AlignIO->new(
-format => 'clustalw',
-file => test_input_file('pep-266.aln')
);
my $pep_aln = $in->next_aln();
isa_ok( $pep_aln, 'Bio::Align::AlignI' );
$in->close();
# aa_to_dna_aln
my $seqin = Bio::SeqIO->new(
-format => 'fasta',
-file => test_input_file('cds-266.fas')
);
my %dna_seq;
while ( my $seq = $seqin->next_seq ) {
$dna_seq{ $seq->display_id } = $seq;
}
my $dna_aln = aa_to_dna_aln( $pep_aln, \%dna_seq );
my @aa_seqs = $pep_aln->each_seq;
for my $dna_seq ( $dna_aln->each_seq ) {
my $peptrans = $dna_seq->translate();
my $aaseq = shift @aa_seqs;
is( $peptrans->seq(), $aaseq->seq() );
}
# dna_to_aa_aln
my $aa_aln = dna_to_aa_aln($dna_aln);
my @pep_seqs = $aa_aln->each_seq;
for my $dna_seq ( $dna_aln->each_seq ) {
my $peptrans = $dna_seq->translate();
my $aaseq = shift @pep_seqs;
is( $peptrans->seq, $aaseq->seq );
}
# bootstrap_replicates
my $bootstraps = bootstrap_replicates( $pep_aln, 10 );
is( scalar @$bootstraps, 10 );
# cat
my $sub_aln1 = $pep_aln->slice( 1, 100 );
my $sub_aln2 = $pep_aln->slice( 101, 200 );
my $sub_aln3 = $pep_aln->slice( 1, 200 );
my $cat_aln = cat( $sub_aln1, $sub_aln2 );
my @seq = $sub_aln3->each_seq;
for my $seq ( $cat_aln->each_seq ) {
my $refseq = shift @seq;
is( $seq->seq, $refseq->seq );
}