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# -*-Perl-*- Test Harness script for Bioperl
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 12);
use_ok('Bio::AlignIO::fasta');
}
my $DEBUG = test_debug();
my ($str,$aln,$strout,$status);
# FASTA
$str = Bio::AlignIO->new(
-file => test_input_file("testaln.fasta"),
-format => 'fasta');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->display_id, 'AK1H_ECOLI/114-431',
"fasta input test ";
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431/1-318',
"fasta input test ";
is ($aln->get_seq_by_pos(1)->description, 'DESCRIPTION HERE',
"fasta input test for description");
is ($aln->get_seq_by_pos(11)->display_id, 'AK_YEAST/134-472',
"fasta input test for id");
is $aln->get_seq_by_pos(11)->get_nse, 'AK_YEAST/134-472/134-472',
"fasta input test, captures formatted start/end";
is ($aln->get_seq_by_pos(2)->end, 318,
"fasta input test for end");
is ($aln->get_seq_by_pos(11)->description, 'A COMMENT FOR YEAST',
"fasta input test for description");
$strout = Bio::AlignIO->new(
'-file' => ">".test_output_file(),
'-format' => 'fasta');
$status = $strout->write_aln($aln);
is $status, 1,"fasta output test";
my $in = Bio::AlignIO->newFh(
'-file' => test_input_file("testaln.fasta"),
'-format' => 'fasta');
my $out = Bio::AlignIO->newFh(
'-file' => ">".test_output_file(),
'-format' => 'pfam');
while ( $aln = <$in>) {
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431/1-318',
"filehandle input test ";
$status = print $out $aln;
last;
}
is $status, 1, "filehandle output test";
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