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# This is -*-Perl-*- code
# $Id: AlignIO.t,v 1.24.2.3 2002/03/18 14:52:19 jason Exp $
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 53;
}
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::IO;
ok (1);
END {
unlink(Bio::Root::IO->catfile("t","data","testout2.pfam"),
Bio::Root::IO->catfile("t","data","testout.selex"),
Bio::Root::IO->catfile("t","data","testout.pfam"),
Bio::Root::IO->catfile("t","data","testout.msf"),
Bio::Root::IO->catfile("t","data","testout.fasta"),
Bio::Root::IO->catfile("t","data","testout.clustal"),
Bio::Root::IO->catfile("t","data","testout.phylip"),
Bio::Root::IO->catfile("t","data","testout.nexus"),
Bio::Root::IO->catfile("t","data","testout.mega"),
);
}
my ($str,$aln,$strout,$status);
# STOCKHOLM
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.stockholm"),
'-format' => 'stockholm');
ok defined($str) && ref($str) && $str->isa('Bio::AlignIO');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246';
# PFAM
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.pfam"));
ok defined($str) && ref($str) && $str->isa('Bio::AlignIO');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246', " failed pfam input test";
$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.pfam"),
'-format' => 'pfam');
$status = $strout->write_aln($aln);
ok $status, 1, " failed pfam output test";
# MSF
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.msf"));
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246', " failed msf input test";
$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.msf"),
'-format' => 'msf');
$status = $strout->write_aln($aln);
ok $status, 1, " failed msf output test";
# FASTA
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.fasta"),
'-format' => 'fasta');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431', " failed fasta input test ";
$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.fasta"),
'-format' => 'fasta');
$status = $strout->write_aln($aln);
ok $status, 1," failed fasta output test";
# SELEX
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.selex"),
'-format' => 'selex');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431', " failed selex format test ";
$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.selex"),
'-format' => 'selex');
$status = $strout->write_aln($aln);
ok $status, 1, " failed selex output test";
# MASE
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.mase"),
'-format' => 'mase');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/1-318', " failed mase input test ";
# PRODOM
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.prodom"),
'-format' => 'prodom');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, 'P04777/1-33', " failed prodom input test ";
# CLUSTAL
$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.clustal"),
'-format' => 'clustalw');
$status = $strout->write_aln($aln);
ok $status, 1, " failed clustalw (.aln) output test";
undef $strout;
$str = Bio::AlignIO->new('-file'=> Bio::Root::IO->catfile("t","data","testout.clustal"),
'-format' => 'clustalw');
$aln = $str->next_aln($aln);
ok $aln->get_seq_by_pos(1)->get_nse, 'P04777/1-33', " failed clustalw (.aln) input test";
# FASTA
my $in = Bio::AlignIO->newFh('-file' => Bio::Root::IO->catfile("t","data","testaln.fasta"),
'-format' => 'fasta');
my $out = Bio::AlignIO->newFh('-file' => ">".Bio::Root::IO->catfile("t","data","testout2.pfam"),
'-format' => 'pfam');
while ( $aln = <$in>) {
ok $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431', " failed filehandle input test ";
$status = print $out $aln;
last;
}
ok $status, 1, " failed filehandle output test";
# BL2SEQ
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","bl2seq.out"),
'-format' => 'bl2seq');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(2)->get_nse, 'ALEU_HORVU/60-360',
"failed BLAST bl2seq format test";
# PHYLIP
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.phylip"),
'-format' => 'phylip');
ok defined($str) && ref($str) && $str->isa('Bio::AlignIO');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, 'Homo_sapie/1-45';
$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.phylip"),
'-format' => 'phylip');
$status = $strout->write_aln($aln);
ok $status, 1, " failed phylip output test";
# NEXUS
$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.nexus"),
'-format' => 'nexus');
ok defined($str) && ref($str) && $str->isa('Bio::AlignIO');
$aln = $str->next_aln();
ok $aln->get_seq_by_pos(1)->get_nse, 'Homo_sapiens/1-45';
$strout = Bio::AlignIO->new('-file' => ">".
Bio::Root::IO->catfile("t", "data", "testout.nexus"),
'-format' => 'nexus', );
$status = $strout->write_aln($aln);
ok $status, 1, " failed nexus output test";
# EMBOSS water
$str = new Bio::AlignIO('-format' => 'emboss',
'-file' => Bio::Root::IO->catfile("t", "data", 'cysprot.water'));
$aln = $str->next_aln();
ok($aln);
ok($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/3-342');
ok($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-331');
ok(sprintf("%.1f",$aln->overall_percentage_identity),33.8);
ok(sprintf("%.1f",$aln->average_percentage_identity),40.1);
ok($aln->get_seq_by_pos(1)->start, 3);
ok($aln->length,364);
# EMBOSS needle
$str = new Bio::AlignIO('-format' => 'emboss',
'-file' => Bio::Root::IO->catfile("t", "data", 'cysprot.needle'));
$aln = $str->next_aln();
ok($aln);
ok($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/1-345');
ok($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-333');
# EMBOSS water 2.2.x
$str = new Bio::AlignIO('-format' => 'emboss',
'-file' => Bio::Root::IO->catfile("t", "data", 'cys1_dicdi.water'));
$aln = $str->next_aln();
ok($aln);
ok($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/1-343');
ok($aln->get_seq_by_pos(2)->get_nse,'CYS1_DICDI-1/1-343');
$aln = $str->next_aln();
ok($aln);
ok($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/29-343');
ok($aln->get_seq_by_pos(2)->get_nse,'ALEU_HORVU/61-360');
# EMBOSS water 2.2.x sparse needle
$str = new Bio::AlignIO(-verbose => 1,
'-format' => 'emboss',
'-file' => Bio::Root::IO->catfile("t", "data", 'sparsealn.needle'));
$aln = $str->next_aln();
ok($aln);
ok(sprintf("%.1f",$aln->overall_percentage_identity), 2.1);
ok(sprintf("%.1f",$aln->average_percentage_identity), 4.6);
ok($aln->get_seq_by_pos(1)->length, 238);
ok($aln->length,238);
ok($aln->get_seq_by_pos(1)->get_nse,'KV1K_HUMAN/1-108');
ok($aln->get_seq_by_pos(2)->get_nse,'IF1Y_HUMAN/1-143');
# MEGA
$str = new Bio::AlignIO('-format' => 'mega',
'-file' => Bio::Root::IO->catfile("t","data","hemoglobinA.meg"));
$aln = $str->next_aln();
ok($aln);
ok($aln->get_seq_by_pos(1)->get_nse,'Human/1-141');
ok($aln->get_seq_by_pos(2)->get_nse,'Horse/1-144');
$aln->unmatch();
ok($aln->get_seq_by_pos(3)->subseq(1,10), 'V-LSAADKGN');
$strout = new Bio::AlignIO('-format' => 'mega',
'-file' => ">" .Bio::Root::IO->catfile("t","data","testout.mega"));
$status = $strout->write_aln($aln);
ok $status, 1, " failed mega output test";
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