# This is -*-Perl-*- code
# $Id: AlignIO.t,v 1.63.2.1 2006/11/08 19:25:18 cjfields Exp $
use strict;
use Data::Dumper;
my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
        eval { require Test::More; };
        if( $@ ) {
                use lib 't/lib';
        }
        use Test::More;
        plan tests => 221;
}
use_ok('Bio::SimpleAlign');
use_ok('Bio::AlignIO');
use_ok('Bio::Root::IO');
END {
    unlink(Bio::Root::IO->catfile("t","data","testout2.pfam"),
           Bio::Root::IO->catfile("t","data","testout.selex"),
           Bio::Root::IO->catfile("t","data","testout.pfam"),
           Bio::Root::IO->catfile("t","data","testout.msf"),
           Bio::Root::IO->catfile("t","data","testout.fasta"),
           Bio::Root::IO->catfile("t","data","testout.clustal"),
           Bio::Root::IO->catfile("t","data","testout.phylip"),
           Bio::Root::IO->catfile("t","data","testout.nexus"),
           Bio::Root::IO->catfile("t","data","testout.mega"),
           Bio::Root::IO->catfile("t","data","testout.po"),
           Bio::Root::IO->catfile("t","data","testout.largemultifasta"),
       Bio::Root::IO->catfile("t","data","testout.stockholm")
          );
}
my ($str,$aln,$strout,$status);
#PSI format  
$str  = new Bio::AlignIO (
    '-file'     => Bio::Root::IO->catfile("t","data","testaln.psi"),
    '-format'   => 'psi');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'QUERY/1-798');
is($aln->no_sequences, 56);
# STOCKHOLM (multiple concatenated files)
# Rfam
$str  = new Bio::AlignIO (
    '-file'     => Bio::Root::IO->catfile("t","data","rfam_tests.stk"),
    '-format'   => 'stockholm');
$strout = Bio::AlignIO->new('-file'  => ">".
                  Bio::Root::IO->catfile("t", "data", "testout.stockholm"),
                '-format' => 'stockholm', );
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'Z11765.1/1-89');
is($aln->accession, 'RF00006');
is($aln->id, 'Vault');
is($aln->description,'Vault RNA');
# annotation
my ($ann) = $aln->annotation->get_Annotations('alignment_comment');
isa_ok($ann, 'Bio::Annotation::Comment');
is($ann->text,'This family of RNAs are found as part of the enigmatic vault'.
   ' ribonucleoprotein complex. The complex consists of a major vault protein'.
   ' (MVP), two minor vault proteins (VPARP and TEP1), and several small '.
   'untranslated RNA molecules. It has been suggested that the vault complex '.
   'is involved in drug resistance. We have identified a putative novel vault '.
   'RNA on chromosome 5 EMBL:AC005219.','Stockholm annotation');
is($ann->tagname,'alignment_comment','Stockholm annotation');
# test output
$status = $strout->write_aln($aln);
is $status, 1, "stockholm output test";
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'L43844.1/2-149');
is($aln->accession, 'RF00007');
is($aln->id, 'U12');
is($aln->description,'U12 minor spliceosomal RNA');
my @anns = $aln->annotation->get_Annotations('reference');
$ann = shift @anns;
isa_ok($ann, 'Bio::Annotation::Reference', 'Stockholm annotation');
$ann = shift @anns;
is($ann->pubmed,'9149533', 'Stockholm annotation');
is($ann->title,
   'Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge.',
   'Stockholm annotation');
is($ann->authors,'Tarn WY, Steitz JA;', 'Stockholm annotation');
is($ann->location,'Trends Biochem Sci 1997;22:132-137.', 'Stockholm annotation');
# alignment meta data
my $meta = $aln->consensus_meta;
isa_ok($meta, 'Bio::Seq::MetaI');
my ($name) = $meta->meta_names;
is($name,'SS_cons', 'Rfam meta data');
my $meta_str = $meta->named_meta($name);
is($meta_str, '...<<<<<..........>>>>>........<<<<......<<<<......>>>>>>>>'.
   '<<<<<.......>>>>>...........<<<<<<<...<<<<<<<.....>>>>>>>.>>>>>>>..<<<'.
   '<<<<<<.........>>>>>>>>>...', 'Rfam meta data');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'AJ295015.1/58-1');
is($aln->accession, 'RF00008');
is($aln->id, 'Hammerhead_3');
is($aln->description,'Hammerhead ribozyme (type III)');
# alignment meta data
$meta = $aln->consensus_meta;
isa_ok($meta, 'Bio::Seq::MetaI');
($name) = $meta->meta_names;
is($name,'SS_cons', 'Rfam meta data');
$meta_str = $meta->named_meta($name);
is($meta_str, '.<<<<<<..<<<<<.........>>>>>.......<<<<.....................'.
   '...........>>>>...>>>>>>.', 'Rfam meta data');
# STOCKHOLM (Pfam)
$str  = new Bio::AlignIO (
    '-file'     => Bio::Root::IO->catfile("t","data","pfam_tests.stk"),
    '-format'   => 'stockholm');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'RAD25_SCHPO/5-240');
is($aln->accession, 'PF00244.9');
is($aln->id, '14-3-3');
is($aln->description,'14-3-3 protein');
($ann) = $aln->annotation->get_Annotations('gathering_threshold');
isa_ok($ann, 'Bio::Annotation::SimpleValue');
is($ann, '25.00 25.00; 25.00 25.00;', 'Pfam annotation');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'COMB_CLOAB/6-235');
is($aln->accession, 'PF04029.4');
is($aln->id, '2-ph_phosp');
is($aln->description,'2-phosphosulpholactate phosphatase');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'Y278_HAEIN/174-219');
is($aln->accession, 'PF03475.3');
is($aln->id, '3-alpha');
is($aln->description,'3-alpha domain');
# alignment meta data
$meta = $aln->consensus_meta;
isa_ok($meta, 'Bio::Seq::MetaI');
my %test_data = ('SA_cons'  => '6000320010013274....3372052026033.108303630350385563',
                 'SS_cons'  => 'SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC',
                 'seq_cons' => 'plTVtclsclhasc......stphLcphLshss.Lupsa+cohpK+lspshs',);
for my $name ($meta->meta_names) {
    ok(exists $test_data{$name}, 'Pfam aln meta data');
    $meta_str = $meta->named_meta($name);
    is($meta_str, $test_data{$name}, 'Pfam aln meta data');
}
%test_data = ();
# sequence meta data
%test_data = ('SA'  => '6000320010013274....3372052026033.108303630350385563',
              'SS'  => 'SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC');
for my $seq ($aln->each_seq) {
    for my $name ($seq->meta_names) {
        ok(exists $test_data{$name}, 'Pfam seq meta data');
        is($seq->named_meta($name), $test_data{$name}, 'Pfam seq meta data');
    }
}
# PFAM format (no annotation)
$str = Bio::AlignIO->new(
          '-file' => Bio::Root::IO->catfile("t","data","testaln.pfam"));
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246');
$strout = Bio::AlignIO->new(
   '-file' => ">".Bio::Root::IO->catfile("t","data","testout.pfam"), 
                            '-format' => 'pfam');
$status = $strout->write_aln($aln);
is($status, 1, " pfam output test");
# MAF
$str = Bio::AlignIO->new(
          '-file' => Bio::Root::IO->catfile("t","data","humor.maf"));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'NM_006987/1-5000', "maf input test";
is $aln->get_seq_by_pos(1)->strand, '-';
# MSF
$str = Bio::AlignIO->new(
    '-file' => Bio::Root::IO->catfile("t","data","testaln.msf"));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246', "msf input test";
$strout = Bio::AlignIO->new(
   '-file' => ">".Bio::Root::IO->catfile("t","data","testout.msf"), 
                            '-format' => 'msf');
$status = $strout->write_aln($aln);
is $status, 1, "msf output test";
# FASTA
$str = Bio::AlignIO->new(
                 -file => Bio::Root::IO->catfile("t","data","testaln.fasta"), 
                 -format => 'fasta');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431', 
  "fasta input test ";
is ($aln->get_seq_by_pos(1)->description, 'DESCRIPTION HERE', 
    "fasta input test for description");
is ($aln->get_seq_by_pos(11)->display_id, 'AK_YEAST',
    "fasta input test for id");
is ($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' => ">".Bio::Root::IO->catfile("t","data","testout.fasta"), 
                              '-format' => 'fasta');
$status = $strout->write_aln($aln);
is $status, 1,"fasta output test";
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>) {
    is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431',
     "filehandle input test  ";
    $status = print $out $aln;
    last;
}
is $status, 1, "filehandle output test";
# SELEX
$str = Bio::AlignIO->new(
    '-file' => Bio::Root::IO->catfile("t","data","testaln.selex"),
                           '-format' => 'selex');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431', "selex format test ";
$strout = Bio::AlignIO->new(
   '-file' => ">".Bio::Root::IO->catfile("t","data","testout.selex"), 
                              '-format' => 'selex');
$status = $strout->write_aln($aln);
is $status, 1, "selex output test";
# MASE
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","testaln.mase"),
                           '-format' => 'mase');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/1-318', "mase input test ";
# PRODOM
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","testaln.prodom"),
                           '-format' => 'prodom');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'P04777/1-33', "prodom input test ";
# CLUSTAL
$strout = Bio::AlignIO->new(
   '-file' => ">".Bio::Root::IO->catfile("t","data","testout.clustal"), 
                              '-format' => 'clustalw');
$status = $strout->write_aln($aln);
is $status, 1, "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);
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'P04777/1-33', "clustalw (.aln) input test";
my $io = Bio::AlignIO->new(
   -file => Bio::Root::IO->catfile("t","data","testaln.aln") );
$aln = $io->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->consensus_string, "MNEGEHQIKLDELFEKLLRARKIFKNKDVLRHSWEPKDLPHRHEQIEA".
"LAQILVPVLRGETMKIIFCGHHACELGEDRGTKGFVIDELKDVDEDRNGKVDVIEINCEHMDTHYRVLPNIAKLF".
"DDCTGIGVPMHGGPTDEVTAKLKQVIDMKERFVIIVLDEIDKLVKKSGDEVLYSLTRINTELKRAKVSVIGISND".
"LKFKEYLDPRVLSSLSEEEVVFPPYDANQLRDILTQRAEEAFYPGVLDEGVIPLCAALAAREHGDARKALDLLRV".
"AGEIAEREGASKVTEKHVWKAQEKIEQDMMEEVIKTLPLQSKVLLYAIVLLDENGDLPANTGDVYAVYRELCEYI".
"DLEPLTQRRISDLINELDMLGIINAKVVSKGRYGRTKEIRLMVTSYKIRNVLRYDYSIQPLLTISLKSEQRRLI",
"clustalw consensus_string test";
# BL2SEQ
$str = Bio::AlignIO->new(
   '-file'   => Bio::Root::IO->catfile("t","data","bl2seq.out"),
                         '-format' => 'bl2seq',
                         '-report_type' => 'blastp');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(2)->get_nse, 'ALEU_HORVU/60-360', 
    "BLAST bl2seq format test";
# PHYLIP interleaved
$str = Bio::AlignIO->new(
    '-file' => Bio::Root::IO->catfile("t","data","testaln.phylip"),
    '-format' => 'phylip');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $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);
is $status, 1, "phylip output test";
# METAFASTA
#print STDERR "Better Metafasta tests needed\n" if $DEBUG;
$io = Bio::AlignIO->new(-verbose => -1, 
   -file => Bio::Root::IO->catfile("t","data","testaln.metafasta"));
$aln = $io->next_aln;
isa_ok($aln,'Bio::Align::AlignI');
is $aln->consensus_string,'CDEFHIJKLMNOPQRSTUVWXYZ', "consensus_string on metafasta";
is $aln->symbol_chars,'23',"symbol_chars() using metafasta";
# NEXUS
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","testaln.nexus"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $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);
is $status, 1, "nexus output test";
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","Bird_Ovomucoids.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","basic-ladder.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","Kingdoms_DNA.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => Bio::Root::IO->catfile("t","data","char-interleave.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","Primate_mtDNA.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","char-matrix-spaces.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","SPAN_Family4nl.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","intrablock-comment.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","SPAN_Family7n.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","long-names.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","SPAN_Family8a.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","multiline-intrablock-comment.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => Bio::Root::IO->catfile("t","data","Treebase-chlamy-dna.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => Bio::Root::IO->catfile("t","data","quoted-strings1.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","UnaSmithHIV-both.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => Bio::Root::IO->catfile("t","data","quoted-strings2.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","barns-combined.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","radical-whitespace.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t","data","basic-bush.nex"),
                          '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => Bio::Root::IO->catfile("t","data","radical-whitespace_02.nex"),
                          '-format' => 'nexus');
# EMBOSS water
$str = new Bio::AlignIO('-format' => 'emboss',
                 '-file'   => Bio::Root::IO->catfile("t", "data", 'cysprot.water'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->score,'501.50');
is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/3-342');
is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-331');
is(sprintf("%.1f",$aln->overall_percentage_identity),33.8);
is(sprintf("%.1f",$aln->average_percentage_identity),40.1);
is($aln->get_seq_by_pos(1)->start, 3);
is($aln->length,364);
# EMBOSS needle
$str = new Bio::AlignIO('-format' => 'emboss',
          '-file'   => Bio::Root::IO->catfile("t", "data", 'cysprot.needle'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->score,'499.50');
is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/1-345');
is($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 = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/1-343');
is($aln->get_seq_by_pos(2)->get_nse,'CYS1_DICDI-1/1-343');
is($aln->score,'1841.0');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/29-343');
is($aln->get_seq_by_pos(2)->get_nse,'ALEU_HORVU/61-360');
# EMBOSS water 2.2.x sparse needle
$str = new Bio::AlignIO(-verbose => $DEBUG,
          '-format' => 'emboss',
        '-file'   => Bio::Root::IO->catfile("t", "data", 'sparsealn.needle'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->score,'18.0');
is(sprintf("%.1f",$aln->overall_percentage_identity), 2.1);
is(sprintf("%.1f",$aln->average_percentage_identity), 38.5);
is($aln->get_seq_by_pos(1)->length, 238);
is($aln->length,238);
is($aln->get_seq_by_pos(1)->get_nse,'KV1K_HUMAN/1-108');
is($aln->get_seq_by_pos(2)->get_nse,'IF1Y_HUMAN/1-143');
is($aln->get_seq_by_pos(1)->seq(), 'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQK'.
   'PGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'.
   '-'x130);
is($aln->get_seq_by_pos(2)->seq(), ('-'x94).'PKNKGKGGK-NRRRGKNENESEKRELVFKE'.
   'DGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEAR'.
   'SLKAYGGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI');
is($aln->is_flush, 1);
# MEGA
$str = new Bio::AlignIO('-format' => 'mega',
        '-file'   => Bio::Root::IO->catfile("t","data","hemoglobinA.meg"));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse,'Human/1-141');
is($aln->get_seq_by_pos(2)->get_nse,'Horse/1-144');
$aln->unmatch();
is($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);
is $status, 1, "mega output test";
# EMBOSS needle
$str = new Bio::AlignIO('-format' => 'emboss',
          '-file'   => Bio::Root::IO->catfile('t','data','gf-s71.needle'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->seq(), 'MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKEVQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKFDKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARALLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKKITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLSRKIRRSSTSNKPVAIVSMQVYVWPSGEEACVATETGGLYLLTLPTLDYKPLSHQTATSINKILFENQFVAVIYHTSNAAVFNSEGLVDEIPFVATLAVR----------PKLVLF--YTSVCVQDITLNCTSPFREFNNEYNPVIKFSKIRFSADLSVING-FRTSSPNSNN-----------------------------------------------');
is($aln->get_seq_by_pos(1)->seq(), 'MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQESQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKFDKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARAVLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENKVTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLSRKIRRSSTSNKPVAIVSMQV----SGDEVCVATETGGLYLLTLPTLESKPLT-QSATSIFKILYEHPYIAVVYHTSNSAIFNSEGLVDEIPFVATLAVRCGAYFIFSNQSRLIIWSMNTRSTVIDENLNCHS-ICSLSND--------------TLQVLDGDFNLNSQSENSATSESENLRISDLQNLRMLKLQNLRTSEFQNFRTSESQYFKKDNGEL');
is($aln->is_flush(), 1);
is($aln->get_seq_by_pos(1)->get_nse,'gf.s71.44/1-448');
is($aln->get_seq_by_pos(2)->get_nse,'Y50C1A.2/1-406');
# PHYLIP sequential/non-interleaved
$strout = Bio::AlignIO->new('-file'  =>
                            Bio::Root::IO->catfile("t","data",
                                                   "noninterleaved.phy"),
                            '-format' => 'phylip');
$aln = $strout->next_aln($aln);
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->seq(), 'CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAA'.
   'AGGTAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGACATGAATT'.
   'TGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGGTTTATCAAAGTAAGACAGTATGATCAGA'.
   'TACCCATAGAGATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCCACACCTGTCAATATAATTG'.
   'GAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT' );
# LARGEMULTIFASTA
$str = Bio::AlignIO->new(
   '-file' => Bio::Root::IO->catfile("t", "data","little.largemultifasta"),
                         '-format' => 'largemultifasta');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'Human:/1-81', "fasta input test ";
is ($aln->get_seq_by_pos(1)->description,
    '72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;',
    "fasta input test for description");
is ($aln->get_seq_by_pos(3)->display_id, 'Rat:',
    "fasta input test for id");
is ($aln->get_seq_by_pos(3)->description,
    '72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;',
    "fasta input test for description");
$strout = Bio::AlignIO->new(
   '-file' => ">".Bio::Root::IO->catfile("t", "data",
                                       "testout.largemultifasta"),
                            '-format' => 'largemultifasta');
$status = $strout->write_aln($aln);
is $status, 1,"fasta output test";
# POA
# just skip on perl 5.6.0 and earlier as it causes a crash on 
# default perl with OS X 10.2
# fink perl 5.6.0 does not seem to have the problem
# can't figure out what it is so just skip for now
if( $^O ne 'darwin' || $] > 5.006 ) {
        $str = new Bio::AlignIO(
                          -file   => Bio::Root::IO->catfile("t", "data", "testaln.po"),
                          -format => 'po',
                          );
        isa_ok($str, 'Bio::AlignIO');
        $aln = $str->next_aln();
        isa_ok($aln,'Bio::Align::AlignI');
        is $aln->no_sequences, 6;
# output is? i.e. does conversion from clustalw to po give the same alignment?
        $str = new Bio::AlignIO(
                  '-file'   => Bio::Root::IO->catfile("t", "data", "testaln.aln"),
                  '-format' => 'clustalw');
        isa_ok($str,'Bio::AlignIO');
        $aln = $str->next_aln();
        isa_ok($aln,'Bio::Align::AlignI');
        $strout = Bio::AlignIO->new(
                 '-file'   => ">" . Bio::Root::IO->catfile("t", "data", "testout.po"),
                 '-format' => 'po');
        $status = $strout->write_aln($aln);
        is $status, 1, "po output test";
        $str = new Bio::AlignIO(
                 '-file'   => Bio::Root::IO->catfile("t", "data", "testaln.po"),
                 '-format' => 'po');
        isa_ok($str,'Bio::AlignIO');
        my $aln2 = $str->next_aln();
        isa_ok($aln2,'Bio::Align::AlignI');
        is $aln2->no_sequences, $aln->no_sequences;
        is $aln2->length, $aln->length;
} else {
        for ( 1..14 ) {
                skip(1,"skipping due to bug in perl 5.6.0 that comes with OS X 10.2");
        }
}
# MEME
# this file has no Strand column
$str = new Bio::AlignIO(
                -file => Bio::Root::IO->catfile("t", "data", "test.meme"),
                -format => 'meme');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');is $aln->length,25;
is $aln->no_sequences,4;
is $aln->get_seq_by_pos(3)->seq(),"CCTTAAAATAAAATCCCCACCACCA";
is $aln->get_seq_by_pos(3)->strand,"1";
# this file has a Strand column
$str = new Bio::AlignIO(
                -file => Bio::Root::IO->catfile("t", "data", "test.meme2"),
                -format => 'meme');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');is $aln->length,20;
is $aln->no_sequences,8;
is $aln->get_seq_by_pos(8)->seq(),"CCAGTCTCCCCTGAATACCC";
is $aln->get_seq_by_pos(7)->strand,"-1";
is $aln->get_seq_by_pos(6)->strand,"1";