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  • Committer: Bazaar Package Importer
  • Author(s): Matt Hope
  • Date: 2004-04-18 14:24:11 UTC
  • mfrom: (1.2.1 upstream) (2.1.1 warty)
  • Revision ID: james.westby@ubuntu.com-20040418142411-gr92uexquw4w8liq
Tags: 1.4-1
* New upstream release
* Examples and working code are installed by default to usr/bin,
  this has been moved to usr/share/doc/bioperl/bin

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t/AlignIO.t
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# This is -*-Perl-*- code
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# $Id: AlignIO.t,v 1.24.2.3 2002/03/18 14:52:19 jason Exp $
 
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# $Id: AlignIO.t,v 1.40 2003/11/25 18:59:42 jason Exp $
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use strict;
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my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
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BEGIN { 
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    eval { require Test; };
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    if( $@ ) { 
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        use lib 't';
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    }
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    use Test;
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    plan tests => 53;
 
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    plan tests => 75;
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}
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use Bio::SimpleAlign;
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END {
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    unlink(Bio::Root::IO->catfile("t","data","testout2.pfam"),
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         Bio::Root::IO->catfile("t","data","testout.selex"),
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         Bio::Root::IO->catfile("t","data","testout.pfam"),
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         Bio::Root::IO->catfile("t","data","testout.msf"),
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         Bio::Root::IO->catfile("t","data","testout.fasta"), 
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         Bio::Root::IO->catfile("t","data","testout.clustal"),
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         Bio::Root::IO->catfile("t","data","testout.phylip"),
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         Bio::Root::IO->catfile("t","data","testout.nexus"),
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         Bio::Root::IO->catfile("t","data","testout.mega"),
 
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           Bio::Root::IO->catfile("t","data","testout.selex"),
 
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           Bio::Root::IO->catfile("t","data","testout.pfam"),
 
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           Bio::Root::IO->catfile("t","data","testout.msf"),
 
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           Bio::Root::IO->catfile("t","data","testout.fasta"), 
 
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           Bio::Root::IO->catfile("t","data","testout.clustal"),
 
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           Bio::Root::IO->catfile("t","data","testout.phylip"),
 
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           Bio::Root::IO->catfile("t","data","testout.nexus"),
 
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           Bio::Root::IO->catfile("t","data","testout.mega"),
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           );
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}
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my ($str,$aln,$strout,$status);
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# STOCKHOLM
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$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.stockholm"),
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                           '-format' => 'stockholm');
 
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# STOCKHOLM (multiple concatenated files, as Pfam flatfile)
 
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ok $str  = new Bio::AlignIO (
 
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    '-file'     => Bio::Root::IO->catfile("t","data","testaln.stockholm"),
 
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    '-format'   => 'stockholm');
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ok defined($str) && ref($str) && $str->isa('Bio::AlignIO');
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$aln = $str->next_aln();
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ok $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246';
 
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$aln = $str->next_aln();
 
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ok $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246';
 
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$aln = $str->next_aln();
 
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ok $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246';
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# PFAM
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$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.pfam"));
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$status = $strout->write_aln($aln);
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ok $status, 1, " failed pfam output test";
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# MAF
 
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$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","humor.maf"));
 
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$aln = $str->next_aln();
 
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ok $aln->get_seq_by_pos(1)->get_nse, 
 
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    'NM_006987/0-5000', " failed maf input test";
 
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# MSF
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$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.msf"));
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$aln = $str->next_aln();
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                           '-format' => 'fasta');
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$aln = $str->next_aln();
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ok $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431', " failed fasta input test ";
 
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ok ($aln->get_seq_by_pos(1)->description, 'DESCRIPTION HERE', 
 
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    " failed fasta input test for description");
 
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ok ($aln->get_seq_by_pos(11)->display_id, 'AK_YEAST',
 
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    " failed fasta input test for id");
 
84
 
 
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ok ($aln->get_seq_by_pos(11)->description, 'A COMMENT FOR YEAST', 
 
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    " failed fasta input test for description");
 
87
 
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$strout = Bio::AlignIO->new('-file' => ">".Bio::Root::IO->catfile("t","data","testout.fasta"), 
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                              '-format' => 'fasta');
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$status = $strout->write_aln($aln);
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                           '-format' => 'clustalw');
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$aln = $str->next_aln($aln);
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ok $aln->get_seq_by_pos(1)->get_nse, 'P04777/1-33', "  failed clustalw (.aln) input test";
 
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my $io = Bio::AlignIO->new(-file => Bio::Root::IO->catfile("t","data","testaln.aln") );
 
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$aln = $io->next_aln();
 
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ok $aln->consensus_string, 'MNEGEHQIKLDELFEKLLRARKIFKNKDVLRHSWEPKDLPHRHEQIEALAQILVPVLRGETMKIIFCGHHACELGEDRGTKGFVIDELKDVDEDRNGKVDVIEINCEHMDTHYRVLPNIAKLFDDCTGIGVPMHGGPTDEVTAKLKQVIDMKERFVIIVLDEIDKLVKKSGDEVLYSLTRINTELKRAKVSVIGISNDLKFKEYLDPRVLSSLSEEEVVFPPYDANQLRDILTQRAEEAFYPGVLDEGVIPLCAALAAREHGDARKALDLLRVAGEIAEREGASKVTEKHVWKAQEKIEQDMMEEVIKTLPLQSKVLLYAIVLLDENGDLPANTGDVYAVYRELCEYIDLEPLTQRRISDLINELDMLGIINAKVVSKGRYGRTKEIRLMVTSYKIRNVLRYDYSIQPLLTISLKSEQRRLI', " failed clustalw consensus_string test";
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# FASTA
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my $in = Bio::AlignIO->newFh('-file'  => Bio::Root::IO->catfile("t","data","testaln.fasta"), 
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# BL2SEQ
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$str = Bio::AlignIO->new('-file'   => Bio::Root::IO->catfile("t","data","bl2seq.out"),
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                           '-format' => 'bl2seq');
 
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                         '-format' => 'bl2seq',
 
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                         '-report_type' => 'blastp');
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$aln = $str->next_aln();
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ok $aln->get_seq_by_pos(2)->get_nse, 'ALEU_HORVU/60-360', 
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    "failed BLAST bl2seq format test";
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$status = $strout->write_aln($aln);
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ok $status, 1, "  failed phylip output test";
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# METAFASTA
 
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$io = Bio::AlignIO->new(-file => Bio::Root::IO->catfile("t","data","testaln.metafasta"));
 
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$aln = $io->next_aln;
 
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ok $aln->consensus_string,'CDEFHIJKLMNOPQRSTUVWXYZhydrophobicIOIOIJOIIOOIOOOOUIIXstructuralABAEEIEIJEIIEOAEEAAUIAX', " failed consensus_string on metafasta";
 
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ok $aln->percentage_identity,'100', " failed percentage_identity using metafasta";
 
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ok $aln->symbol_chars,'39'," failed symbol_chars() using metafasta";
 
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# NEXUS
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$str = Bio::AlignIO->new('-file' => Bio::Root::IO->catfile("t","data","testaln.nexus"),
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                          '-format' => 'nexus');
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# EMBOSS water 2.2.x sparse needle
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$str = new Bio::AlignIO(-verbose => 1,
 
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$str = new Bio::AlignIO(-verbose => $DEBUG,
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                        '-format' => 'emboss',
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                        '-file'   => Bio::Root::IO->catfile("t", "data", 'sparsealn.needle'));
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$aln = $str->next_aln();
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ok($aln);
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ok(sprintf("%.1f",$aln->overall_percentage_identity), 2.1);
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ok(sprintf("%.1f",$aln->average_percentage_identity), 4.6);
 
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ok(sprintf("%.1f",$aln->average_percentage_identity), 38.5);
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ok($aln->get_seq_by_pos(1)->length, 238);
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ok($aln->length,238);
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ok($aln->get_seq_by_pos(1)->get_nse,'KV1K_HUMAN/1-108');
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ok($aln->get_seq_by_pos(2)->get_nse,'IF1Y_HUMAN/1-143');
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ok($aln->get_seq_by_pos(1)->seq(), 'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQKPGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'.'-'x130);
 
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ok($aln->get_seq_by_pos(2)->seq(), ('-'x94).'PKNKGKGGK-NRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI');
 
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ok($aln->is_flush);
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# MEGA
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$str = new Bio::AlignIO('-format' => 'mega',
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$status = $strout->write_aln($aln);
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ok $status, 1, "  failed mega output test";
 
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# 
 
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$str = new Bio::AlignIO('-format' => 'emboss',
 
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                        '-file'   => Bio::Root::IO->catfile('t','data','gf-s71.needle'));
 
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$aln = $str->next_aln();
 
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ok($aln);
 
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ok($aln->get_seq_by_pos(2)->seq(), 'MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKEVQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKFDKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARALLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKKITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLSRKIRRSSTSNKPVAIVSMQVYVWPSGEEACVATETGGLYLLTLPTLDYKPLSHQTATSINKILFENQFVAVIYHTSNAAVFNSEGLVDEIPFVATLAVR----------PKLVLF--YTSVCVQDITLNCTSPFREFNNEYNPVIKFSKIRFSADLSVING-FRTSSPNSNN-----------------------------------------------');
 
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ok($aln->get_seq_by_pos(1)->seq(), 'MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQESQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKFDKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARAVLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENKVTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLSRKIRRSSTSNKPVAIVSMQV----SGDEVCVATETGGLYLLTLPTLESKPLT-QSATSIFKILYEHPYIAVVYHTSNSAIFNSEGLVDEIPFVATLAVRCGAYFIFSNQSRLIIWSMNTRSTVIDENLNCHS-ICSLSND--------------TLQVLDGDFNLNSQSENSATSESENLRISDLQNLRMLKLQNLRTSEFQNFRTSESQYFKKDNGEL');
 
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ok($aln->is_flush());
 
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ok($aln->get_seq_by_pos(1)->get_nse,'gf.s71.44/1-448');
 
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ok($aln->get_seq_by_pos(2)->get_nse,'Y50C1A.2/1-406');
 
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# Let's parse Phylip non-interleaved
 
269
$strout = Bio::AlignIO->new('-file'  =>
 
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                            Bio::Root::IO->catfile("t","data",
 
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                                                   "noninterleaved.phy"),
 
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                            '-format' => 'phylip');
 
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$aln = $strout->next_aln($aln);
 
274
ok($aln);
 
275
ok($aln->get_seq_by_pos(2)->seq(), 'CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGACATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGGTTTATCAAAGTAAGACAGTATGATCAGATACCCATAGAGATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCCACACCTGTCAATATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT' );