t/AlignIO/emboss.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id: emboss.t 14971 2008-10-28 16:08:52Z cjfields $
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 37);
  10
  11         use_ok('Bio::AlignIO::emboss');
  12 }
  13
  14 my $DEBUG = test_debug();
  15
  16 my ($str,$aln,$strout,$status);
  17
  18 # EMBOSS water
  19 $str = Bio::AlignIO->new('-format' => 'emboss',
  20                  '-file'   => test_input_file('cysprot.water'));
  21 $aln = $str->next_aln();
  22 isa_ok($aln,'Bio::Align::AlignI');
  23 is($aln->score,'501.50');
  24 is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/3-342');
  25 is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-331');
  26 is(sprintf("%.1f",$aln->overall_percentage_identity),33.8);
  27 is(sprintf("%.1f",$aln->average_percentage_identity),40.1);
  28
  29 is($aln->get_seq_by_pos(1)->start, 3);
  30 is($aln->length,364);
  31
  32
  33 # EMBOSS needle
  34 $str = Bio::AlignIO->new('-format' => 'emboss',
  35           '-file'   => test_input_file('cysprot.needle'));
  36 $aln = $str->next_aln();
  37 isa_ok($aln,'Bio::Align::AlignI');
  38 is($aln->score,'499.50');
  39 is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/1-345');
  40 is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-333');
  41
  42
  43 # EMBOSS water 2.2.x
  44 $str = Bio::AlignIO->new('-format' => 'emboss',
  45          '-file'   => test_input_file('cys1_dicdi.water'));
  46 $aln = $str->next_aln();
  47 isa_ok($aln,'Bio::Align::AlignI');
  48 is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/1-343');
  49 is($aln->get_seq_by_pos(2)->get_nse,'CYS1_DICDI-1/1-343');
  50 is($aln->score,'1841.0');
  51 $aln = $str->next_aln();
  52 isa_ok($aln,'Bio::Align::AlignI');
  53 is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/29-343');
  54 is($aln->get_seq_by_pos(2)->get_nse,'ALEU_HORVU/61-360');
  55
  56
  57 # EMBOSS water 2.2.x sparse needle
  58 $str = Bio::AlignIO->new(-verbose => $DEBUG,
  59           '-format' => 'emboss',
  60         '-file'   => test_input_file('sparsealn.needle'));
  61 $aln = $str->next_aln();
  62 isa_ok($aln,'Bio::Align::AlignI');
  63 is($aln->score,'18.0');
  64 is(sprintf("%.1f",$aln->overall_percentage_identity), 2.1);
  65 is(sprintf("%.1f",$aln->average_percentage_identity), 38.5);
  66 is($aln->get_seq_by_pos(1)->length, 238);
  67 is($aln->length,238);
  68 is($aln->get_seq_by_pos(1)->get_nse,'KV1K_HUMAN/1-108');
  69 is($aln->get_seq_by_pos(2)->get_nse,'IF1Y_HUMAN/1-143');
  70 is($aln->get_seq_by_pos(1)->seq(), 'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQK'.
  71    'PGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'.
  72    '-'x130);
  73 is($aln->get_seq_by_pos(2)->seq(), ('-'x94).'PKNKGKGGK-NRRRGKNENESEKRELVFKE'.
  74    'DGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEAR'.
  75    'SLKAYGGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI');
  76 is($aln->is_flush, 1);
  77
  78 # EMBOSS needle
  79 $str = Bio::AlignIO->new('-format' => 'emboss',
  80           '-file'   => test_input_file('gf-s71.needle'));
  81 $aln = $str->next_aln();
  82 isa_ok($aln,'Bio::Align::AlignI');
  83 is($aln->get_seq_by_pos(2)->seq(), 'MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKEVQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKFDKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARALLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKKITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLSRKIRRSSTSNKPVAIVSMQVYVWPSGEEACVATETGGLYLLTLPTLDYKPLSHQTATSINKILFENQFVAVIYHTSNAAVFNSEGLVDEIPFVATLAVR----------PKLVLF--YTSVCVQDITLNCTSPFREFNNEYNPVIKFSKIRFSADLSVING-FRTSSPNSNN-----------------------------------------------');
  84 is($aln->get_seq_by_pos(1)->seq(), 'MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQESQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKFDKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARAVLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENKVTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLSRKIRRSSTSNKPVAIVSMQV----SGDEVCVATETGGLYLLTLPTLESKPLT-QSATSIFKILYEHPYIAVVYHTSNSAIFNSEGLVDEIPFVATLAVRCGAYFIFSNQSRLIIWSMNTRSTVIDENLNCHS-ICSLSND--------------TLQVLDGDFNLNSQSENSATSESENLRISDLQNLRMLKLQNLRTSEFQNFRTSESQYFKKDNGEL');
  85 is($aln->is_flush(), 1);
  86 is($aln->get_seq_by_pos(1)->get_nse,'gf.s71.44/1-448');
  87 is($aln->get_seq_by_pos(2)->get_nse,'Y50C1A.2/1-406');
  88