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 lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 37);
  11
  12         use_ok('Bio::AlignIO::emboss');
  13 }
  14
  15 my $DEBUG = test_debug();
  16
  17 my ($str,$aln,$strout,$status);
  18
  19 # EMBOSS water
  20 $str = Bio::AlignIO->new('-format' => 'emboss',
  21                  '-file'   => test_input_file('cysprot.water'));
  22 $aln = $str->next_aln();
  23 isa_ok($aln,'Bio::Align::AlignI');
  24 is($aln->score,'501.50');
  25 is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/3-342');
  26 is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-331');
  27 is(sprintf("%.1f",$aln->overall_percentage_identity),33.8);
  28 is(sprintf("%.1f",$aln->average_percentage_identity),40.1);
  29
  30 is($aln->get_seq_by_pos(1)->start, 3);
  31 is($aln->length,364);
  32
  33
  34 # EMBOSS needle
  35 $str = Bio::AlignIO->new('-format' => 'emboss',
  36           '-file'   => test_input_file('cysprot.needle'));
  37 $aln = $str->next_aln();
  38 isa_ok($aln,'Bio::Align::AlignI');
  39 is($aln->score,'499.50');
  40 is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/1-345');
  41 is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-333');
  42
  43
  44 # EMBOSS water 2.2.x
  45 $str = Bio::AlignIO->new('-format' => 'emboss',
  46          '-file'   => test_input_file('cys1_dicdi.water'));
  47 $aln = $str->next_aln();
  48 isa_ok($aln,'Bio::Align::AlignI');
  49 is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/1-343');
  50 is($aln->get_seq_by_pos(2)->get_nse,'CYS1_DICDI-1/1-343');
  51 is($aln->score,'1841.0');
  52 $aln = $str->next_aln();
  53 isa_ok($aln,'Bio::Align::AlignI');
  54 is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/29-343');
  55 is($aln->get_seq_by_pos(2)->get_nse,'ALEU_HORVU/61-360');
  56
  57
  58 # EMBOSS water 2.2.x sparse needle
  59 $str = Bio::AlignIO->new(-verbose => $DEBUG,
  60           '-format' => 'emboss',
  61         '-file'   => test_input_file('sparsealn.needle'));
  62 $aln = $str->next_aln();
  63 isa_ok($aln,'Bio::Align::AlignI');
  64 is($aln->score,'18.0');
  65 is(sprintf("%.1f",$aln->overall_percentage_identity), 2.1);
  66 is(sprintf("%.1f",$aln->average_percentage_identity), 38.5);
  67 is($aln->get_seq_by_pos(1)->length, 238);
  68 is($aln->length,238);
  69 is($aln->get_seq_by_pos(1)->get_nse,'KV1K_HUMAN/1-108');
  70 is($aln->get_seq_by_pos(2)->get_nse,'IF1Y_HUMAN/1-143');
  71 is($aln->get_seq_by_pos(1)->seq(), 'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQK'.
  72    'PGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'.
  73    '-'x130);
  74 is($aln->get_seq_by_pos(2)->seq(), ('-'x94).'PKNKGKGGK-NRRRGKNENESEKRELVFKE'.
  75    'DGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEAR'.
  76    'SLKAYGGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI');
  77 is($aln->is_flush, 1);
  78
  79 # EMBOSS needle
  80 $str = Bio::AlignIO->new('-format' => 'emboss',
  81           '-file'   => test_input_file('gf-s71.needle'));
  82 $aln = $str->next_aln();
  83 isa_ok($aln,'Bio::Align::AlignI');
  84 is($aln->get_seq_by_pos(2)->seq(), 'MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKEVQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKFDKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARALLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKKITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLSRKIRRSSTSNKPVAIVSMQVYVWPSGEEACVATETGGLYLLTLPTLDYKPLSHQTATSINKILFENQFVAVIYHTSNAAVFNSEGLVDEIPFVATLAVR----------PKLVLF--YTSVCVQDITLNCTSPFREFNNEYNPVIKFSKIRFSADLSVING-FRTSSPNSNN-----------------------------------------------');
  85 is($aln->get_seq_by_pos(1)->seq(), 'MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQESQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKFDKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARAVLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENKVTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLSRKIRRSSTSNKPVAIVSMQV----SGDEVCVATETGGLYLLTLPTLESKPLT-QSATSIFKILYEHPYIAVVYHTSNSAIFNSEGLVDEIPFVATLAVRCGAYFIFSNQSRLIIWSMNTRSTVIDENLNCHS-ICSLSND--------------TLQVLDGDFNLNSQSENSATSESENLRISDLQNLRMLKLQNLRTSEFQNFRTSESQYFKKDNGEL');
  86 is($aln->is_flush(), 1);
  87 is($aln->get_seq_by_pos(1)->get_nse,'gf.s71.44/1-448');
  88 is($aln->get_seq_by_pos(2)->get_nse,'Y50C1A.2/1-406');
  89