t/EMBOSS.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4 # Before `./Build install' is performed this script should be runnable with
   5 # `./Build test'. After `./Build install' it should work as `perl test.t'
   6
   7 use strict;
   8 BEGIN {
   9     use Bio::Root::Test;
  10     test_begin(-tests => 32,
  11                            -requires_modules => [qw(XML::Twig)]);
  12         use_ok('Bio::Root::IO');
  13         use_ok('Bio::SeqIO');
  14         use_ok('Bio::AlignIO');
  15         use_ok('Bio::Factory::EMBOSS');
  16 }
  17
  18 my $compseqoutfile = test_output_file();
  19 my $wateroutfile   = test_output_file();
  20 my $consoutfile    = test_output_file();
  21 my $verbose = test_debug();
  22
  23 ## End of black magic.
  24 ##
  25 ## Insert additional test code below but remember to change
  26 ## the print "1..x\n" in the BEGIN block to reflect the
  27 ## total number of tests that will be run.
  28
  29 my $factory = Bio::Factory::EMBOSS->new();
  30 ok($factory);
  31
  32 SKIP: {
  33         my $compseqapp = $factory->program('compseq');
  34
  35     $factory->verbose($verbose);
  36
  37         skip('EMBOSS not installed',27) if !$compseqapp;
  38
  39         my $version = $factory->version;
  40
  41         my %input = ( '-word' => 4,
  42                           '-sequence' => test_input_file('dna1.fa'),
  43                           '-outfile' => $compseqoutfile);
  44         $compseqapp->run(\%input);
  45         ok(-e $compseqoutfile);
  46
  47         my $water = $factory->program('water');
  48
  49         ok ($water);
  50
  51         # testing in-memory use of
  52         my $in = Bio::SeqIO->new(-format => 'fasta',
  53                                 -file =>  test_input_file('cysprot1a.fa'));
  54         my $seq = $in->next_seq();
  55         ok($seq);
  56         my @amino;
  57         $in = Bio::SeqIO->new(-format => 'fasta',
  58                                  -file =>  test_input_file('amino.fa'));
  59         while( my $s = $in->next_seq) {
  60                 push @amino, $s;
  61         }
  62
  63         my %expected;
  64         if( $version ge '2.8.0' ) {
  65                 $water->run({ '-asequence' => $seq,
  66                           '-bsequence'    => \@amino,
  67                           '-gapopen'   => '10.0',
  68                           '-gapextend' => '0.5',
  69                           '-outfile'   => $wateroutfile});
  70                 %expected = ( 'alnlen' => 394,
  71                           'opid'    => '30.71',
  72                           'apid'    => '40.20');
  73
  74         } else {
  75                 $water->run({ '-sequencea' => $seq,
  76                           '-seqall'    => \@amino,
  77                           '-gapopen'   => '10.0',
  78                           '-gapextend' => '0.5',
  79                           '-outfile'   => $wateroutfile});
  80                 %expected = ( 'alnlen' => 339,
  81                           'opid'    => '33.04',
  82                           'apid'    => '40.58');
  83
  84         }
  85         ok(-e $wateroutfile);
  86
  87         my $alnin = Bio::AlignIO->new(-format => 'emboss',
  88                                         -file   => $wateroutfile);
  89
  90         ok( $alnin);
  91         my $aln = $alnin->next_aln;
  92         ok($aln);
  93         is($aln->length, 43);
  94         is($aln->overall_percentage_identity, 100);
  95         is($aln->average_percentage_identity, 100);
  96
  97         my ($first) = $aln->each_seq();
  98         ok($first->seq(), 'SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE');
  99         $aln = $alnin->next_aln;
 100         ok($aln);
 101
 102         is($aln->length, $expected{'alnlen'});
 103         is(sprintf("%.2f",$aln->overall_percentage_identity), $expected{'opid'});
 104         is(sprintf("%.2f",$aln->average_percentage_identity), $expected{'apid'});
 105
 106
 107         my $cons = $factory->program('cons');
 108         $cons->verbose(0);
 109         $in = Bio::AlignIO->new(-format => 'msf',
 110                                    -file   => test_input_file('cysprot.msf'));
 111         my $aln2 = $in->next_aln;
 112         if( $version ge '2.8.0' ) {
 113                 $cons->run({ '-sequence' => $aln2,
 114                          '-outseq'   => $consoutfile});
 115         } else {
 116                 $cons->run({ '-msf'   => $aln2,
 117                          '-outseq'=> $consoutfile});
 118         }
 119         ok(-e $consoutfile);
 120
 121         # testing acd parsing and EMBOSSacd methods
 122
 123         $compseqapp = $factory->program('compseq');
 124
 125         ok my $acd = $compseqapp->acd;
 126         is $compseqapp->acd->name, 'compseq';
 127         ok my $compseq_mand_acd = $compseqapp->acd->mandatory;
 128         ok $compseq_mand_acd->mandatory->qualifier('-word');
 129         is $compseq_mand_acd->mandatory->qualifier('-supper1'), 0;
 130         is $acd->qualifier('-ppppppp'), 0;
 131         ok $acd->qualifier('-reverse');
 132         is $acd->category('-reverse'), 'optional';
 133         like $acd->values('-reverse'), qr/(?:Yes\/No|true)/;
 134         like $acd->descr('-reverse'), qr/(?:boolean|true)/;
 135         is $acd->unnamed('-reverse'), 0;
 136         like $acd->default('-reverse'), qr/(?:Yes\/No|true)/;
 137 }
 138
 139 __END__
 140
 141 ## comparing input and ACD qualifiers
 142 ## commented out because verbose > 1 prints error messages
 143 ## that would confuse users running tests
 144
 145 $compseqapp->verbose(1);
 146 %input = ( '-word' => 4,
 147        '-outfile' => $compseqoutfile);
 148 eval {
 149     my $a = $compseqapp->run(\%input);
 150 };
 151 ok 1 if $@; # '-sequence' missing
 152
 153  %input = ( '-word' => 4,
 154        '-incorrect_option' => 'no value',
 155        '-sequence' => test_input_file('dna1.fa'),
 156        '-outfile' => $compseqoutfile);
 157 eval {
 158     $compseqapp->run(\%input);
 159 };
 160 ok 1 if $@; # -incorrect_option is incorrect