t/EMBOSS.t

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