t/Coil.t

   1 #!/usr/local/bin/perl
   2 #-*-Perl-*-
   3 # ## Bioperl Test Harness Script for Modules
   4 # #
   5 use strict;
   6 BEGIN {
   7    eval { require Test; };
   8    if( $@ ) {
   9       use lib 't';
  10    }
  11    use Test;
  12    use vars qw($NTESTS);
  13    $NTESTS = 4;
  14    plan tests => $NTESTS;
  15 }
  16
  17 END {
  18    foreach ( $Test::ntest..$NTESTS ) {
  19        skip('Unable to run Coil tests, exe may not be installed or configured properly',1);
  20    }
  21 }
  22 use Bio::Tools::Run::Coil;
  23 use Bio::Root::IO;
  24 use Bio::SeqIO;
  25
  26 if(! $ENV{'COILSDIR'}){
  27         warn("Need to define env variable COILSDIR to run test");
  28         exit(0);
  29 }
  30
  31 my  $factory = Bio::Tools::Run::Coil->new();
  32 ok $factory->isa('Bio::Tools::Run::Coil');
  33
  34 my $prot_file=  Bio::Root::IO->catfile("t","data","coil_protein_input");
  35
  36 my $seq1 = Bio::Seq->new();
  37 my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta');
  38 $seq1 = $seqstream->next_seq();
  39
  40 my $coil_present = $factory->executable();
  41
  42 unless ($coil_present) {
  43        warn("coil  program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  44        exit 0;
  45 }
  46 $factory->quiet(1);
  47 my @feat = $factory->predict_protein_features($seq1);
  48
  49 ok $feat[0]->isa('Bio::SeqFeatureI');
  50 ok ($feat[0]->start,71);
  51 ok ($feat[0]->end,91);
  52