t/Phrap.t

   1 #!/usr/local/bin/perl
   2 #-*-Perl-*-
   3 # ## Bioperl Test Harness Script for Modules
   4 # #
   5 use strict;
   6 my $DBEUG = $ENV{'BIOPERLDEBUG'} || 0;
   7 BEGIN {
   8    eval { require Test; };
   9    if( $@ ) {
  10       use lib 't';
  11    }
  12    use Test;
  13    use vars qw($NTESTS);
  14    $NTESTS = 5;
  15    plan tests => $NTESTS;
  16 }
  17
  18 END {
  19    foreach ( $Test::ntest..$NTESTS ) {
  20        skip('Unable to run Phrap tests, exe may not be installed',1);
  21    }
  22 }
  23 ok(1);
  24 use Bio::Tools::Run::Phrap;
  25 use Bio::Root::IO;
  26 use Bio::SeqIO;
  27 use Bio::AlignIO;
  28 use Bio::Seq;
  29
  30 my $input =  Bio::Root::IO->catfile("t","data","Phrap.fa");
  31 my @params = (-verbose => $DBEUG,
  32               arguments=>'-penalty -3 -minmatch 15');
  33
  34 my  $factory = Bio::Tools::Run::Phrap->new(@params);
  35 ok $factory->isa('Bio::Tools::Run::Phrap');
  36 ok $factory->arguments, '-penalty -3 -minmatch 15';
  37
  38 my $phrap_present = $factory->executable();
  39
  40 unless ($phrap_present) {
  41        warn("Phrap program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  42        exit 0;
  43 }
  44
  45 my $assembly = $factory->run($input);
  46
  47 foreach my $contig($assembly->all_contigs){
  48   my $collection = $contig->get_features_collection;
  49   my @sf = $collection->get_all_features;
  50
  51   ok $sf[1]->start, 601;
  52   ok $sf[1]->end,   963;
  53 }
  54
  55
  56 1;
  57