t/Phrap.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 = 5;
  14    plan tests => $NTESTS;
  15 }
  16
  17 END {
  18    foreach ( $Test::ntest..$NTESTS ) {
  19        skip('Unable to run Phrap tests, exe may not be installed',1);
  20    }
  21 }
  22 ok(1);
  23 use Bio::Tools::Run::Phrap;
  24 use Bio::Root::IO;
  25 use Bio::SeqIO;
  26 use Bio::AlignIO;
  27 use Bio::Seq;
  28
  29 my $input =  Bio::Root::IO->catfile("t","data","Phrap.fa");
  30 my @params = (arguments=>'-penalty -3 -minmatch 15');
  31
  32 my  $factory = Bio::Tools::Run::Phrap->new(@params);
  33 ok $factory->isa('Bio::Tools::Run::Phrap');
  34 ok $factory->arguments, '-penalty -3 -minmatch 15';
  35
  36 my $phrap_present = $factory->executable();
  37
  38 unless ($phrap_present) {
  39        warn("Phrap program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  40        exit 0;
  41 }
  42
  43 my $assembly = $factory->run($input);
  44
  45 foreach my $contig($assembly->all_contigs){
  46   my $collection = $contig->get_features_collection;
  47   my @sf = $collection->get_all_features;
  48   ok $sf[0]->start,601;
  49   ok $sf[0]->end,963;
  50 }
  51
  52
  53 1;
  54