t/abi.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7         use lib 't/lib';
   8     use BioperlTest;
   9
  10     test_begin(-tests => 7,
  11                            -requires_module => 'Bio::SeqIO::staden::read 1.52');
  12
  13         use_ok('Bio::SeqIO');
  14 }
  15
  16 my $verbose = test_debug();
  17
  18 my $io = Bio::SeqIO->new(-format => 'abi',
  19                                                                  -verbose => $verbose,
  20                                                                  -file => test_input_file('readtest.abi',),
  21                                                                  -get_trace_data => 1);
  22 my $seq = $io->next_seq;
  23 isa_ok($seq, 'Bio::PrimarySeqI');
  24 is($seq->seq, "GCNTATGACGTGGATTNCGAATTCTNNNNNCGGTAGNNGAAAATCCCCGGNCAAGNTTNNCCCTGCAAANGGAANAANNTGGCCGAGCGCTACGGGCTGATCTGGGTGTGCCTGTTTCCCCCGGCCGGGGGGAGNGATGCAGGACATCCAAGTATCCCGCCNATGGNGGGCTGAGGACGAGGACGGCTTCCATCAGATCAGTGTGCCCGGNCTTCGACATCGGCGGCAGCGCCGCGCGCCAACTGGAAGGCTTCATCGACGTGNAGCATTTTGNCTTCNTGCGCACCGCTACCTTCACCCANCCGGACAAGCGCNAANTGCNGNCCTACACCACCACNGAAACACCGACCGGNTTNAATGCCGATTACCTGAGNNGCGTGGCAAATTATTCGGNGGACNTGCCGCTGNCGGACGTGGACCCGAACTTCCAATGGCTGCGTCATTNCTAGGTGAATCTGCCTTTCACCGCCACGCTCACCATCCACTTCCCGGTGCCGGGCAAGCGGTTGGTGATNATGAATGCCGCCAGACCGGTGTCCAAGCACACCANCCGCCTGNTGGTGCCGATCGNCCGCTAATTTCGACACCCATCTGCCNGNGGGAAGACGTACATGNGTTCAACCTTGCACNTNGTTCNAAAAAAACCNTGCCATGGTGGNAANCGCAAGCGGNCCGGAAATATCNGCCGGNTTGACCCGCNTGNTTGGAAAGTGCATATTCCCCNCCGATNCNCAATTTCGAT");
  25 # trace data points, only added if get_trace_data is invoked
  26 is($seq->get_trace_graph( -trace => 'a' ), 8793);
  27 is($seq->get_trace_graph( -trace => 't' ), 8793);
  28 is($seq->get_trace_graph( -trace => 'g' ), 8793);
  29 is($seq->get_trace_graph( -trace => 'c' ), 8793);