t/Variation/Variation_IO.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 26,
  11                            -requires_modules => ['Text::Wrap 98', 'XML::Writer']);
  12
  13         use_ok('Bio::Variation::IO');
  14 }
  15
  16 sub io {
  17     my ($t_file, $o_file, $out_format) = @_;
  18     my $res;
  19
  20     my ($o_ext) = $out_format eq 'flat' ? 'dat' : 'xml';
  21     my ($o_format) = $out_format;
  22     my ($t_name) = $t_file =~ /(.*)....$/;
  23
  24     my( $before );
  25     {
  26         local $/ = undef;
  27         local *BEFORE;
  28         open(BEFORE, "$t_name.$o_ext") || die "couldn't open $t_name.$o_ext\n";;
  29         $before = <BEFORE>;
  30         close BEFORE;
  31     }
  32
  33     ok $before;#"Error in reading input file [$t_name.$o_ext]";
  34
  35     my $in = Bio::Variation::IO->new( -file => $t_file);
  36     my  @entries ;
  37     while (my $e = $in->next) {
  38         push @entries, $e;
  39     }
  40     my $count = scalar @entries;
  41     cmp_ok @entries, '>', 0;# "No SeqDiff objects [$count]";
  42
  43     my $out = Bio::Variation::IO->new( -FILE => ">$o_file",
  44                                        -FORMAT => $o_format);
  45     my $out_ok = 1;
  46     foreach my $e (@entries) {
  47         $out->write($e) or $out_ok = 0;
  48     }
  49     undef($out);  # Flush to disk
  50     ok $out_ok;#  "error writing variants";
  51
  52     my( $after );
  53     {
  54         local $/ = undef;
  55         local *AFTER;
  56         open AFTER, $o_file;
  57         $after = <AFTER>;
  58         close AFTER;
  59     }
  60
  61     ok $after;# "Error in reading in again the output file [$o_file]";
  62     is $before, $after, "test output file compared to input";
  63     print STDERR `diff $t_file $o_file` if $before ne $after;
  64 }
  65
  66 io  (test_input_file('mutations.dat'),
  67      test_output_file(), 'flat'); #1..5
  68 io  (test_input_file('polymorphism.dat'),
  69      test_output_file(), 'flat'); #6..10
  70
  71 SKIP: {
  72         test_skip(-tests => 15, -requires_modules => [qw(XML::Twig
  73                                                                                                      XML::Writer
  74                                                                                                      IO::String)]);
  75
  76         eval {
  77                 if( $XML::Writer::VERSION >= 0.5 ) {
  78                 io  (test_input_file('mutations.xml'),
  79                          test_output_file(), 'xml'); #10..12
  80                 } else {
  81                 io  (test_input_file('mutations.old.xml'),
  82                          test_output_file(), 'xml'); #10..12
  83                 }
  84         };
  85
  86         eval {
  87                 if( $XML::Writer::VERSION >= 0.5 ) {
  88                 io  (test_input_file('polymorphism.xml'),
  89                          test_output_file(), 'xml'); #13..14
  90                 } else {
  91                 io  (test_input_file('polymorphism.old.xml'),
  92                          test_output_file(), 'xml'); #13..14
  93
  94                 }
  95         };
  96
  97         eval {
  98                 if( $XML::Writer::VERSION >= 0.5 ) {
  99                 io  (test_input_file('mutations.dat'),
 100                          test_output_file(), 'xml'); #15..25
 101                 } else {
 102                 io  (test_input_file('mutations.old.dat'),
 103                          test_output_file(), 'xml'); #15..25
 104                 }
 105         };
 106 }