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Viewing changes to t/Variation/Variation_IO.t

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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t/Variation/Variation_IO.t
 
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# -*-Perl-*- Test Harness script for Bioperl
 
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# $Id: Variation_IO.t 15112 2008-12-08 18:12:38Z sendu $
 
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use strict;
 
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BEGIN { 
 
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    use lib '.';
 
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    use Bio::Root::Test;
 
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    test_begin(-tests => 26,
 
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                           -requires_modules => ['Text::Wrap 98', 'XML::Writer']);
 
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        use_ok('Bio::Variation::IO');
 
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}
 
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sub io {
 
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    my ($t_file, $o_file, $out_format) = @_; 
 
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    my $res;
 
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    my ($o_ext) = $out_format eq 'flat' ? 'dat' : 'xml';
 
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    my ($o_format) = $out_format;
 
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    my ($t_name) = $t_file =~ /(.*)....$/;
 
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    my( $before );
 
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    {
 
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        local $/ = undef;
 
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        local *BEFORE;
 
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        open(BEFORE, "$t_name.$o_ext") || die "couldn't open $t_name.$o_ext\n";;
 
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        $before = <BEFORE>;
 
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        close BEFORE;
 
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    }
 
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    ok $before;#"Error in reading input file [$t_name.$o_ext]";
 
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    my $in = Bio::Variation::IO->new( -file => $t_file);
 
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    my  @entries ;
 
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    while (my $e = $in->next) {
 
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        push @entries, $e;
 
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    }
 
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    my $count = scalar @entries;
 
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    cmp_ok @entries, '>', 0;# "No SeqDiff objects [$count]";
 
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    my $out = Bio::Variation::IO->new( -FILE => ">$o_file", 
 
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                                       -FORMAT => $o_format);
 
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    my $out_ok = 1;
 
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    foreach my $e (@entries) {
 
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        $out->write($e) or $out_ok = 0;
 
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    }
 
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    undef($out);  # Flush to disk
 
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    ok $out_ok;#  "error writing variants";
 
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    my( $after );
 
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    {
 
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        local $/ = undef;
 
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        local *AFTER;
 
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        open AFTER, $o_file;
 
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        $after = <AFTER>;
 
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        close AFTER;
 
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    }
 
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    ok $after;# "Error in reading in again the output file [$o_file]";
 
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    is $before, $after, "test output file compared to input";
 
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    print STDERR `diff $t_file $o_file` if $before ne $after;
 
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}
 
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io  (test_input_file('mutations.dat'), 
 
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     test_output_file(), 'flat'); #1..5
 
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io  (test_input_file('polymorphism.dat'), 
 
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     test_output_file(), 'flat'); #6..10
 
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SKIP: {
 
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        test_skip(-tests => 15, -requires_modules => [qw(XML::Twig
 
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                                                                                                     XML::Writer
 
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                                                                                                     IO::String)]);
 
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        eval {
 
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                if( $XML::Writer::VERSION >= 0.5 ) { 
 
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                io  (test_input_file('mutations.xml'), 
 
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                         test_output_file(), 'xml'); #10..12
 
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                } else { 
 
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                io  (test_input_file('mutations.old.xml'), 
 
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                         test_output_file(), 'xml'); #10..12
 
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                }
 
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        };
 
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        eval {
 
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                if( $XML::Writer::VERSION >= 0.5 ) { 
 
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                io  (test_input_file('polymorphism.xml'), 
 
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                         test_output_file(), 'xml'); #13..14
 
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                } else { 
 
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                io  (test_input_file('polymorphism.old.xml'), 
 
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                         test_output_file(), 'xml'); #13..14
 
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                }
 
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        };
 
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        eval { 
 
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                if( $XML::Writer::VERSION >= 0.5 ) { 
 
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                io  (test_input_file('mutations.dat'), 
 
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                         test_output_file(), 'xml'); #15..25
 
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                } else { 
 
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                io  (test_input_file('mutations.old.dat'), 
 
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                         test_output_file(), 'xml'); #15..25
 
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                }
 
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        };
 
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}