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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2008-03-18 14:44:57 UTC
  • mfrom: (4 hardy)
  • mto: This revision was merged to the branch mainline in revision 6.
  • Revision ID: james.westby@ubuntu.com-20080318144457-1jjoztrvqwf0gruk
http://bugs.debian.org/448890
* debian/control:
  - Removed MIA Matt Hope (dopey) from the Uploaders field.
    Thank you for your work, Matt. I hope you are doing well.
  - Downgraded some recommended package to the 'Suggests' priority,
    according to the following discussion on Upstream's mail list.
    http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
    (Closes: #448890)
* debian/copyright converted to machine-readable format.

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t/Variation_IO.t
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# -*-Perl-*-
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## Bioperl Test Harness Script for Modules
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## $Id: Variation_IO.t,v 1.13 2001/12/14 17:52:44 jason Exp $
 
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## $Id: Variation_IO.t,v 1.20 2005/09/17 02:11:21 bosborne Exp $
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use strict;
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use vars qw($NUMTESTS);
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BEGIN { 
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    eval { require Test; };
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    if( $@ ) {
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        use lib 't';
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    }
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    use Test;
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    eval { require 'Text/Wrap.pm' };
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    if( $@ || $Text::Wrap::VERSION < 98 ) {
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        print STDERR "Must have at least Text::Wrap 98 installed\n";
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        plan tests => 1;
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        ok(1);
 
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BEGIN {
 
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        use vars qw($NUMTESTS $error);
 
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        $error = 0;
 
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        eval { require Test; };
 
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        if( $@ ) {
 
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                use lib 't';
 
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        }
 
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        use Test;
 
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        eval {
 
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                require Text::Wrap;
 
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                require XML::Writer;
 
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        };
 
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        if ( $@ || $Text::Wrap::VERSION < 98 ) {
 
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                print STDERR "Skip tests - missing Text::Wrap 98 installed or XML::Writer\n";
 
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                $error = 1;
 
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        }
 
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        $NUMTESTS = 25;
 
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        plan tests => $NUMTESTS;
 
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}
 
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END {
 
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        foreach ( $Test::ntest..$NUMTESTS) {
 
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                skip("Cannot complete Variation_IO tests",1);
 
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        }
 
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}
 
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if ($error == 1 ) {
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        exit(0);
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    }
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    $NUMTESTS = 25;
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    plan tests => $NUMTESTS;
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}
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use Text::Wrap 98;
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use Bio::Variation::IO;
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use Bio::Root::IO;
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sub fileformat ($) {
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    my ($file) = shift;
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    my $format;
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    if ($file =~ /.*dat$/) {
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        $format = 'flat';
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    }
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    elsif ($file =~ /.*xml$/ ) {
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        $format = 'xml';
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    } else {
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        print "Wrong extension! [$file]";
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        exit;
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    }
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    return $format;
 
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        my ($file) = shift;
 
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        my $format;
 
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        if ($file =~ /.*dat$/) {
 
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                $format = 'flat';
 
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        }
 
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        elsif ($file =~ /.*xml$/ ) {
 
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                $format = 'xml';
 
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        } else {
 
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                print "Wrong extension! [$file]";
 
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                exit;
 
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        }
 
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        return $format;
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}
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sub ext ($) {
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    my ($file) = @_;
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    my ($name) = $file =~ /.*.(...)$/;
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    return $name;
 
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        my ($file) = @_;
 
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        my ($name) = $file =~ /.*.(...)$/;
 
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        return $name;
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}
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sub filename ($) {
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    my ($file) = @_;
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    my ($name) = $file =~ /(.*)....$/;
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    return $name;
 
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        my ($file) = @_;
 
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        my ($name) = $file =~ /(.*)....$/;
 
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        return $name;
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}
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sub io {
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    }
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    my $count = scalar @entries;
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    ok @entries > 0;# "No SeqDiff objects [$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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    }
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    ok $after;# "Error in reading in again the output file [$o_file]";
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    ok $before, $after, "test output file differs from input";
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    print STDERR `diff $t_file $o_file` if $before ne $after;
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    unlink($o_file); 
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}
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io  (Bio::Root::IO->catfile("t","data","mutations.dat"), 
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   Bio::Root::IO->catfile("t","data","mutations.out.dat")); #1..5
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     Bio::Root::IO->catfile("t","data","mutations.out.dat")); #1..5
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io  (Bio::Root::IO->catfile("t","data","polymorphism.dat"), 
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   Bio::Root::IO->catfile("t","data","polymorphism.out.dat")); #6..10
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     Bio::Root::IO->catfile("t","data","polymorphism.out.dat")); #6..10
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eval {
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    require Bio::Variation::IO::xml;
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}
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eval {
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    io  (Bio::Root::IO->catfile("t","data","mutations.xml"), 
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        Bio::Root::IO->catfile("t","data","mutations.out.xml")); #10..12
 
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    if( $XML::Writer::VERSION >= 0.5 ) { 
 
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        io  (Bio::Root::IO->catfile("t","data","mutations.xml"), 
 
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             Bio::Root::IO->catfile("t","data","mutations.out.xml")); #10..12
 
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    } else { 
 
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        io  (Bio::Root::IO->catfile("t","data","mutations.old.xml"), 
 
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             Bio::Root::IO->catfile("t","data","mutations.out.xml")); #10..12
 
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    }
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};
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eval {
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    io  (Bio::Root::IO->catfile("t","data","polymorphism.xml"), 
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        Bio::Root::IO->catfile("t","data","polymorphism.out.xml")); #13..14
 
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    if( $XML::Writer::VERSION >= 0.5 ) { 
 
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        io  (Bio::Root::IO->catfile("t","data","polymorphism.xml"), 
 
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             Bio::Root::IO->catfile("t","data","polymorphism.out.xml")); #13..14
 
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    } else { 
 
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        io  (Bio::Root::IO->catfile("t","data","polymorphism.old.xml"), 
 
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             Bio::Root::IO->catfile("t","data","polymorphism.out.xml")); #13..14
 
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    }
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};
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eval { 
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         io  (Bio::Root::IO->catfile("t","data","mutations.dat"), 
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            Bio::Root::IO->catfile("t","data","mutations.out.xml")); #15..25
 
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    if( $XML::Writer::VERSION >= 0.5 ) { 
 
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        io  (Bio::Root::IO->catfile("t","data","mutations.dat"), 
 
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             Bio::Root::IO->catfile("t","data","mutations.out.xml")); #15..25
 
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    } else { 
 
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        io  (Bio::Root::IO->catfile("t","data","mutations.old.dat"), 
 
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             Bio::Root::IO->catfile("t","data","mutations.old.out.xml")); #15..25
 
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    }
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};
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