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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Variation_IO.t,v 1.13 2001/12/14 17:52:44 jason Exp $
use strict;
use vars qw($NUMTESTS);
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
eval { require 'Text/Wrap.pm' };
if( $@ || $Text::Wrap::VERSION < 98 ) {
print STDERR "Must have at least Text::Wrap 98 installed\n";
plan tests => 1;
ok(1);
exit(0);
}
$NUMTESTS = 25;
plan tests => $NUMTESTS;
}
use Text::Wrap 98;
use Bio::Variation::IO;
use Bio::Root::IO;
sub fileformat ($) {
my ($file) = shift;
my $format;
if ($file =~ /.*dat$/) {
$format = 'flat';
}
elsif ($file =~ /.*xml$/ ) {
$format = 'xml';
} else {
print "Wrong extension! [$file]";
exit;
}
return $format;
}
sub ext ($) {
my ($file) = @_;
my ($name) = $file =~ /.*.(...)$/;
return $name;
}
sub filename ($) {
my ($file) = @_;
my ($name) = $file =~ /(.*)....$/;
return $name;
}
sub io {
my ($t_file, $o_file) = @_;
my $res;
my ($t_ext) = ext ($t_file);
my ($o_ext) = ext ($o_file);
my ($t_format) = fileformat ($t_file);
my ($o_format) = fileformat ($o_file);
my ($t_name) = filename($t_file);
my ($o_name) = filename($o_file);
my( $before );
{
local $/ = undef;
local *BEFORE;
open BEFORE, "$t_name.$o_ext";
$before = <BEFORE>;
close BEFORE;
}
ok $before;#"Error in reading input file [$t_name.$o_ext]";
my $in = Bio::Variation::IO->new( -file => $t_file);
my @entries ;
while (my $e = $in->next) {
push @entries, $e;
}
my $count = scalar @entries;
ok @entries > 0;# "No SeqDiff objects [$count]";
my $out = Bio::Variation::IO->new( -FILE => "> $o_file",
-FORMAT => $o_format);
my $out_ok = 1;
foreach my $e (@entries) {
$out->write($e) or $out_ok = 0;
}
undef($out); # Flush to disk
ok $out_ok;# "error writing variants";
my( $after );
{
local $/ = undef;
local *AFTER;
open AFTER, $o_file;
$after = <AFTER>;
close AFTER;
}
ok $after;# "Error in reading in again the output file [$o_file]";
ok $before, $after, "test output file differs from input";
print STDERR `diff $t_file $o_file` if $before ne $after;
unlink($o_file);
}
io (Bio::Root::IO->catfile("t","data","mutations.dat"),
Bio::Root::IO->catfile("t","data","mutations.out.dat")); #1..5
io (Bio::Root::IO->catfile("t","data","polymorphism.dat"),
Bio::Root::IO->catfile("t","data","polymorphism.out.dat")); #6..10
eval {
require Bio::Variation::IO::xml;
};
if( $@ ) {
print STDERR
"\nThe XML-format conversion requires the CPAN modules ",
"XML::Twig, XML::Writer, and IO::String to be installed ",
"on your system, which they probably aren't. Skipping these tests.\n";
for( $Test::ntest..$NUMTESTS) {
skip("No XML::Twig installed", 1);
}
exit(0);
}
eval {
io (Bio::Root::IO->catfile("t","data","mutations.xml"),
Bio::Root::IO->catfile("t","data","mutations.out.xml")); #10..12
};
eval {
io (Bio::Root::IO->catfile("t","data","polymorphism.xml"),
Bio::Root::IO->catfile("t","data","polymorphism.out.xml")); #13..14
};
eval {
io (Bio::Root::IO->catfile("t","data","mutations.dat"),
Bio::Root::IO->catfile("t","data","mutations.out.xml")); #15..25
};
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