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# -*-Perl-*- Test Harness script for Bioperl
# $Id: IO.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 18);
use_ok('Bio::Restriction::IO');
}
#
# default enz set
#
ok my $in = Bio::Restriction::IO->new();
ok my $renzs = $in->read;
is $renzs->each_enzyme, 532;
ok my $e = $renzs->get_enzyme('AccI');
is $e->name, 'AccI';
my $outfile = test_output_file();
ok my $out = Bio::Restriction::IO->new(-format => 'base', -file => ">$outfile");
TODO: {
local $TODO = "writing to a file doesn't seem to work? prints to STDOUT!";
#$out->write($renzs);
ok -s $outfile;
#map {print $_->name, "\t", $_->site, "\t", $_->overhang, "\n"} $renzs->each_enzyme;
}
#
# withrefm, 31
#
ok $in = Bio::Restriction::IO->new
(-format=> 'withrefm',
-verbose => 0,
-file => test_input_file('rebase.withrefm'));
ok $renzs = $in->read;
is $renzs->each_enzyme, 11;
#
# itype2, 8
#
#enzyme name [tab] prototype [tab] recognition sequence with cleavage site
# [tab] methylation site and type [tab] commercial source [tab] references
ok $in = Bio::Restriction::IO->new
(-format=> 'itype2', -verbose => 0,
-file => test_input_file('rebase.itype2'));
ok $renzs = $in->read;
is $renzs->each_enzyme, 16;
ok $out = Bio::Restriction::IO->new(-format=>'base');
SKIP: {
test_skip(-tests => 3, -requires_networking => 1);
#test_skip(-tests => 2, -requires_module => 'LWP::UserAgent');
ok $in = Bio::Restriction::IO->new(-format=>'prototype',
-current => 1);
ok my $coll = $in->read;
cmp_ok $coll->each_enzyme, '>=', 307;
}
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