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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 325);
use_ok('Bio::Factory::FTLocationFactory');
}
my $simple_impl = "Bio::Location::Simple";
my $fuzzy_impl = "Bio::Location::Fuzzy";
my $split_impl = "Bio::Location::Split";
# Holds strings and results. The latter is an array of expected class name,
# min/max start position and position type, min/max end position and position
# type, location type, the number of locations, and the strand.
#
my %testcases = (
# note: the following are directly taken from
# http://www.insdc.org/documents/feature_table.html#3.4.3
"467"
=> [$simple_impl, 467, 467, "EXACT",
467, 467, "EXACT",
"EXACT", 1, 1],
"340..565"
=> [$simple_impl, 340, 340, "EXACT",
565, 565, "EXACT",
"EXACT", 1, 1],
"<345..500"
=> [$fuzzy_impl, undef, 345, "BEFORE",
500, 500, "EXACT",
"EXACT", 1, 1],
"<1..888"
=> [$fuzzy_impl, undef, 1, "BEFORE",
888, 888, "EXACT",
"EXACT", 1, 1],
"1..>888"
=> [$fuzzy_impl, 1, 1, "EXACT",
888, undef, "AFTER",
"EXACT", 1, 1],
"(102.110)"
=> [$fuzzy_impl, 102, 102, "EXACT",
110, 110, "EXACT",
"WITHIN", 1, 1],
"(23.45)..600"
=> [$fuzzy_impl, 23, 45, "WITHIN",
600, 600, "EXACT",
"EXACT", 1, 1],
"(122.133)..(204.221)"
=> [$fuzzy_impl, 122, 133, "WITHIN",
204, 221, "WITHIN",
"EXACT", 1, 1],
"123^124"
=> [$simple_impl, 123, 123, "EXACT",
124, 124, "EXACT",
"IN-BETWEEN", 1, 1],
"145^177"
=> [$fuzzy_impl, 145, 145, "EXACT",
177, 177, "EXACT",
"IN-BETWEEN", 1, 1],
"join(12..78,134..202)"
=> [$split_impl, 12, 12, "EXACT",
202, 202, "EXACT",
"EXACT", 2, 1],
"complement(join(2691..4571,4918..5163))"
=> [$split_impl, 2691, 2691, "EXACT",
5163, 5163, "EXACT",
"EXACT", 2, -1],
# Partial frameshifted gene at the end of a contig
"complement(join(94468..94578,94578..>94889))"
=> [$split_impl, 94468, 94468, "EXACT",
94889, undef, "AFTER",
"EXACT", 2, -1],
"complement(34..(122.126))"
=> [$fuzzy_impl, 34, 34, "EXACT",
122, 126, "WITHIN",
"EXACT", 1, -1],
"J00194:100..202"
=> [$simple_impl, 100, 100, "EXACT",
202, 202, "EXACT",
"EXACT", 1, 1],
"join(1..100,J00194.1:100..202)"
=> [$split_impl, 1, 1, "EXACT",
100, 100, "EXACT",
"EXACT", 2, 1],
# this variant is not really allowed by the FT definition
# document but we want to be able to cope with it
"J00194:(100..202)"
=> [$simple_impl, 100, 100, "EXACT",
202, 202, "EXACT",
"EXACT", 1, 1],
"((122.133)..(204.221))"
=> [$fuzzy_impl, 122, 133, "WITHIN",
204, 221, "WITHIN",
"EXACT", 1, 1],
"join(AY016290.1:108..185,AY016291.1:1546..1599)"
=> [$split_impl, 108, 108, "EXACT",
185, 185, "EXACT",
"EXACT", 2, 1],
# UNCERTAIN locations and positions (Swissprot)
"?2465..2774"
=> [$fuzzy_impl, 2465, 2465, "UNCERTAIN",
2774, 2774, "EXACT",
"EXACT", 1, 1],
"22..?64"
=> [$fuzzy_impl, 22, 22, "EXACT",
64, 64, "UNCERTAIN",
"EXACT", 1, 1],
"?22..?64"
=> [$fuzzy_impl, 22, 22, "UNCERTAIN",
64, 64, "UNCERTAIN",
"EXACT", 1, 1],
"?..>393"
=> [$fuzzy_impl, undef, undef, "UNCERTAIN",
393, undef, "AFTER",
"UNCERTAIN", 1, 1],
"<1..?"
=> [$fuzzy_impl, undef, 1, "BEFORE",
undef, undef, "UNCERTAIN",
"UNCERTAIN", 1, 1],
"?..536"
=> [$fuzzy_impl, undef, undef, "UNCERTAIN",
536, 536, "EXACT",
"UNCERTAIN", 1, 1],
"1..?"
=> [$fuzzy_impl, 1, 1, "EXACT",
undef, undef, "UNCERTAIN",
"UNCERTAIN", 1, 1],
"?..?"
=> [$fuzzy_impl, undef, undef, "UNCERTAIN",
undef, undef, "UNCERTAIN",
"UNCERTAIN", 1, 1],
"?1..12"
=> [$fuzzy_impl, 1, 1, "UNCERTAIN",
12, 12, "EXACT",
"EXACT", 1, 1]
);
my $locfac = Bio::Factory::FTLocationFactory->new();
isa_ok($locfac,'Bio::Factory::LocationFactoryI');
# sorting is to keep the order constant from one run to the next
foreach my $locstr (keys %testcases) {
my $loc = $locfac->from_string($locstr);
if($locstr eq "join(AY016290.1:108..185,AY016291.1:1546..1599)") {
$loc->seq_id("AY016295.1");
}
if($locstr eq "join(1..100,J00194.1:100..202)") {
$loc->seq_id("unknown");
}
my @res = @{$testcases{$locstr}};
is(ref($loc), $res[0], $res[0]);
is($loc->min_start(), $res[1]);
is($loc->max_start(), $res[2]);
is($loc->start_pos_type(), $res[3]);
is($loc->min_end(), $res[4]);
is($loc->max_end(), $res[5]);
is($loc->end_pos_type(), $res[6]);
is($loc->location_type(), $res[7]);
my @locs = $loc->each_Location();
is(@locs, $res[8]);
my $ftstr = $loc->to_FTstring();
# this is a somewhat ugly hack, but we want clean output from to_FTstring()
# Umm, then these should really fail, correct?
# Should we be engineering workarounds for tests?
$locstr = "J00194:100..202" if $locstr eq "J00194:(100..202)";
$locstr = "(122.133)..(204.221)" if $locstr eq "((122.133)..(204.221))";
# now test
is($ftstr, $locstr, "Location String: $locstr");
# test strand production
is($loc->strand(), $res[9]);
}
SKIP: {
skip('nested matches in regex only supported in v5.6.1 and higher', 8) unless $^V gt v5.6.0;
# Tests based on location definition (http://www.insdc.org/documents/feature_table.html#3.4)
my $string1 = 'complement(join(2691..4571,4918..5163))';
my $string2 = 'join(complement(4918..5163),complement(2691..4571))';
my $loc1 = $locfac->from_string($string1);
my $loc2 = $locfac->from_string($string2);
my $loc1_str = $loc1->to_FTstring;
my $loc2_str = $loc2->to_FTstring;
is($loc1_str, $string1, $string1);
is($loc2_str, $string1, $string2);
is($loc1_str, $loc2_str, 'equivalent remote location strings');
# Test for equivalent reverse strand locations adding one remote component
$string1 = 'complement(join(TEST0001.1:2691..4571,4918..5163))';
$string2 = 'join(complement(4918..5163),complement(TEST0001.1:2691..4571))';
$loc1 = $locfac->from_string($string1);
$loc2 = $locfac->from_string($string2);
$loc1_str = $loc1->to_FTstring;
$loc2_str = $loc2->to_FTstring;
is($loc1_str, $string1, $string1);
is($loc2_str, $string1, $string2);
is($loc1_str, $loc2_str, 'equivalent remote location strings');
# Test for equivalent reverse strand locations adding two remote components
$string1 = 'complement(join(TEST0001.1:2691..4571,TEST0008.1:4918..5163))';
$string2 = 'join(complement(TEST0008.1:4918..5163),complement(TEST0001.1:2691..4571))';
$loc1 = $locfac->from_string($string1);
$loc2 = $locfac->from_string($string2);
$loc1_str = $loc1->to_FTstring;
$loc2_str = $loc2->to_FTstring;
is($loc1_str, $string1, $string1);
is($loc2_str, $string1, $string2);
is($loc1_str, $loc2_str, 'equivalent remote location strings');
# bug #1674, #1765, 2101
# EMBL-like (BAC19856.3 protein)
# join(20464..20694,21548..22763,join(complement(314652..314672),complement(232596..232990),complement(231520..231669)))
# GenBank-like
# join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))
# Note that
# join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)
# is the same as
# join(1000..2000,3000..4000,5000..6000,7000..8000,9000..10000)
my @expected = (# intentionally testing same expected string twice
# as I am providing two different encodings
# that should mean the same thing
'join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))',
'join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))',
# ditto
'join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))',
'join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))',
# this is just seen once
'join(1000..2000,3000..4000,5000..6000,7000..8000,9000..10000)',
'order(S67862.1:72..75,join(S67863.1:1..788,1..19))'
);
for my $locstr (
'join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294)))',
'join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))',
'join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))',
'join(20464..20694,21548..22763,join(complement(314652..314672),complement(232596..232990),complement(231520..231669)))',
'join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)',
'order(S67862.1:72..75,join(S67863.1:1..788,1..19))'
) {
my $loc = $locfac->from_string($locstr);
my $ftstr = $loc->to_FTstring();
is($ftstr, shift @expected, $locstr);
}
}
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