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#-*-perl-*-
# $Id: Analysis-refac.t 16090 2009-09-15 21:57:56Z cjfields $
use strict;
use warnings;
use Bio::Root::Test;
use Bio::PrimarySeq;
use lib '.';
test_begin(-tests => 29);
use_ok( 'Bio::Restriction::IO' );
use_ok( 'Bio::Restriction::Analysis' );
# recog sites (not nec. cut sites!) in lc
my $seq = new Bio::PrimarySeq(
-seq => 'gtcGaagcttAGCAAACGGTTTCTACgacgttatcgtcATTCGGGgcaagcgTCGGCGATTCGGACGTGcacctgcAAAtGCGCGGCgTTAgcgaggtgGCGAgacttttatgtcCCCCTgaagcggttattggTTATATGGTGTTCGTgaccgaTCTAATCCATATTTATTTTTGGCAGTGCtgggtgTTACgacTCGCGA',
-primary_id => 'test',
-molecule => 'dna'
);
# the test enzymes [rebase characterization]:
# nonambig intrasite cutter: HindIII [ A^AGCTT ]
# ambig intrasite cutter: AasI [ GACNNNN^NNGTC ]
# nonambig extrasite cutter: AarI [ CACCTGC(4/8) ]
# ambig extrasite cutter: BceSI [ SSAAGCG(27/27) ]
# ambig center cutter: AjuI [ (7/12)GAANNNNNNNTTGG(11/6) ]
# multi extrasite cutter: TaqII [ GACCGA(11/9),CACCCA(11/9) ]
# the test sequence *cut* (not site) map (recog sites in lc)
#+ AasI(circ)
#+ HindIII AasI
# 1 CTCGaagcttAGCAAACGGTTTCTACgacgttatcgtcATTCGGGgcaagcgTCGGCGAT 60
#- IIIdniH IsaA
#+ BceSI AjuI
#+ AarI AasI
# 61 TCGGACGTGcacctgcAAATGCGCGGCgTTAgcgaggtgGCGAgacttttatgtcCCCCT 120
#- IraA IsaA
#- ISecB IujA
#+ IIqaT
#+ AjuI TaqII
# 121 gaagcggttattggTTATATGGTGTTCGTgaccgaTCTAATCCATATTTATTTTTGGCAG 180
#- IujA IIqaT
#- TaqII
#+
# 181 TGCtgggtgTTACgacTCGCGA 202
#- (cric)IsaA
# so we have +/- cut sites (tpi's, not nt's), in positive strand
# coordinates:
# HindIII : (5, 9)
# AasI : (33, 31), (110,108)
# AasI : (200,202=0) when circularized
# BceSI : (79, 79)
# AarI : (80, 84)
# AjuI : (145, 140) / (113, 108)
# TaqII : (166, 164) / (174, 172)
ok( my $rebase_io = Bio::Restriction::IO->new(
-file => test_input_file('withrefm.906'),
-format => 'withrefm',
), 'read withrefm file');
ok( my $rebase_cln = $rebase_io->read, 'parse withrefm file');
# examples
# ambiguous, nonamibiguous X intrasite, extrasite
ok( my $ninz = $rebase_cln->get_enzyme('HindIII'), 'HindIII: nonambiguous intrasite cutter');
ok( my $nexz = $rebase_cln->get_enzyme('AarI'), 'AarI: nonambiguous extrasite cutter');
ok( my $ainz = $rebase_cln->get_enzyme('AasI'), 'AasI: ambiguous intrasite cutter' );
ok( my $aexz = $rebase_cln->get_enzyme('BceSI'), 'BceSI: ambiguous extrasite cutter' );
# central recognition site: (s/t)[site](m/n)
ok( my $cenz = $rebase_cln->get_enzyme('AjuI'), 'AjuI: cutter with central recog site');
# multisite extrasite:
ok (my $menz = $rebase_cln->get_enzyme('TaqII'), 'TaqII: multi-extrasite cutter');
ok (my $examples = Bio::Restriction::EnzymeCollection->new(
-enzymes=>[$ninz,$ainz, $ainz, $aexz, $cenz, $menz]
) );
# build pretend analysis object to test internals
my $an = {};
bless($an, 'Bio::Restriction::Analysis');
$an->seq($seq);
my ($plus_sites, $minus_sites);
# intrasite cutters
$plus_sites = $an->_make_cuts( $seq->seq, $ninz );
$minus_sites = $an->_make_cuts( $seq->seq, $ninz,'COMP' );
is_deeply( $plus_sites, [5], 'HindIII plus');
is_deeply( $minus_sites, [9], 'HindIII minus');
$plus_sites = $an->_make_cuts( $seq->seq, $ainz );
$minus_sites = $an->_make_cuts( $seq->seq, $ainz,'COMP' );
is_deeply( $plus_sites, [33, 110], 'AasI plus');
is_deeply( $minus_sites, [31, 108], 'AasI minus');
# extrasite cutters
$plus_sites = $an->_make_cuts( $seq->seq, $nexz );
$minus_sites = $an->_make_cuts( $seq->seq, $nexz, 'COMP');
is_deeply( $plus_sites, [80], 'AarI plus');
is_deeply( $minus_sites, [84], 'AarI minus');
$plus_sites = $an->_make_cuts( $seq->seq, $aexz );
$minus_sites = $an->_make_cuts( $seq->seq, $aexz, 'COMP');
is_deeply( $plus_sites, [79], 'BceSI plus');
is_deeply( $minus_sites, [79], 'BceSI minus');
# central site cutter
$plus_sites = $an->_make_cuts( $seq->seq, $cenz );
$minus_sites = $an->_make_cuts( $seq->seq, $cenz, 'COMP');
is_deeply( $plus_sites, [145, 113], 'AjuI plus');
is_deeply( $minus_sites, [140, 108], 'AjuI minus');
# multisite extrasite cutter
$plus_sites = $an->_make_cuts( $seq->seq, $menz );
$minus_sites = $an->_make_cuts( $seq->seq, $menz, 'COMP' );
is_deeply( $plus_sites, [166, 174], 'TaqII plus');
is_deeply( $minus_sites, [164, 172], 'TaqII minus');
# real Analysis object
# start restriction analysis
ok( my $analysis = Bio::Restriction::Analysis->new(
-seq => $seq,
-enzymes => $rebase_cln
), "build real B:R::Analysis object");
# retrieve fragment map
my @fm = $analysis->fragment_maps($examples);
is( @fm, 13, '13 fragments');
# circularize
ok( $seq->is_circular(1), 'circularize');
ok( $analysis->cut, 'recut');
@fm = $analysis->fragment_maps($examples);
is_deeply( [$analysis->positions('AasI')], [33, 110, 200], 'circ: AasI
site at origin' );
is( @fm, 13, 'circ: still 13 fragments (cut site at origin)');
1;
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