1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqFeaturePrimer.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 8);
use_ok('Bio::SeqFeature::Primer');
}
my $DEBUG = test_debug();
print("Checking to see if a BSFP object can be created:\n") if $DEBUG;
# yes sure, but first scope a few variables
my $seqsequence = "gcatcgatctagctagcta";
my $primersequence = "aaaaaacgatcgatcgtagctagct";
my $seqname = "chads_nifty_sequence";
my $primername = "chads_nifty_primer";
# ok, and what about variables governing where the feature is located?
# check the primer3docs, luke...
# TARGET=513,26
# PRIMER_FIRST_BASE_INDEX=1
# PRIMER_LEFT=484,20
print("Checking to see if the BSFP object can be constructed with a bio::seq object\n") if $DEBUG;
my $seq = Bio::Seq->new( -seq => $seqsequence, -id =>$seqname);
my $bsfp_seq = Bio::SeqFeature::Primer->new( -sequence => $seq,
-TARGET => '5,3' );
isa_ok $bsfp_seq, "Bio::SeqFeature::Primer";
print("Checking to see if the BSFP object can be constructed with scalars\n") if $DEBUG;
my $bsfp_scalar = Bio::SeqFeature::Primer->new( -sequence => $primersequence,
-id => $primername,
-TARGET => '5,3' );
isa_ok $bsfp_scalar, "Bio::SeqFeature::Primer";
print("Checking to see that seq() returns a Bio::Seq object and that the object is the right one.\n") if $DEBUG;
isa_ok $bsfp_scalar->seq(), "Bio::Seq";
print("First for the scalar-ily created one.\n") if $DEBUG;
print("id ok?\n") if $DEBUG;
is $bsfp_scalar->seq()->id(), $primername;
print("sequence ok?\n") if $DEBUG;
is $bsfp_scalar->seq()->seq(), $primersequence;
print("Now for the seq-ily created one\n") if $DEBUG;
print("id ok?\n") if $DEBUG;
is $bsfp_seq->seq()->display_id(), $seqname;
print("sequence ok?\n") if $DEBUG;
is $bsfp_seq->seq()->seq(), $seqsequence;
|
