| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
|
1
|
|
|
|
|
|
|
#!/usr/bin/env perl |
|
2
|
|
|
|
|
|
|
# Copyright (c) 2016 by Weigang Qiu Lab |
|
3
|
|
|
|
|
|
|
|
|
4
|
|
|
|
|
|
|
package Bio::BPWrapper; |
|
5
|
|
|
|
|
|
|
|
|
6
|
63
|
|
|
63
|
|
468
|
use strict; |
|
|
63
|
|
|
|
|
141
|
|
|
|
63
|
|
|
|
|
2745
|
|
|
7
|
63
|
|
|
63
|
|
320
|
use warnings; |
|
|
63
|
|
|
|
|
104
|
|
|
|
63
|
|
|
|
|
3811
|
|
|
8
|
63
|
|
|
63
|
|
1126
|
use 5.010; |
|
|
63
|
|
|
|
|
257
|
|
|
9
|
|
|
|
|
|
|
our $VERSION = '1.15'; |
|
10
|
|
|
|
|
|
|
|
|
11
|
63
|
|
|
63
|
|
373
|
use constant PROGRAM => 'Bio::BPWrapper'; |
|
|
63
|
|
|
|
|
133
|
|
|
|
63
|
|
|
|
|
9064
|
|
|
12
|
|
|
|
|
|
|
|
|
13
|
|
|
|
|
|
|
=pod |
|
14
|
|
|
|
|
|
|
|
|
15
|
|
|
|
|
|
|
=head2 Common Subroutines |
|
16
|
|
|
|
|
|
|
|
|
17
|
|
|
|
|
|
|
=head3 print_version $program_name |
|
18
|
|
|
|
|
|
|
|
|
19
|
|
|
|
|
|
|
Show program name and version and exit |
|
20
|
|
|
|
|
|
|
|
|
21
|
|
|
|
|
|
|
=cut |
|
22
|
|
|
|
|
|
|
|
|
23
|
|
|
|
|
|
|
|
|
24
|
|
|
|
|
|
|
sub print_version($) |
|
25
|
|
|
|
|
|
|
{ |
|
26
|
0
|
|
|
0
|
0
|
0
|
my $program = shift; |
|
27
|
0
|
|
|
|
|
0
|
say "${program}, version $Bio::BPWrapper::VERSION"; |
|
28
|
0
|
|
|
|
|
0
|
exit; |
|
29
|
|
|
|
|
|
|
} |
|
30
|
|
|
|
|
|
|
|
|
31
|
63
|
|
|
63
|
|
456
|
use Pod::Usage; |
|
|
63
|
|
|
|
|
278
|
|
|
|
63
|
|
|
|
|
14697
|
|
|
32
|
|
|
|
|
|
|
|
|
33
|
|
|
|
|
|
|
=head3 common_opts $opts |
|
34
|
|
|
|
|
|
|
|
|
35
|
|
|
|
|
|
|
Handle some common options: |
|
36
|
|
|
|
|
|
|
|
|
37
|
|
|
|
|
|
|
=over 4 |
|
38
|
|
|
|
|
|
|
|
|
39
|
|
|
|
|
|
|
=item C<--help>, C<-h> |
|
40
|
|
|
|
|
|
|
|
|
41
|
|
|
|
|
|
|
Show usage help |
|
42
|
|
|
|
|
|
|
|
|
43
|
|
|
|
|
|
|
=item C<--man> |
|
44
|
|
|
|
|
|
|
|
|
45
|
|
|
|
|
|
|
Show a manual page via L |
|
46
|
|
|
|
|
|
|
|
|
47
|
|
|
|
|
|
|
=back |
|
48
|
|
|
|
|
|
|
|
|
49
|
|
|
|
|
|
|
=cut |
|
50
|
|
|
|
|
|
|
|
|
51
|
|
|
|
|
|
|
sub common_opts($) |
|
52
|
|
|
|
|
|
|
{ |
|
53
|
63
|
|
|
63
|
0
|
139
|
my $opts = shift; |
|
54
|
63
|
50
|
|
|
|
257
|
pod2usage(1) if $opts->{"help"}; |
|
55
|
63
|
50
|
|
|
|
297
|
pod2usage(-exitstatus => 0, -verbose => 2) if $opts->{"man"}; |
|
56
|
|
|
|
|
|
|
} |
|
57
|
|
|
|
|
|
|
|
|
58
|
|
|
|
|
|
|
|
|
59
|
|
|
|
|
|
|
unless (caller) { |
|
60
|
|
|
|
|
|
|
print "Pssst... this is a module. Invoke via bioaln, bioseq, biopop, or biotree.\n"; |
|
61
|
|
|
|
|
|
|
} |
|
62
|
|
|
|
|
|
|
1; |