File Coverage

line	stmt	bran	sub	pod	time	code
1						package App::Sandy::Role::SeqID;
2						# ABSTRACT: Role for seqid standardization
3
4	6		6		4562	use App::Sandy::Base 'role';
	6				12
	6				44
5
6						our $VERSION = '0.24'; # VERSION
7
8						my $SEQID_REGEX = qr/^chr(?=\w+$)/ia;
9						my $MT_REGEX = qr/^MT$/ia;
10
11						sub with_std_seqid {
12	100		100	0	245	my ($self, $seqid) = @_;
13
14	100	50			205	croak "No seqid defined" if not defined $seqid;
15
16	100				505	$seqid =~ s/$SEQID_REGEX//;
17	100				260	$seqid =~ s/$MT_REGEX/M/;
18
19	100				300	return uc $seqid;
20						}
21
22						__END__
23
24						=pod
25
26						=encoding UTF-8
27
28						=head1 NAME
29
30						App::Sandy::Role::SeqID - Role for seqid standardization
31
32						=head1 VERSION
33
34						version 0.24
35
36						=head1 AUTHORS
37
38						=over 4
39
40						=item *
41
42						Thiago L. A. Miller <tmiller@mochsl.org.br>
43
44						=item *
45
46						J. Leonel Buzzo <lbuzzo@mochsl.org.br>
47
48						=item *
49
50						Felipe R. C. dos Santos <fsantos@mochsl.org.br>
51
52						=item *
53
54						Helena B. Conceição <hconceicao@mochsl.org.br>
55
56						=item *
57
58						Rodrigo Barreiro <rbarreiro@mochsl.org.br>
59
60						=item *
61
62						Gabriela Guardia <gguardia@mochsl.org.br>
63
64						=item *
65
66						Fernanda Orpinelli <forpinelli@mochsl.org.br>
67
68						=item *
69
70						Rafael Mercuri <rmercuri@mochsl.org.br>
71
72						=item *
73
74						Rodrigo Barreiro <rbarreiro@mochsl.org.br>
75
76						=item *
77
78						Pedro A. F. Galante <pgalante@mochsl.org.br>
79
80						=back
81
82						=head1 COPYRIGHT AND LICENSE
83
84						This software is Copyright (c) 2023 by Teaching and Research Institute from Sírio-Libanês Hospital.
85
86						This is free software, licensed under:
87
88						The GNU General Public License, Version 3, June 2007
89
90						=cut