| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
|
1
|
|
|
|
|
|
|
package Bio::MUST::Apps::TwoScalp; |
|
2
|
|
|
|
|
|
|
# ABSTRACT: Main class for two-scalp tool |
|
3
|
|
|
|
|
|
|
$Bio::MUST::Apps::TwoScalp::VERSION = '0.231010'; |
|
4
|
1
|
|
|
1
|
|
263349
|
use strict; |
|
|
1
|
|
|
|
|
7
|
|
|
|
1
|
|
|
|
|
28
|
|
|
5
|
1
|
|
|
1
|
|
6
|
use warnings; |
|
|
1
|
|
|
|
|
12
|
|
|
|
1
|
|
|
|
|
32
|
|
|
6
|
|
|
|
|
|
|
|
|
7
|
1
|
|
|
1
|
|
577
|
use Bio::MUST::Apps::SlaveAligner::Local; |
|
|
1
|
|
|
|
|
4767058
|
|
|
|
1
|
|
|
|
|
38
|
|
|
8
|
1
|
|
|
1
|
|
724
|
use Bio::MUST::Apps::TwoScalp::Seq2Seq; |
|
|
1
|
|
|
|
|
8
|
|
|
|
1
|
|
|
|
|
44
|
|
|
9
|
1
|
|
|
1
|
|
691
|
use Bio::MUST::Apps::TwoScalp::Profile2Profile; |
|
|
1
|
|
|
|
|
5
|
|
|
|
1
|
|
|
|
|
47
|
|
|
10
|
1
|
|
|
1
|
|
686
|
use Bio::MUST::Apps::TwoScalp::Seqs2Profile; |
|
|
1
|
|
|
|
|
4
|
|
|
|
1
|
|
|
|
|
43
|
|
|
11
|
1
|
|
|
1
|
|
571
|
use Bio::MUST::Apps::TwoScalp::AlignAll; |
|
|
1
|
|
|
|
|
4
|
|
|
|
1
|
|
|
|
|
53
|
|
|
12
|
|
|
|
|
|
|
|
|
13
|
|
|
|
|
|
|
1; |
|
14
|
|
|
|
|
|
|
|
|
15
|
|
|
|
|
|
|
__END__ |
|
16
|
|
|
|
|
|
|
|
|
17
|
|
|
|
|
|
|
=pod |
|
18
|
|
|
|
|
|
|
|
|
19
|
|
|
|
|
|
|
=head1 NAME |
|
20
|
|
|
|
|
|
|
|
|
21
|
|
|
|
|
|
|
Bio::MUST::Apps::TwoScalp - Main class for two-scalp tool |
|
22
|
|
|
|
|
|
|
|
|
23
|
|
|
|
|
|
|
=head1 VERSION |
|
24
|
|
|
|
|
|
|
|
|
25
|
|
|
|
|
|
|
version 0.231010 |
|
26
|
|
|
|
|
|
|
|
|
27
|
|
|
|
|
|
|
=head1 SYNOPSIS |
|
28
|
|
|
|
|
|
|
|
|
29
|
|
|
|
|
|
|
# get documentation |
|
30
|
|
|
|
|
|
|
$ two-scalp.pl --man |
|
31
|
|
|
|
|
|
|
|
|
32
|
|
|
|
|
|
|
# align unaligned sequences within provided example ALI file |
|
33
|
|
|
|
|
|
|
$ two-scalp.pl test/PTHR22663.ali --out=-ts |
|
34
|
|
|
|
|
|
|
|
|
35
|
|
|
|
|
|
|
=head1 DESCRIPTION |
|
36
|
|
|
|
|
|
|
|
|
37
|
|
|
|
|
|
|
C<two-scapl.pl> is an application to align or re-align sequences in existing |
|
38
|
|
|
|
|
|
|
multiple sequences alignments (FASTA or ALI file formats). Its main engine is |
|
39
|
|
|
|
|
|
|
BLAST L<https://blast.ncbi.nlm.nih.gov/>. |
|
40
|
|
|
|
|
|
|
|
|
41
|
|
|
|
|
|
|
Note that only alignable regions of the sequences are added to the alignment, |
|
42
|
|
|
|
|
|
|
which may lead to discarding low-conserved regions. Moreover, some sequences |
|
43
|
|
|
|
|
|
|
can generate multiple aligned fragments (BLAST HSPs). If you do not like this |
|
44
|
|
|
|
|
|
|
behavior, C<two-scalp.pl> is not for you! |
|
45
|
|
|
|
|
|
|
|
|
46
|
|
|
|
|
|
|
=head1 AUTHOR |
|
47
|
|
|
|
|
|
|
|
|
48
|
|
|
|
|
|
|
Denis BAURAIN <denis.baurain@uliege.be> |
|
49
|
|
|
|
|
|
|
|
|
50
|
|
|
|
|
|
|
=head1 COPYRIGHT AND LICENSE |
|
51
|
|
|
|
|
|
|
|
|
52
|
|
|
|
|
|
|
This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN. |
|
53
|
|
|
|
|
|
|
|
|
54
|
|
|
|
|
|
|
This is free software; you can redistribute it and/or modify it under |
|
55
|
|
|
|
|
|
|
the same terms as the Perl 5 programming language system itself. |
|
56
|
|
|
|
|
|
|
|
|
57
|
|
|
|
|
|
|
=cut |