| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
|
1
|
|
|
|
|
|
|
# -*-CPerl-*- |
|
2
|
|
|
|
|
|
|
# Last changed Time-stamp: <2015-02-06 16:27:32 mtw> |
|
3
|
|
|
|
|
|
|
|
|
4
|
|
|
|
|
|
|
package Bio::ViennaNGS::Tutorial; |
|
5
|
|
|
|
|
|
|
|
|
6
|
1
|
|
|
1
|
|
1356
|
use Exporter; |
|
|
1
|
|
|
|
|
2
|
|
|
|
1
|
|
|
|
|
49
|
|
|
7
|
1
|
|
|
1
|
|
6
|
use version; our $VERSION = qv('0.12_15'); |
|
|
1
|
|
|
|
|
2
|
|
|
|
1
|
|
|
|
|
7
|
|
|
8
|
1
|
|
|
1
|
|
90
|
use strict; |
|
|
1
|
|
|
|
|
2
|
|
|
|
1
|
|
|
|
|
36
|
|
|
9
|
1
|
|
|
1
|
|
6
|
use warnings; |
|
|
1
|
|
|
|
|
3
|
|
|
|
1
|
|
|
|
|
85
|
|
|
10
|
|
|
|
|
|
|
|
|
11
|
|
|
|
|
|
|
our @ISA = qw(Exporter); |
|
12
|
|
|
|
|
|
|
our @EXPORT = (); |
|
13
|
|
|
|
|
|
|
|
|
14
|
|
|
|
|
|
|
our @EXPORT_OK = qw (); |
|
15
|
|
|
|
|
|
|
|
|
16
|
|
|
|
|
|
|
1; |
|
17
|
|
|
|
|
|
|
__END__ |
|
18
|
|
|
|
|
|
|
|
|
19
|
|
|
|
|
|
|
=head1 NAME |
|
20
|
|
|
|
|
|
|
|
|
21
|
|
|
|
|
|
|
Bio::ViennaNGS::Tutorial - A collection of basic tutorials |
|
22
|
|
|
|
|
|
|
demonstrating of the core components and features of the |
|
23
|
|
|
|
|
|
|
L<Bio::ViennaNGS> suite |
|
24
|
|
|
|
|
|
|
|
|
25
|
|
|
|
|
|
|
=head1 DESCRIPTION |
|
26
|
|
|
|
|
|
|
|
|
27
|
|
|
|
|
|
|
The L<Bio::ViennaNGS> tutorial is a collection of fully documented |
|
28
|
|
|
|
|
|
|
pipeline scripts that have been built as a showcase for the usage of |
|
29
|
|
|
|
|
|
|
the L<Bio::ViennaNGS> distribution with real NGS data. |
|
30
|
|
|
|
|
|
|
|
|
31
|
|
|
|
|
|
|
=head2 DISCLAIMER |
|
32
|
|
|
|
|
|
|
|
|
33
|
|
|
|
|
|
|
Many example pipelines covered here work and depend on fairly large |
|
34
|
|
|
|
|
|
|
real world NGS data sets in the gigabyte scale. Be prepared that each |
|
35
|
|
|
|
|
|
|
tutorial takes a couple of hours of CPU time to finish. When running |
|
36
|
|
|
|
|
|
|
the scripts locally you need to ensure that your system has enough |
|
37
|
|
|
|
|
|
|
hardware resources available. |
|
38
|
|
|
|
|
|
|
|
|
39
|
|
|
|
|
|
|
=head2 DATA DOWNLOAD |
|
40
|
|
|
|
|
|
|
|
|
41
|
|
|
|
|
|
|
All input data required for the individual tutorial pipelines can be |
|
42
|
|
|
|
|
|
|
downloaded from the L<ViennaNGS data |
|
43
|
|
|
|
|
|
|
repository|http://nibiru.tbi.univie.ac.at/ViennaNGS/>. |
|
44
|
|
|
|
|
|
|
|
|
45
|
|
|
|
|
|
|
=head1 TUTORIALS |
|
46
|
|
|
|
|
|
|
|
|
47
|
|
|
|
|
|
|
=over |
|
48
|
|
|
|
|
|
|
|
|
49
|
|
|
|
|
|
|
=item L<Tutorial 00|http://search.cpan.org/dist/Bio-ViennaNGS/scripts/Tutorial_pipeline00.pl>: Inferring detailed mapping statistics from BAM files |
|
50
|
|
|
|
|
|
|
|
|
51
|
|
|
|
|
|
|
=item L<Tutorial 01|http://search.cpan.org/dist/Bio-ViennaNGS/scripts/Tutorial_pipeline01.pl>: Finding sequence motifs in close proximity to gene starts in a set of human protein coding genes |
|
52
|
|
|
|
|
|
|
|
|
53
|
|
|
|
|
|
|
=item L<Tutorial 02|http://search.cpan.org/dist/Bio-ViennaNGS/scripts/Tutorial_pipeline02.pl>: Automatic generation of UCSC genome browser Track Hubs for visualization of ENCODE RNA-seq data |
|
54
|
|
|
|
|
|
|
|
|
55
|
|
|
|
|
|
|
=back |
|
56
|
|
|
|
|
|
|
|
|
57
|
|
|
|
|
|
|
|
|
58
|
|
|
|
|
|
|
=head1 AUTHORS |
|
59
|
|
|
|
|
|
|
|
|
60
|
|
|
|
|
|
|
=over |
|
61
|
|
|
|
|
|
|
|
|
62
|
|
|
|
|
|
|
=item Michael T. Wolfinger E<lt>michael@wolfinger.euE<gt> |
|
63
|
|
|
|
|
|
|
|
|
64
|
|
|
|
|
|
|
=item Joerg Fallmann E<lt>fall@tbi.univie.ac.atE<gt> |
|
65
|
|
|
|
|
|
|
|
|
66
|
|
|
|
|
|
|
=item Florian Eggenhofer E<lt>florian.eggenhofer@tbi.univie.ac.atE<gt> |
|
67
|
|
|
|
|
|
|
|
|
68
|
|
|
|
|
|
|
=item Fabian Amman E<lt>fabian@tbi.univie.ac.at<gt> |
|
69
|
|
|
|
|
|
|
|
|
70
|
|
|
|
|
|
|
=back |
|
71
|
|
|
|
|
|
|
|
|
72
|
|
|
|
|
|
|
=head1 COPYRIGHT AND LICENSE |
|
73
|
|
|
|
|
|
|
|
|
74
|
|
|
|
|
|
|
Copyright (C) 2014-2015 Michael T. Wolfinger |
|
75
|
|
|
|
|
|
|
E<lt>michael@wolfinger.euE<gt> |
|
76
|
|
|
|
|
|
|
|
|
77
|
|
|
|
|
|
|
This library is free software; you can redistribute it and/or modify |
|
78
|
|
|
|
|
|
|
it under the same terms as Perl itself, either Perl version 5.10.0 or, |
|
79
|
|
|
|
|
|
|
at your option, any later version of Perl 5 you may have available. |
|
80
|
|
|
|
|
|
|
|
|
81
|
|
|
|
|
|
|
This software is distributed in the hope that it will be useful, but |
|
82
|
|
|
|
|
|
|
WITHOUT ANY WARRANTY; without even the implied warranty of |
|
83
|
|
|
|
|
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. |
|
84
|
|
|
|
|
|
|
|
|
85
|
|
|
|
|
|
|
=cut |
|
86
|
|
|
|
|
|
|
|
|
87
|
|
|
|
|
|
|
|