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Uploaded v0.0.3, first stable release.
author peterjc
date Thu, 06 Mar 2014 08:58:13 -0500
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1 Galaxy tool to back-translate a protein alignment to nucleotides
2 ================================================================
3
4 This tool is copyright 2012-2014 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence).
7
8 This tool is a short Python script (using Biopython library functions) to
9 load a protein alignment, and matching nucleotide FASTA file of unaligned
10 sequences, which are threaded onto the protein alignment in order to produce
11 a codon aware nucleotide alignment - which can be viewed as a back translation.
12
13 This tool is available from the Galaxy Tool Shed at:
14
15 * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
16
17
18 Automated Installation
19 ======================
20
21 This should be straightforward using the Galaxy Tool Shed, which should be
22 able to automatically install the dependency on Biopython, and then install
23 this tool and run its unit tests.
24
25
26 Manual Installation
27 ===================
28
29 There are just two files to install to use this tool from within Galaxy:
30
31 * ``align_back_trans.py`` (the Python script)
32 * ``align_back_trans.xml`` (the Galaxy tool definition)
33
34 The suggested location is in a dedicated ``tools/align_back_trans`` folder.
35
36 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
37 the tool. One suggested location is in the multiple alignments section. Simply
38 add the line::
39
40 <tool file="align_back_trans/align_back_trans.xml" />
41
42 You will also need to install Biopython 1.62 or later. If you want to run
43 the unit tests, include this line in ``tools_conf.xml.sample`` and the sample
44 FASTA files under the ``test-data`` directory. Then::
45
46 ./run_functional_tests.sh -id align_back_trans
47
48 That's it.
49
50
51 History
52 =======
53
54 ======= ======================================================================
55 Version Changes
56 ------- ----------------------------------------------------------------------
57 v0.0.1 - Initial version, based on a previously written Python script
58 v0.0.2 - Optionally check the translation is consistent
59 ======= ======================================================================
60
61
62 Developers
63 ==========
64
65 This script was initially developed on this repository:
66 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
67
68 With the addition of a Galaxy wrapper, developement moved here:
69 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
70
71 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
72 the following command from the Galaxy root folder::
73
74 $ tar -czf align_back_trans.tar.gz tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml test-data/demo_nucs.fasta test-data/demo_nucs_trailing_stop.fasta test-data/demo_prot_align.fasta test-data/demo_nuc_align.fasta
75
76 Check this worked::
77
78 $ tar -tzf align_back_trans.tar.gz
79 tools/align_back_trans/README.rst
80 tools/align_back_trans/align_back_trans.py
81 tools/align_back_trans/align_back_trans.xml
82 tools/align_back_trans/tool_dependencies.xml
83 test-data/demo_nucs.fasta
84 test-data/demo_nucs_trailing_stop.fasta
85 test-data/demo_prot_align.fasta
86 test-data/demo_nuc_align.fasta
87
88
89 Licence (MIT)
90 =============
91
92 Permission is hereby granted, free of charge, to any person obtaining a copy
93 of this software and associated documentation files (the "Software"), to deal
94 in the Software without restriction, including without limitation the rights
95 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
96 copies of the Software, and to permit persons to whom the Software is
97 furnished to do so, subject to the following conditions:
98
99 The above copyright notice and this permission notice shall be included in
100 all copies or substantial portions of the Software.
101
102 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
103 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
104 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
105 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
106 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
107 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
108 THE SOFTWARE.