|
4
|
1 Galaxy tool to back-translate a protein alignment to nucleotides
|
|
|
2 ================================================================
|
|
|
3
|
|
|
4 This tool is copyright 2012-2015 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 The underlying Python script can also be used outside of Galaxy, for
|
|
|
18 details run::
|
|
|
19
|
|
|
20 $ python align_back_trans.py
|
|
|
21
|
|
|
22 Automated Installation
|
|
|
23 ======================
|
|
|
24
|
|
|
25 This should be straightforward using the Galaxy Tool Shed, which should be
|
|
|
26 able to automatically install the dependency on Biopython, and then install
|
|
|
27 this tool and run its unit tests.
|
|
|
28
|
|
|
29
|
|
|
30 Manual Installation
|
|
|
31 ===================
|
|
|
32
|
|
|
33 There are just two files to install to use this tool from within Galaxy:
|
|
|
34
|
|
|
35 * ``align_back_trans.py`` (the Python script)
|
|
|
36 * ``align_back_trans.xml`` (the Galaxy tool definition)
|
|
|
37
|
|
|
38 The suggested location is in a dedicated ``tools/align_back_trans`` folder.
|
|
|
39
|
|
|
40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
|
|
|
41 the tool. One suggested location is in the multiple alignments section. Simply
|
|
|
42 add the line::
|
|
|
43
|
|
|
44 <tool file="align_back_trans/align_back_trans.xml" />
|
|
|
45
|
|
|
46 You will also need to install Biopython 1.62 or later.
|
|
|
47
|
|
|
48 If you wish to run the unit tests, also move/copy the ``test-data/`` files
|
|
|
49 under Galaxy's ``test-data/`` folder. Then::
|
|
|
50
|
|
|
51 ./run_tests.sh -id align_back_trans
|
|
|
52
|
|
|
53 That's it.
|
|
|
54
|
|
|
55
|
|
|
56 History
|
|
|
57 =======
|
|
|
58
|
|
|
59 ======= ======================================================================
|
|
|
60 Version Changes
|
|
|
61 ------- ----------------------------------------------------------------------
|
|
|
62 v0.0.1 - Initial version, based on a previously written Python script
|
|
|
63 v0.0.2 - Optionally check the translation is consistent
|
|
|
64 v0.0.3 - First official release
|
|
|
65 v0.0.4 - Simplified XML to apply input format to output data.
|
|
|
66 - Fixed error message when sequence length not a multiple of three.
|
|
|
67 v0.0.5 - More explicit error messages when seqences lengths do not match.
|
|
|
68 - Tool definition now embeds citation information.
|
|
|
69 v0.0.6 - Reorder XML elements (internal change only).
|
|
|
70 - Use ``format_source=...`` tag.
|
|
|
71 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
|
|
|
72 ======= ======================================================================
|
|
|
73
|
|
|
74
|
|
|
75 Developers
|
|
|
76 ==========
|
|
|
77
|
|
|
78 This script was initially developed on this repository:
|
|
|
79 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
|
|
|
80
|
|
|
81 With the addition of a Galaxy wrapper, developement moved here:
|
|
|
82 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
|
|
|
83
|
|
|
84 For pushing a release to the test or main "Galaxy Tool Shed", use the following
|
|
|
85 Planemo commands (which requires you have set your Tool Shed access details in
|
|
|
86 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
|
|
|
87
|
|
|
88 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
|
|
|
89 ...
|
|
|
90
|
|
|
91 or::
|
|
|
92
|
|
|
93 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
|
|
|
94 ...
|
|
|
95
|
|
|
96 To just build and check the tar ball, use::
|
|
|
97
|
|
|
98 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/
|
|
|
99 ...
|
|
|
100 $ tar -tzf shed_upload.tar.gz
|
|
|
101 test-data/demo_nucs.fasta
|
|
|
102 test-data/demo_nucs_trailing_stop.fasta
|
|
|
103 test-data/demo_prot_align.fasta
|
|
|
104 test-data/demo_nuc_align.fasta
|
|
|
105 tools/align_back_trans/README.rst
|
|
|
106 tools/align_back_trans/align_back_trans.py
|
|
|
107 tools/align_back_trans/align_back_trans.xml
|
|
|
108 tools/align_back_trans/tool_dependencies.xml
|
|
|
109
|
|
|
110
|
|
|
111 Licence (MIT)
|
|
|
112 =============
|
|
|
113
|
|
|
114 Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
|
115 of this software and associated documentation files (the "Software"), to deal
|
|
|
116 in the Software without restriction, including without limitation the rights
|
|
|
117 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
|
118 copies of the Software, and to permit persons to whom the Software is
|
|
|
119 furnished to do so, subject to the following conditions:
|
|
|
120
|
|
|
121 The above copyright notice and this permission notice shall be included in
|
|
|
122 all copies or substantial portions of the Software.
|
|
|
123
|
|
|
124 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
|
125 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
|
126 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
|
127 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
|
128 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
|
129 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
|
|
130 THE SOFTWARE.
|
