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