Mercurial > repos > peterjc > seq_select_by_id
annotate tools/seq_select_by_id/README.rst @ 5:1a83f5ab9e95 draft
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author | peterjc |
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date | Thu, 21 Nov 2013 04:54:59 -0500 |
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4
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1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID |
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2 =============================================================== |
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3 |
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4 This tool is copyright 2011-2013 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. |
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7 |
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8 This tool is a short Python script (using Biopython library functions) to extract |
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9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given |
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10 by a column of a tabular file. The output order follows that of the tabular file, |
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11 and if there are duplicates in the tabular file, there will be duplicates in the |
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12 output sequence file. |
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13 |
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14 This tool is available from the Galaxy Tool Shed at: |
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15 |
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16 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id |
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17 |
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18 See also the sister tools to filter sequence files according to IDs from column(s) |
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19 of a tabular file (where the output order follows the sequence file, and any |
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20 duplicate IDs are ignored) and rename sequences: |
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21 |
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22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id |
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23 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename |
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24 |
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25 |
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26 Automated Installation |
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27 ====================== |
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28 |
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29 This should be straightforward using the Galaxy Tool Shed, which should be |
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30 able to automatically install the dependency on Biopython, and then install |
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31 this tool and run its unit tests. |
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32 |
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33 |
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34 Manual Installation |
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35 =================== |
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36 |
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37 There are just two files to install to use this tool from within Galaxy: |
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38 |
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39 * seq_select_by_id.py (the Python script) |
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40 * seq_select_by_id.xml (the Galaxy tool definition) |
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41 |
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42 The suggested location is a dedicated tools/seq_select_by_id folder. |
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43 |
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44 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the |
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45 tool. One suggested location is in the filters section. Simply add the line:: |
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46 |
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47 <tool file="seq_select_by_id/seq_select_by_id.xml" /> |
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48 |
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49 If you wish to run the unit tests, also add this to tools_conf.xml.sample |
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50 and move/copy the test-data files under Galaxy's test-data folder. Then:: |
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51 |
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52 $ ./run_functional_tests.sh -id seq_select_by_id |
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53 |
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54 You will also need to install Biopython 1.54 or later. That's it. |
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55 |
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56 |
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57 History |
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58 ======= |
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59 |
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60 ======= ====================================================================== |
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61 Version Changes |
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62 ------- ---------------------------------------------------------------------- |
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63 v0.0.1 - Initial version. |
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64 v0.0.3 - Ignore blank lines in input. |
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65 v0.0.4 - Record script version when run from Galaxy. |
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66 - Basic unit test included. |
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67 v0.0.5 - Check for errors using Python script's return code. |
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68 v0.0.6 - Link to Tool Shed added to help text and this documentation. |
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69 - Automatic installation of Biopython dependency. |
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70 - Use reStructuredText for this README file. |
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71 - Adopt standard MIT License. |
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72 v0.0.7 - Updated citation information (Cock et al. 2013). |
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73 - Fixed Biopython dependency setup. |
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74 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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75 - Renamed folder and adopted README.rst naming. |
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76 v0.0.8 - Corrected automated dependency definition |
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77 ======= ====================================================================== |
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78 |
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79 |
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80 Developers |
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81 ========== |
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82 |
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83 This script and related tools were initially developed on the following hg branch: |
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84 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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85 |
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86 Development has now moved to a dedicated GitHub repository: |
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87 https://github.com/peterjc/pico_galaxy/tree/master/tools |
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88 |
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89 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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90 the following command from the Galaxy root folder:: |
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91 |
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92 $ tar -czf seq_select_by_id.tar.gz tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.* tools/seq_select_by_id/tool_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular |
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93 |
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94 Check this worked:: |
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95 |
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96 $ tar -tzf seq_select_by_id.tar.gz |
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97 tools/seq_select_by_id/README.rst |
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98 tools/seq_select_by_id/seq_select_by_id.py |
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99 tools/seq_select_by_id/seq_select_by_id.xml |
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100 tools/seq_select_by_id/tool_dependencies.xml |
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101 test-data/k12_ten_proteins.fasta |
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102 test-data/k12_hypothetical.fasta |
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103 test-data/k12_hypothetical.tabular |
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104 |
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105 |
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106 Licence (MIT) |
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107 ============= |
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108 |
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109 Permission is hereby granted, free of charge, to any person obtaining a copy |
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110 of this software and associated documentation files (the "Software"), to deal |
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111 in the Software without restriction, including without limitation the rights |
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112 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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113 copies of the Software, and to permit persons to whom the Software is |
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114 furnished to do so, subject to the following conditions: |
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115 |
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116 The above copyright notice and this permission notice shall be included in |
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117 all copies or substantial portions of the Software. |
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118 |
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119 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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120 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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121 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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122 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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123 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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124 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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125 THE SOFTWARE. |