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0
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1 Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences
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2 =========================================================
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3
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4 This tool is copyright 2011-2017 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 rename
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9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as
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10 two columns of a tabular file. The output order follows that of the sequence file,
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11 and if there are duplicates in the input sequence file, there will be duplicates
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12 in the output sequence file.
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13
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14 This tool is available from the Galaxy Tool Shed,
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15
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16 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_length
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17
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18 See also the sister tools to filter or select sequence files according to IDs
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19 from column(s) of tabular file:
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20
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21 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
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23
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24
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25 Automated Installation
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26 ======================
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27
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28 This should be straightforward using the Galaxy Tool Shed, which should be
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29 able to automatically install the dependency on Biopython, and then install
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30 this tool and run its unit tests.
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31
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32
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33 Manual Installation
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34 ===================
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35
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36 There are just two files to install to use this tool from within Galaxy:
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37
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38 * ``seq_length.py`` (the Python script)
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39 * ``seq_length.xml`` (the Galaxy tool definition)
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40
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41 The suggested location is in a dedicated ``tools/seq_length`` folder.
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42
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43 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
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44 tool. One suggested location is in the filters section. Simply add the line::
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45
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46 <tool file="seq_length/seq_length.xml" />
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47
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48 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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49 under Galaxy's ``test-data/`` folder. Then::
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50
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51 $ ./run_tests.sh -id seq_length
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52
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53 You will also need to install Biopython 1.54 or later. That's it.
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54
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55
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56 History
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57 =======
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58
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59 ======= ======================================================================
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60 Version Changes
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61 ------- ----------------------------------------------------------------------
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62 v0.0.1 - Initial version.
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1
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63 v0.0.2 - Faster for FASTA and FASTQ.
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64 - Fixed typo.
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2
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65 v0.0.3 - Improved command line usage (outside of Galaxy).
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66 - More tests (now covers SFF as well).
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67 - Fix requesting SFF format.
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0
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68 ======= ======================================================================
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69
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70
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71 Developers
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72 ==========
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73
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74 Development is here:
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75
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76 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length
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77
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78 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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79 Planemo commands (which requires you have set your Tool Shed access details in
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80 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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81
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82 $ planemo shed_update -t testtoolshed --check_diff tools/seq_length/
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83 ...
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84
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85 or::
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86
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87 $ planemo shed_update -t toolshed --check_diff tools/seq_length/
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88 ...
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89
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90 To just build and check the tar ball, use::
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91
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92 $ planemo shed_upload --tar_only tools/seq_length/
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93 ...
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94 $ tar -tzf shed_upload.tar.gz
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95 test-data/SRR639755_sample_strict.fastq
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96 test-data/SRR639755_sample_strict.length.tabular
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97 test-data/four_human_proteins.fasta
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98 test-data/four_human_proteins.length.tabular
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99 tools/seq_length/README.rst
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100 tools/seq_length/seq_length.py
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101 tools/seq_length/seq_length.xml
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102 tools/seq_length/tool_dependencies.xml
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103
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104
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105 Licence (MIT)
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106 =============
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107
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108 Permission is hereby granted, free of charge, to any person obtaining a copy
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109 of this software and associated documentation files (the "Software"), to deal
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110 in the Software without restriction, including without limitation the rights
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111 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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112 copies of the Software, and to permit persons to whom the Software is
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113 furnished to do so, subject to the following conditions:
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114
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115 The above copyright notice and this permission notice shall be included in
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116 all copies or substantial portions of the Software.
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117
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118 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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119 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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120 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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121 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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122 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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123 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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124 THE SOFTWARE.
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