Mercurial > repos > peterjc > seq_select_by_id
comparison tools/filters/seq_select_by_id.rst @ 3:19e26966ed3e draft
Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
No functional changes.
author | peterjc |
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date | Mon, 29 Jul 2013 09:13:13 -0400 |
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1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID | |
2 =============================================================== | |
3 | |
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 This tool is a short Python script (using Biopython library functions) to extract | |
9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given | |
10 by a column of a tabular file. The output order follows that of the tabular file, | |
11 and if there are duplicates in the tabular file, there will be duplicates in the | |
12 output sequence file. | |
13 | |
14 This tool is available from the Galaxy Tool Shed at: | |
15 | |
16 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id | |
17 | |
18 See also the sister tools to filter sequence files according to IDs from column(s) | |
19 of a tabular file (where the output order follows the sequence file, and any | |
20 duplicate IDs are ignored) and rename sequences: | |
21 | |
22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
23 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename | |
24 | |
25 | |
26 Automated Installation | |
27 ====================== | |
28 | |
29 This should be straightforward using the Galaxy Tool Shed, which should be | |
30 able to automatically install the dependency on Biopython, and then install | |
31 this tool and run its unit tests. | |
32 | |
33 | |
34 Manual Installation | |
35 =================== | |
36 | |
37 There are just two files to install to use this tool from within Galaxy: | |
38 | |
39 * seq_select_by_id.py (the Python script) | |
40 * seq_select_by_id.xml (the Galaxy tool definition) | |
41 | |
42 The suggested location is in the Galaxy folder tools/filters next to the tool | |
43 for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. | |
44 | |
45 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
46 tool. One suggested location is in the filters section. Simply add the line:: | |
47 | |
48 <tool file="filters/seq_select_by_id.xml" /> | |
49 | |
50 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
51 and move/copy the test-data files under Galaxy's test-data folder. Then:: | |
52 | |
53 $ ./run_functional_tests.sh -id seq_select_by_id | |
54 | |
55 You will also need to install Biopython 1.54 or later. That's it. | |
56 | |
57 | |
58 History | |
59 ======= | |
60 | |
61 ======= ====================================================================== | |
62 Version Changes | |
63 ------- ---------------------------------------------------------------------- | |
64 v0.0.1 - Initial version. | |
65 v0.0.3 - Ignore blank lines in input. | |
66 v0.0.4 - Record script version when run from Galaxy. | |
67 - Basic unit test included. | |
68 v0.0.5 - Check for errors using Python script's return code. | |
69 v0.0.6 - Link to Tool Shed added to help text and this documentation. | |
70 - Automatic installation of Biopython dependency. | |
71 - Use reStructuredText for this README file. | |
72 - Adopt standard MIT License. | |
73 ======= ====================================================================== | |
74 | |
75 | |
76 Developers | |
77 ========== | |
78 | |
79 This script and related tools are being developed on the following hg branch: | |
80 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
81 | |
82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
83 the following command from the Galaxy root folder:: | |
84 | |
85 $ tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* tools/filters/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular | |
86 | |
87 Check this worked:: | |
88 | |
89 $ tar -tzf seq_select_by_id.tar.gz | |
90 tools/filters/seq_select_by_id.py | |
91 tools/filters/seq_select_by_id.rst | |
92 tools/filter/seq_select_by_id.xml | |
93 tools/filters/repository_dependencies.xml | |
94 test-data/k12_ten_proteins.fasta | |
95 test-data/k12_hypothetical.fasta | |
96 test-data/k12_hypothetical.tabular | |
97 | |
98 | |
99 Licence (MIT) | |
100 ============= | |
101 | |
102 Permission is hereby granted, free of charge, to any person obtaining a copy | |
103 of this software and associated documentation files (the "Software"), to deal | |
104 in the Software without restriction, including without limitation the rights | |
105 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
106 copies of the Software, and to permit persons to whom the Software is | |
107 furnished to do so, subject to the following conditions: | |
108 | |
109 The above copyright notice and this permission notice shall be included in | |
110 all copies or substantial portions of the Software. | |
111 | |
112 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
113 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
114 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
115 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
116 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
117 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
118 THE SOFTWARE. |