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1 Galaxy tool to find ORFs or simple CDSs
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2 =======================================
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3
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4 This tool is copyright 2011 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)
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9 to search nucleotide sequences for open reading frames (ORFs) or coding
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10 sequences (CDSs) where the first potential start codon is used. See the
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11 help text in the XML file for more information.
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12
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13 There are just two files to install:
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14
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15 * get_orfs_or_cdss.py (the Python script)
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16 * get_orfs_or_cdss.xml (the Galaxy tool definition)
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17
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18 The suggested location is in the Galaxy folder tools/filters next to the tool
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19 for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL.
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20
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21 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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22 tool. One suggested location is in the filters section. Simply add the line:
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23
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24 <tool file="filters/get_orfs_or_cdss.xml" />
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25
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26 You will also need to install Biopython 1.54 or later. If you want to run
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27 the unit tests, include this line in tools_conf.xml.sample and the sample
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28 FASTA files under the test-data directory. That's it.
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29
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30
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31 History
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32 =======
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33
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34 v0.0.1 - Initial version.
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35
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36
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37 Developers
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38 ==========
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39
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40 This script and related tools are being developed on the following hg branch:
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41 http://bitbucket.org/peterjc/galaxy-central/src/tools
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42
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43 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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44 the following command from the Galaxy root folder:
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45
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46 tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.*
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47
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48 Check this worked:
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49
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50 $ tar -tzf get_orfs_or_cdss.tar.gz
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51 filter/get_orfs_or_cdss.py
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52 filter/get_orfs_or_cdss.txt
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53 filter/get_orfs_or_cdss.xml
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54
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55
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56 Licence (MIT/BSD style)
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57 =======================
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58
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59 Permission to use, copy, modify, and distribute this software and its
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60 documentation with or without modifications and for any purpose and
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61 without fee is hereby granted, provided that any copyright notices
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62 appear in all copies and that both those copyright notices and this
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63 permission notice appear in supporting documentation, and that the
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64 names of the contributors or copyright holders not be used in
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65 advertising or publicity pertaining to distribution of the software
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66 without specific prior permission.
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67
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68 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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69 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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70 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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71 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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72 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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73 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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74 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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75 OR PERFORMANCE OF THIS SOFTWARE.
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