Mercurial > repos > peterjc > seq_select_by_id

annotate tools/filters/seq_select_by_id.txt @ 2:28d52478ace9 draft

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Uploaded v0.0.4 which adds a unit test.
author peterjc
date Mon, 15 Apr 2013 12:28:51 -0400
parents 50a8a6917a9c
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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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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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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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14 See also the sister tool to filter sequence files according to IDs from column(s)
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15 of a tabular file, where the output order follows the sequence file, and any
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16 duplicate IDs are ignored.
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17
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18 There are just two files to install:
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20 * seq_select_by_id.py (the Python script)
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21 * seq_select_by_id.xml (the Galaxy tool definition)
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23 The suggested location is in the Galaxy folder tools/filters next to the tool
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24 for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL.
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26 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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27 tool. One suggested location is in the filters section. Simply add the line:
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28
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29 <tool file="filters/seq_select_by_id.xml" />
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31 You will also need to install Biopython 1.54 or later. That's it.
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34 History
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35 =======
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36
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37 v0.0.1 - Initial version.
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38 v0.0.3 - Ignore blank lines in input.
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39 v0.0.4 - Record script version when run from Galaxy.
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40 - Basic unit test included.
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43 Developers
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44 ==========
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45
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46 This script and related tools are being developed on the following hg branch:
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47 http://bitbucket.org/peterjc/galaxy-central/src/tools
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48
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49 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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50 the following command from the Galaxy root folder:
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51
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52 $ tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
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54 Check this worked:
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55
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56 $ tar -tzf seq_select_by_id.tar.gz
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57 filter/seq_select_by_id.py
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58 filter/seq_select_by_id.txt
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59 filter/seq_select_by_id.xml
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60 test-data/k12_ten_proteins.fasta
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61 test-data/k12_hypothetical.fasta
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62 test-data/k12_hypothetical.tabular
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64
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65 Licence (MIT/BSD style)
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66 =======================
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67
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68 Permission to use, copy, modify, and distribute this software and its
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69 documentation with or without modifications and for any purpose and
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70 without fee is hereby granted, provided that any copyright notices
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71 appear in all copies and that both those copyright notices and this
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72 permission notice appear in supporting documentation, and that the
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73 names of the contributors or copyright holders not be used in
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74 advertising or publicity pertaining to distribution of the software
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75 without specific prior permission.
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76
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77 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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78 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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79 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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80 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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81 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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82 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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83 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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84 OR PERFORMANCE OF THIS SOFTWARE.