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1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
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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 the Galaxy library functions and
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9 Biopython). There are just two files to install:
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10
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11 * seq_primer_clip.py (the Python script)
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12 * seq_primer_clip.xml (the Galaxy tool definition)
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13
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14 The suggested location is a new tools/primers folder. You will also need to
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15 modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
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16 this to tools_conf.xml.sample in order to run the tests:
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17
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18 <tool file="primers/seq_primer_clip.xml" />
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19
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20 There are optionally some example files required to run the functional tests,
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21 put these in the test-data/primers folder.
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22
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23 test-data/primers/dop_primers.fasta
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24 test-data/primers/MID4_GLZRM4E04_rnd30.fasta
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25 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
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26 test-data/primers/MID4_GLZRM4E04_rnd30.sff
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27 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
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28 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
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29 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
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30
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31 You should then be able to run the tests with:
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32
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33 sh run_functional_tests.sh -id seq_primer_clip
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34
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35 You will also need to install Biopython 1.54 or later. That's it.
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36
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37
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38 History
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39 =======
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40
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41 v0.0.1 - Initial version (not publicly released)
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42 v0.0.2 - Sort primers by length (longest and therefore most specific first)
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43 v0.0.3 - Consider missing bases at start/end of read as mismatches
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44 v0.0.4 - Apply minimum length to sequences with no match too
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45 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes
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46 v0.0.6 - Added some functional tests
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47 v0.0.7 - Added error check for bad filename arguments
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48 v0.0.8 - Record version of Python script when run from Galaxy.
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49 - Check for errors using Python script's return code.
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50
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51
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52 Developers
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53 ==========
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54
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55 This script and related tools are being developed on the following hg branch:
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56 http://bitbucket.org/peterjc/galaxy-central/src/tools
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57
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58 This incorporates the previously used hg branch:
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59 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
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60
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61 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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62 the following command from the Galaxy root folder:
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63
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64 $ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/*
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65
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66 Check this worked:
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67
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68 $ tar -tzf seq_primer_clip.tar.gz
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69 tools/primers/seq_primer_clip.py
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70 tools/primers/seq_primer_clip.txt
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71 tools/primers/seq_primer_clip.xml
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72 test-data/primers/dop_primers.fasta
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73 test-data/primers/MID4_GLZRM4E04_rnd30.fasta
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74 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
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75 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
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76 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
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77 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
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78 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta
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79 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
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80 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff
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81 test-data/primers/MID4_GLZRM4E04_rnd30.sff
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82
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83
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84 Licence (MIT/BSD style)
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85 =======================
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86
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87 Permission to use, copy, modify, and distribute this software and its
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88 documentation with or without modifications and for any purpose and
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89 without fee is hereby granted, provided that any copyright notices
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90 appear in all copies and that both those copyright notices and this
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91 permission notice appear in supporting documentation, and that the
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92 names of the contributors or copyright holders not be used in
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93 advertising or publicity pertaining to distribution of the software
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94 without specific prior permission.
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95
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96 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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97 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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98 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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99 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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100 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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101 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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102 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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103 OR PERFORMANCE OF THIS SOFTWARE.
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