Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/README.rst @ 4:d8d9a9069586 draft
v0.1.11 using BLAST+ 2.5.0 and Biopython 1.67
author | peterjc |
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date | Wed, 19 Apr 2017 07:44:47 -0400 |
parents | 9ba8ebb636f4 |
children | 8f4500f6f2aa |
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1 | 1 Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper |
2 ========================================================== | |
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3 |
4 | 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 to run reciprocal BLAST searches on a |
1 | 9 pair of sequence files, and extract the reciprocal best hits. The script |
10 ``blast_rbh.py`` can be used directly (without Galaxy) as long as NCBI | |
11 BLAST+ is installed. | |
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1 | 13 It comes with an optional Galaxy tool definition file ``blast_rbh.xml`` |
14 allowing the Python script to be run from within Galaxy. It is available | |
15 from the Galaxy Tool Shed at: | |
16 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh | |
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17 |
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18 |
2 | 19 Citation |
20 ======== | |
21 | |
22 Please cite the following paper: | |
23 | |
24 NCBI BLAST+ integrated into Galaxy. | |
25 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo | |
26 *GigaScience* 2015, 4:39 | |
27 DOI: http://dx.doi.org/10.1186/s13742-015-0080-7 | |
28 | |
29 You should also cite the NCBI BLAST+ tools: | |
30 | |
31 BLAST+: architecture and applications. | |
32 C. Camacho et al. *BMC Bioinformatics* 2009, 10:421. | |
33 DOI: http://dx.doi.org/10.1186/1471-2105-10-421 | |
34 | |
35 | |
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36 Automated Installation |
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37 ====================== |
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38 |
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39 Installation via the Galaxy Tool Shed should take care of the Galaxy side of |
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40 things, including the dependency the NCBI BLAST+ binaries. |
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41 |
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42 |
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43 Manual Installation |
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44 =================== |
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45 |
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46 There are just two files to install: |
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47 |
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48 - ``blast_rbh.py`` (the Python script) |
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49 - ``blast_rbh.xml`` (the Galaxy tool definition) |
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50 |
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51 The suggested location is in a ``tools/blast_rbh/`` folder. You will then |
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52 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool |
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53 by adding the line:: |
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54 |
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55 <tool file="blast_rbh/blast_rbh.xml" /> |
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56 |
1 | 57 If you want to run the functional tests, copy the sample test files under |
58 sample test files under Galaxy's ``test-data/`` directory. Then:: | |
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59 |
1 | 60 ./run_tests.sh -id blast_reciprocal_best_hits |
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61 |
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62 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``. |
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63 |
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64 |
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65 History |
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66 ======= |
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67 |
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68 ======= ====================================================================== |
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69 Version Changes |
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70 ------- ---------------------------------------------------------------------- |
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71 v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29 |
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72 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates. |
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73 v0.1.2 - Using optparse for command line API. |
1 | 74 - Tool definition now embeds citation information. |
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75 - Fixed Tool Shed dependency definition. |
1 | 76 v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency). |
77 - Avoid extra database and BLAST search in self-comparison mode. | |
78 v0.1.4 - Check for duplicate FASTA identifiers (workaround for makeblastdb | |
79 not treating this as an error, leading to confusing RBH output). | |
80 v0.1.5 - Clarify documentation for using the Python script outside Galaxy. | |
81 - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install. | |
2 | 82 v0.1.6 - Offer the new blastp-fast task added in BLAST+ 2.2.30. |
83 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. | |
84 v0.1.7 - Reorder XML elements (internal change only). | |
85 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
86 - Updated citation information with GigaScience paper. | |
4 | 87 v0.1.8 - Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install. |
88 v0.1.9 - Updates to the command line API for the Python script. | |
89 - PEP8 style updates to the Python script (internal change only). | |
90 - Fix parameter help text which was not being displayed. | |
91 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. | |
92 - Update Biopython dependency. | |
93 - Tweak Python script to work under Python 2 or Python 3. | |
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94 ======= ====================================================================== |
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95 |
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96 |
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97 Developers |
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98 ========== |
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99 |
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100 This tool is developed on the following GitHub repository: |
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101 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
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102 |
2 | 103 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
104 Planemo commands (which requires you have set your Tool Shed access details in | |
105 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
106 | |
4 | 107 $ planemo shed_update -t testtoolshed --check_diff tools/blast_rbh/ |
2 | 108 ... |
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109 |
2 | 110 or:: |
111 | |
4 | 112 $ planemo shed_update -t toolshed --check_diff tools/blast_rbh/ |
2 | 113 ... |
114 | |
115 To just build and check the tar ball, use:: | |
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116 |
4 | 117 $ planemo shed_upload --tar_only tools/blast_rbh/ |
2 | 118 ... |
119 $ tar -tzf shed_upload.tar.gz | |
120 test-data/four_human_proteins.fasta | |
121 test-data/k12_edited_proteins.fasta | |
122 test-data/k12_ten_proteins.fasta | |
123 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular | |
124 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular | |
125 test-data/rbh_blastp_k12.tabular | |
126 test-data/rbh_blastp_k12_self.tabular | |
127 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular | |
128 test-data/rbh_none.tabular | |
129 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular | |
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130 test-data/rhodopsin_nucs.fasta |
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131 test-data/rhodopsin_proteins.fasta |
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132 test-data/three_human_mRNA.fasta |
2 | 133 tools/blast_rbh/README.rst |
134 tools/blast_rbh/blast_rbh.py | |
135 tools/blast_rbh/blast_rbh.xml | |
136 tools/blast_rbh/tool_dependencies.xml | |
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137 |
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138 |
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139 Licence (MIT) |
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140 ============= |
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141 |
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142 Permission is hereby granted, free of charge, to any person obtaining a copy |
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143 of this software and associated documentation files (the "Software"), to deal |
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144 in the Software without restriction, including without limitation the rights |
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145 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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146 copies of the Software, and to permit persons to whom the Software is |
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147 furnished to do so, subject to the following conditions: |
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148 |
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149 The above copyright notice and this permission notice shall be included in |
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150 all copies or substantial portions of the Software. |
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151 |
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152 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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153 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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154 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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155 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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156 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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157 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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158 THE SOFTWARE. |