Mercurial > repos > peterjc > seq_filter_by_id

annotate tools/seq_filter_by_id/README.rst @ 8:2d4537dbf0bc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.2.6 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
author peterjc
date Wed, 10 May 2017 13:18:01 -0400
parents fb1313d79396
children 141612f8c3e3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
1 Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
2 =========================================================
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
3
8
2d4537dbf0bc v0.2.6 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
peterjc
parents: 7
diff changeset
4 This tool is copyright 2010-2017 by Peter Cock, The James Hutton Institute
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
6 See the licence text below.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
7
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
8 This tool is a short Python script (using both Biopython library functions)
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
9 which divides a FASTA, FASTQ, or SFF file in two, those sequences with or
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
10 without an ID present in the specified column(s) of a tabular file. Example
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
11 uses include filtering based on search results from a tool like NCBI BLAST
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
12 before assembly.
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
13
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
14 This tool is available from the Galaxy Tool Shed at:
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
15
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
16 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
17
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
18 See also sister tools:
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
19
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
20 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
21 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
23
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
24
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
25 Automated Installation
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
26 ======================
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
27
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
28 This should be straightforward using the Galaxy Tool Shed, which should be
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
29 able to automatically install the dependency on Biopython, and then install
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
30 this tool and run its unit tests.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
31
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
32
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
33 Manual Installation
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
34 ===================
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
35
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
36 There are just two files to install to use this tool from within Galaxy:
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
37
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
38 * ``seq_filter_by_id.py`` (the Python script)
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
39 * ``seq_filter_by_id.xml`` (the Galaxy tool definition)
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
40
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
41 The suggested location is a dedicated ``tools/seq_filter_by_id`` folder.
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
42
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
43 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
44 tool. One suggested location is in the filters section. Simply add the line::
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
45
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
46 <tool file="seq_filter_by_id/seq_filter_by_id.xml" />
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
47
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
48 If you wish to run the unit tests, also move/copy the ``test-data/`` files
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
49 under Galaxy's ``test-data/`` folder. Then::
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
50
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
51 $ ./run_tests.sh -id seq_filter_by_id
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
52
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
53 You will also need to install Biopython 1.54 or later. That's it.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
54
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
55
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
56 History
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
57 =======
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
58
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
59 ======= ======================================================================
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
60 Version Changes
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
61 ------- ----------------------------------------------------------------------
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
62 v0.0.1 - Initial version, combining three separate scripts for each file format.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
63 v0.0.4 - Record script version when run from Galaxy.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
64 - Faster FASTA code which preserves the original line wrapping.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
65 - Basic unit test included.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
66 v0.0.5 - Check for errors using Python script's return code.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
67 - Cope with malformed FASTA entries without an identifier.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
68 v0.0.6 - Link to Tool Shed added to help text and this documentation.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
69 - Automated installation of the Biopython dependency.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
70 - Use reStructuredText for this README file.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
71 - Adopt standard MIT License.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
72 - Updated citation information (Cock et al. 2013).
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
73 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
74 - Renamed folder and adopted README.rst naming.
4
1c36cf8ef133 Uploaded v0.0.7 fixed dependency on Biopython 1.62
peterjc
parents: 3
diff changeset
75 v0.0.7 - Correct automated dependency definition.
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
76 v0.0.8 - Simplified XML to apply input format to output data.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
77 v0.2.0 - Can supply ID list as a text parameter (instead of in a file)
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
78 - Using ``optparse`` for the Python command line API.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
79 - Advanced option to ignore paired read suffices.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
80 - Updated dependencies to use Biopython 1.64.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
81 v0.2.1 - Use Biopython instead of Galaxy for FASTQ handling.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
82 - Tool definition now embeds citation information.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
83 - Include input dataset name in output dataset names.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
84 - If white space is found in the requested tabular field then only
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
85 the first word is used as the identifier (with a warning to stderr).
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
86 v0.2.2 - Use the ``format_source=...`` tag.
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
87 - Reorder XML elements (internal change only).
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
88 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
6
03e134cae41a v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
peterjc
parents: 5
diff changeset
89 v0.2.3 - Ignore blank lines in ID file (contributed by Gildas Le Corguillé).
03e134cae41a v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
peterjc
parents: 5
diff changeset
90 - Defensive quoting of filenames etc in the command definition
03e134cae41a v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
peterjc
parents: 5
diff changeset
91 (internal change only).
7
fb1313d79396 Uploaded v0.2.5, ignore blank names in tabular files (based on contribution from Gildas Le Corguille)
peterjc
parents: 6
diff changeset
92 v0.2.4 - Corrected error message wording.
fb1313d79396 Uploaded v0.2.5, ignore blank names in tabular files (based on contribution from Gildas Le Corguille)
peterjc
parents: 6
diff changeset
93 v0.2.5 - Ignore empty names, common in R output (Gildas Le Corguillé).
8
2d4537dbf0bc v0.2.6 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
peterjc
parents: 7
diff changeset
94 v0.2.6 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
95 ======= ======================================================================
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
96
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
97
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
98 Developers
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
99 ==========
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
100
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
101 This script and related tools were initially developed on the following hg branches:
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
102 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
103 http://bitbucket.org/peterjc/galaxy-central/src/tools
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
104
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
105 Development has now moved to a dedicated GitHub repository:
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
106 https://github.com/peterjc/pico_galaxy/tree/master/tools
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
107
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
108 For pushing a release to the test or main "Galaxy Tool Shed", use the following
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
109 Planemo commands (which requires you have set your Tool Shed access details in
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
110 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
111
6
03e134cae41a v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
peterjc
parents: 5
diff changeset
112 $ planemo shed_update -t testtoolshed --check_diff tools/seq_filter_by_id/ -m "New release"
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
113 ...
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
114
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
115 or::
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
116
6
03e134cae41a v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
peterjc
parents: 5
diff changeset
117 $ planemo shed_update -t toolshed --check_diff tools/seq_filter_by_id/ -m "New release"
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
118 ...
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
119
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
120 To just build and check the tar ball, use::
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
121
6
03e134cae41a v0.2.3, ignore blank lines in ID file (contributed by Gildas Le Corguille)
peterjc
parents: 5
diff changeset
122 $ planemo shed_upload --tar_only tools/seq_filter_by_id/
5
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
123 ...
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
124 $ tar -tzf shed_upload.tar.gz
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
125 test-data/empty_file.dat
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
126 test-data/k12_hypothetical.fasta
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
127 test-data/k12_hypothetical.tabular
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
128 test-data/k12_hypothetical_alt.tabular
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
129 test-data/k12_ten_proteins.fasta
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
130 test-data/sanger-pairs-mixed.fastq
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
131 test-data/sanger-pairs-names.tabular
832c1fd57852 v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
peterjc
parents: 4
diff changeset
132 test-data/sanger-sample.fastq
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
133 tools/seq_filter_by_id/README.rst
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
134 tools/seq_filter_by_id/seq_filter_by_id.py
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
135 tools/seq_filter_by_id/seq_filter_by_id.xml
4
1c36cf8ef133 Uploaded v0.0.7 fixed dependency on Biopython 1.62
peterjc
parents: 3
diff changeset
136 tools/seq_filter_by_id/tool_dependencies.xml
3
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
137
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
138
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
139 Licence (MIT)
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
140 =============
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
141
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
142 Permission is hereby granted, free of charge, to any person obtaining a copy
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
143 of this software and associated documentation files (the "Software"), to deal
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
144 in the Software without restriction, including without limitation the rights
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
145 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
146 copies of the Software, and to permit persons to whom the Software is
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
147 furnished to do so, subject to the following conditions:
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
148
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
149 The above copyright notice and this permission notice shall be included in
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
150 all copies or substantial portions of the Software.
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
151
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
152 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
153 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
154 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
155 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
156 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
157 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
44ab4c0f7683 Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
peterjc
parents:
diff changeset
158 THE SOFTWARE.