thapbi-pict 0.1.6

THAPBI Phytophthora ITS1 Classifier Tool (PICT).

THAPBI Phytophthora ITS1 Classifier Tool (PICT)

Phytophthora (from Greek meaning plant-destroyer) species are economically important plant pathogens, important in both agriculture and forestry. ITS1 is short for Internal Transcribed Spacer one, which is a region of eukaryotes genomes between the 18S and 5.8S rRNA genes. This is commonly used for molecular barcoding, where sequencing this short region can identify species.

This repository is for development of ITS1-based diagnostic/profiling tools for the Tree Health and Plant Biosecurity Initiative (THAPBI) Phyto-Threats project, funded by the UK's BBSRC.

This continues earlier work including:

• https://github.com/widdowquinn/THAPBI
• https://github.com/widdowquinn/THAPBI-pycits
• https://github.com/peterthorpe5/THAPBI-pycits
• https://github.com/peterthorpe5/public_scripts/tree/master/metapy
• https://github.com/peterthorpe5/public_scripts/tree/master/metapy_tools

Installation

In the near future we intend to release this software as a BioConda package, meaning the follwing command will install it along with all the dependencies:

$ conda install thapbi_pict

Until then, since the software is on the Python Package Index (PyPI), the following command will install it along with its Python dependencies:

$ pip install thapbi_pict

However, in this case you will still need to install various external command line tools like hmmer, and others which are only used for some classifiers (like blast and swarm). If you have BioConda setup, use the following:

$ conda install blast cutadapt flash hmmer swarm trimmomatic

On a typical Linux system most of the tools listed will be available via the default distribution packages, although not always under the same package name.

If you want to install the very latest unreleased code, you should download the source code from GitHub, and decompress it if required. Then load the plain text SQL dump of the default database into SQLite3 by running sqlite3 thapb_pict/ITS1_DB.sqlite < database/ITS1_DB.sql, and next run pip3 install . which should automatically get our Python dependencies.

Once installed, you should be able to run the tool using:

$ thapbi_pict

This should automatically find the installed copy of the Python code. Use thapbi_pict -v to report the version, or thapbi_pict -h for help.

Release History

Version	Date	Notes
v0.0.1	2019-01-17	Initial framework with identity and swarm classifiers.
v0.0.2	2019-01-21	Added assess command.
v0.0.3	2019-01-22	Simplified generated filenames.
v0.0.4	2019-01-24	Added seq-import command, blast classifier, multi-taxon predictions.
v0.0.5	2019-02-06	Hamming Loss in assessement output.
v0.0.6	2019-02-07	Misc. cleanup and import fixes.
v0.0.7	2019-02-12	Added plate-summary command, onebp classifier.
v0.0.8	2019-02-21	Fix multi-class TN under-counting. New loss metric, swarmid classifier.
v0.0.9	2019-03-05	Looks for expected primers, discards mismatches. Caches HMM files locally.
v0.0.10	2019-03-06	Replace primer code allowing only 1bp differences with cutadapt.
v0.0.11	2019-03-08	Speed up FASTQ preparation by using flash instead of pear v0.9.6.
v0.0.12	2019-03-11	Fixed bug in swarmid classifier.
v0.0.13	2019-03-22	Remove conserved 32bp when primer trim. Assess at sample level by default.
v0.0.14	2019-04-01	MD5 in dump output. Fixed importing sequences failing taxonomic validation.
v0.0.15	2019-04-03	Support for genus-level only entries in the database.
v0.1.0	2019-04-04	Include a bundled ITS1 database.
v0.1.1	2019-04-16	Expand default taxonomy and database from Peronosporaceae to Peronosporales.
v0.1.2	2019-04-17	Keep searching if onebp classifier perfect match is at genus-level only.
v0.1.3	2019-04-24	Can optionally display sample metadata from TSV file in summary reports.
v0.1.4	2019-04-25	Sort samples using the optional metadata fields requested in reports.
v0.1.5	2019-04-29	Reworked optional metadata integration and its display in summary reports.
v0.1.6	2019-04-30	Include ready to use binary ITS1 database in source tar-ball & wheel files.

Development Notes

Please see the CONTRIBUTING.md file for details of the development setup including Python style conventions, git pre-commit hook, continuous integration and test coverage.

For a release, start from a clean git checkout (to reduce the chance of bundling any stray local files despite a cautious MANIFEST.in).

rm -rf thapbi_pict/ITS1_DB.sqlite
sqlite3 thapbi_pict/ITS1_DB.sqlite < database/ITS1_DB.sql
chmod a-w thapbi_pict/ITS1_DB.sqlite
python setup.py sdist --formats=gztar
python setup.py bdist_wheel
twine upload dist/thapbi_pict-X.Y.Z.tar.gz dist/thapbi_pict-X.Y.Z-py3-none-any.whl
git tag -vX.Y.Z
git push origin master --tags