thapbi-pict 0.2.4

THAPBI Phytophthora ITS1 Classifier Tool (PICT).

THAPBI Phytophthora ITS1 Classifier Tool (PICT)

THAPBI PICT an ITS1-based diagnostic/profiling tool from the UK BBSRC funded Tree Health and Plant Biosecurity Initiative (THAPBI) Phyto-Threats project, focused on identifying Phytophthora species present in Illumina sequenced environmental samples.

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 software repository 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

We recommend installing this tool on Linux using the Conda packaging system, via the BioConda channel, which will handle all the dependencies:

$ conda install thapbi_pict

The same should work on macOS, but the command line dependencies likely rule out using Windows directly.

Alternatively, 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.

On Debian (with the efforts of DebianMed), or Ubuntu Linux, try:

$ sudo apt-get install ncbi-blast+ cutadapt hmmer swarm trimmomatic

If you want to install the very latest unreleased code, you must download the source code from GitHub - see the CONTRIBUTING.md file for more details.

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
v0.2.4	2019-06-21	Synthetic controls in DB, fixed 3 Hyaloperonospora also in Peronospora.
v0.2.3	2019-06-18	Sample count rather than total read abundance for node size in edit-graph.
v0.2.2	2019-06-12	New edit-graph command for use with Cytoscape etc, or PDF via GraphViz.
v0.2.1	2019-05-27	Cope better with multiple (short) ITS1 fragments during classification.
v0.2.0	2019-05-14	Limit ITS1 length, 100 to 250bp. Exclude uncultured NCBI entries from DB.
v0.1.12	2019-05-09	Sort read-summary output by species. Set coloring group at command line.
v0.1.11	2019-05-06	Excel output from read-summary with formatting applied.
v0.1.10	2019-05-03	Tweaking command line API, renamed plate-summary to read-summary.
v0.1.9	2019-05-02	Implemented pipeline subcommand (prepare reads, classify, and report).
v0.1.8	2019-05-01	Standard errors for missing external tools; versions logged in verbose mode.
v0.1.7	2019-05-01	Changed default classifier method from 'identity' to more lienient 'onebp'.
v0.1.6	2019-04-30	Include ready to use binary ITS1 database in source tar-ball & wheel files.
v0.1.5	2019-04-29	Reworked optional metadata integration and its display in summary reports.
v0.1.4	2019-04-25	Sort samples using the optional metadata fields requested in reports.
v0.1.3	2019-04-24	Can optionally display sample metadata from TSV file in summary reports.
v0.1.2	2019-04-17	Keep searching if onebp classifier perfect match is at genus-level only.
v0.1.1	2019-04-16	Expand default taxonomy and database from Peronosporaceae to Peronosporales.
v0.1.0	2019-04-04	Include a bundled ITS1 database.
v0.0.15	2019-04-03	Support for genus-level only entries in the database.
v0.0.14	2019-04-01	MD5 in dump output. Fixed importing sequences failing taxonomic validation.
v0.0.13	2019-03-22	Remove conserved 32bp when primer trim. Assess at sample level by default.
v0.0.12	2019-03-11	Fixed bug in swarmid classifier.
v0.0.11	2019-03-08	Speed up FASTQ preparation by using flash instead of pear v0.9.6.
v0.0.10	2019-03-06	Replace primer code allowing only 1bp differences with cutadapt.
v0.0.9	2019-03-05	Looks for expected primers, discards mismatches. Caches HMM files locally.
v0.0.8	2019-02-21	Fix multi-class TN under-counting. New loss metric, swarmid classifier.
v0.0.7	2019-02-12	Added plate-summary command, onebp classifier.
v0.0.6	2019-02-07	Misc. cleanup and import fixes.
v0.0.5	2019-02-06	Hamming Loss in assessement output.
v0.0.4	2019-01-24	Added seq-import command, blast classifier, multi-taxon predictions.
v0.0.3	2019-01-22	Simplified generated filenames.
v0.0.2	2019-01-21	Added assess command.
v0.0.1	2019-01-17	Initial framework with identity and swarm classifiers.

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, and release process.