THAPBI Phytophthora ITS1 Classifier Tool (PICT).

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for peterjc from gravatar.com peterjc

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: Freely Distributable, MIT License
  • Author: Peter Cock
  • Requires: Python >=3.5
Classifiers

Project description

THAPBI PICT on the Python Package Index (PyPI) THAPBI PICT on BioConda THAPBI PICT TravisCI build status THAPBI PICT CircleCI build status Documentation Status Code style: black

THAPBI Phytophthora ITS1 Classifier Tool (PICT)

About

THAPBI PICT is a sequence based diagnostic/profiling tool from the UK 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.

With appropriate primer and HMM settings, and a custom database, THAPBI PICT can be applied to other organisms and/or barcode marker sequences - not just ITS1.

Installation

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

$ conda install thapbi_pict

Sadly 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. See INSTALL.rst for more details, and if you want to modify the software read CONTRIBUTING.rst as well.

Quick Start

Once installed, you should be able to run the tool at the command line 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.

Documentation

The tool documentation is hosted by Read The Docs, generated automatically from the docs/ folder.

Funding

The Phyto-Threats project was supported from 2016 to 2019 under the Tree Health and Plant Biosecurity Initiative (THAPBI), jointly funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Department for Environment, Food and Rural affairs (DEFRA), Economic and Social Research Council (ESRC), Forestry Commission, Natural Environment Research Council (NERC) and Scottish Government.

Background

THAPBI PICT continues earlier work including:

Release History

See the CHANGELOG.rst file (it was getting too long to include here).

Development Notes

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

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for peterjc from gravatar.com peterjc

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: Freely Distributable, MIT License
  • Author: Peter Cock
  • Requires: Python >=3.5
Classifiers

Release history Release notifications | RSS feed

1.0.18

1.0.17

1.0.16

1.0.15

1.0.14

1.0.13

1.0.12

1.0.11

1.0.10

1.0.9

1.0.8

1.0.7

1.0.6

1.0.5

1.0.4

1.0.3

1.0.2

1.0.1

1.0.0

0.14.1

0.14.0

0.13.6

0.13.5

0.13.4

0.13.3

0.13.2

0.13.1

0.13.0

0.12.9

0.12.8

0.12.7

0.12.6

0.12.5

0.12.4

0.12.3

0.12.2

0.12.1

0.12.0

0.11.6

0.11.5

0.11.4

0.11.3

0.11.2

0.11.1

0.11.0

0.10.6

0.10.5

0.10.4

0.10.3

0.10.2

0.10.1

0.10.0

0.9.9

0.9.8

0.9.7

0.9.6

0.9.5

0.9.4

0.9.3

0.9.2

0.9.1

0.9.0

0.8.4

0.8.3

0.8.2

0.8.1

0.8.0

0.7.11

0.7.10

0.7.9

0.7.8

0.7.7

0.7.6

0.7.5

0.7.4

0.7.3

0.7.2

0.7.1

0.7.0

0.6.15

0.6.14

0.6.13

0.6.12

0.6.11

0.6.10

0.6.9

0.6.8

0.6.7

0.6.6

0.6.5

This version

0.6.4

0.6.3

0.6.2

0.6.1

0.6.0

0.5.8

0.5.7

0.5.6

0.5.5

0.5.4

0.5.1

0.5.0

0.4.19

0.4.18

0.4.17

0.4.15

0.4.13

0.4.12

0.4.11

0.4.10

0.4.9

0.4.8

0.4.7

0.4.6

0.4.5

0.4.4

0.4.2

0.4.1

0.4.0

0.3.12

0.3.11

0.3.10

0.3.9

0.3.8

0.3.7

0.3.4

0.3.3

0.3.2

0.3.1

0.3.0

0.2.5

0.2.4

0.2.3

0.2.2

0.2.1

0.2.0

0.1.12

0.1.11

0.1.10

0.1.9

0.1.8

0.1.7

0.1.6

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

thapbi_pict-0.6.4.tar.gz (3.7 MB view details)

Uploaded Source

Built Distributions

thapbi_pict-0.6.4-py3.7.egg (1.3 MB view details)

Uploaded Source

thapbi_pict-0.6.4-py3-none-any.whl (1.2 MB view details)

Uploaded Python 3

File details

Details for the file thapbi_pict-0.6.4.tar.gz.

File metadata

  • Download URL: thapbi_pict-0.6.4.tar.gz
  • Upload date:
  • Size: 3.7 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/45.0.0.post20200113 requests-toolbelt/0.9.1 tqdm/4.41.1 CPython/3.7.6

File hashes

Hashes for thapbi_pict-0.6.4.tar.gz
Algorithm Hash digest
SHA256 f2ad6f0a63bb7e0aae35a6996ba21daff5972779b9f0372b71810da0aa938f1a
MD5 786b1fb9cf905c05641a7dbe84db164b
BLAKE2b-256 62afcf12d65dccee82ac93e701b714d519a480e3d630b930615825c3526fc0f7

See more details on using hashes here.

File details

Details for the file thapbi_pict-0.6.4-py3.7.egg.

File metadata

  • Download URL: thapbi_pict-0.6.4-py3.7.egg
  • Upload date:
  • Size: 1.3 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/45.0.0.post20200113 requests-toolbelt/0.9.1 tqdm/4.41.1 CPython/3.7.6

File hashes

Hashes for thapbi_pict-0.6.4-py3.7.egg
Algorithm Hash digest
SHA256 20641cd7c1da080c6421cd5db77c37ae3673c240fb42d47424101a917b1598e9
MD5 ec2cd8f0c3c9986c6a37aabc01ab54f5
BLAKE2b-256 3ea255e2f2530173d44d4ab0104ccc1ed427d1b96579ad07bfe7d1fd7ee30a38

See more details on using hashes here.

File details

Details for the file thapbi_pict-0.6.4-py3-none-any.whl.

File metadata

  • Download URL: thapbi_pict-0.6.4-py3-none-any.whl
  • Upload date:
  • Size: 1.2 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/45.0.0.post20200113 requests-toolbelt/0.9.1 tqdm/4.41.1 CPython/3.7.6

File hashes

Hashes for thapbi_pict-0.6.4-py3-none-any.whl
Algorithm Hash digest
SHA256 ca91a1e3e6c59de868d9d629c9670fe67fdda21f3f0d9a25bcd9c157e32b1e36
MD5 d7dd044135f774a445a73ed053bdd04e
BLAKE2b-256 f619055d3d2083bb86533e35f819e818c9f0f5487c5979bcf74498f64b44dfe6

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page