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)

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.

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

This continues earlier work including:

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. 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.

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

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

This version

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-0.3.3.tar.gz (2.9 MB view details)

Uploaded Source

Built Distribution

thapbi_pict-0.3.3-py3-none-any.whl (1.2 MB view details)

Uploaded Python 3

File details

Details for the file thapbi_pict-0.3.3.tar.gz.

File metadata

  • Download URL: thapbi_pict-0.3.3.tar.gz
  • Upload date:
  • Size: 2.9 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.5.0.1 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.31.1 CPython/3.7.2

File hashes

Hashes for thapbi_pict-0.3.3.tar.gz
Algorithm Hash digest
SHA256 5b9100972b34871d7acf1b0a26f1fa29481b0d237e476c64a06b1f8e3bdb9f55
MD5 fcefb1f765d0a53f1bb1ac99e7c97260
BLAKE2b-256 fe45958b8ccd260382d5af2d8a2cd5bae7958738f8d84caaa43bf0c0fb50cabb

See more details on using hashes here.

File details

Details for the file thapbi_pict-0.3.3-py3-none-any.whl.

File metadata

  • Download URL: thapbi_pict-0.3.3-py3-none-any.whl
  • Upload date:
  • Size: 1.2 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.5.0.1 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.31.1 CPython/3.7.2

File hashes

Hashes for thapbi_pict-0.3.3-py3-none-any.whl
Algorithm Hash digest
SHA256 f0e13f4581b700b6a8ca78624049f1a469e3682ad23ead6dbb437b5ea1d79e33
MD5 1b387364584f39a0cacfbdf53a0c4427
BLAKE2b-256 7c1fa76edfd1f0254be4a14678980f07272eed7940fd82aac1a48ef35d0edd74

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