Skip to main content

BOLDigger as a command-line tool

Project description

BOLDigger-commandline

BOLDigger as a command-line tool for easy implementation into bioinformatic pipelines.

Before using please check that you have updated to the latest version of BOLDigger since BOLDigger-cline heavily relies on the current code of BOLDigger.

For a detailed explanation of the different functions BOLDigger offers please visit: https://github.com/DominikBuchner/BOLDigger

Installation

BOLDigger-commandline requires Python version 3.6 or higher and can be easily installed by using pip in any command line:

pip install boldigger_cline

will install BOLDigger-commandline as well as all needed dependencies.

To update BOLDigger-commandline type:

pip install --upgrade boldigger_cline

How to cite

Buchner D, Leese F (2020) BOLDigger – a Python package to identify and organise sequences with the Barcode of Life Data systems. Metabarcoding and Metagenomics 4: e53535. https://doi.org/10.3897/mbmg.4.53535

Usage

BOLDigger commandline offers all functions of BOLDigger as a command line tool.

For documentation on how to use type:

boldigger-cline -h

Returns:

usage: boldigger-cline [-h] [--version]
                       {ie_coi,ie_its,ie_rbcl,add_metadata,first_hit,jamp_hit,digger_hit}
                       ...

BOLDigger as a command line tool, https://github.com/DominikBuchner/BOLDigger-

commandline

positional arguments:
  {ie_coi,ie_its,ie_rbcl,add_metadata,first_hit,jamp_hit,digger_hit}
    ie_coi              COI identification engine
    ie_its              ITS identification engine
    ie_rbcl             rbcl identification engine
    add_metadata        additional data download
    first_hit           use the first hit as top hit
    jamp_hit            determine the top hit with the JAMP method
    digger_hit          determine the top hit with the BOLDigger method

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

The help function also works for all sub-functions of BOLDigger-commandline:

boldigger-cline ie_coi -h

Returns:

usage: boldigger-cline ie_coi [-h]
                              username password fasta_path output_folder

                              [batch_size]

positional arguments:
  username       Username for boldsystems login
  password       Password for boldsystems login
  fasta_path     Path to the fasta file to be blasted
  output_folder  Path to the output folder
  batch_size     Batch size to be blasted.

optional arguments:
  -h, --help     show this help message and exit

Identification engine - Example usage

To run the identification engine for COI type:

boldigger-cline ie_coi username password fasta_path output_folder [batch size](optional)

Additional data download and top hit determination

All other function of BOLDigger commandline just need a filepath to the BOLDResult file as an argument.

Project details


Download files

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

Source Distribution

boldigger-cline-2.2.2.tar.gz (13.9 kB view details)

Uploaded Source

Built Distribution

boldigger_cline-2.2.2-py3-none-any.whl (17.0 kB view details)

Uploaded Python 3

File details

Details for the file boldigger-cline-2.2.2.tar.gz.

File metadata

  • Download URL: boldigger-cline-2.2.2.tar.gz
  • Upload date:
  • Size: 13.9 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.6

File hashes

Hashes for boldigger-cline-2.2.2.tar.gz
Algorithm Hash digest
SHA256 1e9e2743a8a7a2dee8b0e8e5e61b9172285045690a835a43ffddc2ee7c7f1b38
MD5 7475b6ef127f1af63e3dd78ca3c885bb
BLAKE2b-256 36f6f9f272d1d47b9934d5274342aaac6d61259df125adb47d7514bb0e9f44d4

See more details on using hashes here.

File details

Details for the file boldigger_cline-2.2.2-py3-none-any.whl.

File metadata

File hashes

Hashes for boldigger_cline-2.2.2-py3-none-any.whl
Algorithm Hash digest
SHA256 e0f49355ce93c82f95e6049370e7ee17d4ddf26185d2859451b2cbcbc89a4a82
MD5 29362b9cb8a63fe4ebbb00c6a16298e8
BLAKE2b-256 29e9aa0d6ca9de6e7fbe772e0f2491633a84d7f3a9d73d6a8ff3938e2649799f

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