Skip to main content
Join the official 2020 Python Developers SurveyStart the survey!

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.

Files for boldigger-cline, version 1.0.1
Filename, size File type Python version Upload date Hashes
Filename, size boldigger_cline-1.0.1-py3-none-any.whl (16.1 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size boldigger-cline-1.0.1.tar.gz (11.8 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page