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.
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