Metadata-Version: 2.1
Name: boldigger-cline
Version: 1.1.0
Summary: BOLDigger as a command-line tool
Home-page: https://github.com/DominikBuchner/BOLDigger-commandline
Author: Dominik Buchner
Author-email: dominik.buchner524@googlemail.com
License: MIT
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 â€“ 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.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
