Metadata-Version: 2.1
Name: clinker
Version: 0.0.2
Summary: UNKNOWN
Home-page: https://github.com/gamcil/clinker
Author: Cameron Gilchrist
License: UNKNOWN
Description: # clinker
        Gene cluster comparison figure generator
        
        ## What is it?
        clinker is a pipeline for easily generating publication-quality gene cluster
        comparison figures.
        
        <img src="images/figure.png" alt="bua cluster and homologues" width=700>
        
        Given a set of GenBank files, clinker will automatically extract protein translations,
        perform global alignments between sequences in each cluster, determine the
        optimal display order based on cluster similarity, and generate an interactive
        visualisation (using ![clustermap.js](https://github.com/gamcil/clustermap.js))
        that can be extensively tweaked before being exported as an SVG file.
        
        ## Installation
        clinker can be installed directly through pip:
        
        `pip install clinker`
        
        Or by cloning the source code from GitHub:
        
        ```
        git clone https://github.com/gamcil/clinker.git
        cd clinker
        pip install .
        ```
        
        ## Usage
        Running clinker can be as simple as:
        
        `clinker clusters/*.gbk`
        
        This will run the clinker pipeline on all GenBank files within the
        folder and open a new tab in your web browser with the visualisation
        application.
        
        See `-h/--help` for more information:
        
        ```
        usage: clinker [-h] [-i IDENTITY] [-f] [-o OUTPUT] [-dl DELIMITER]
                       [-dc DECIMALS] [-hl] [-ha]
                       files [files ...]
        
        clinker: Automatic creation of publication-ready gene cluster comparison figures.
        
        clinker generates gene cluster comparison figures from GenBank files.
        It performs pairwise local or global alignments between every sequence
        in every unique pair of clusters and generates interactive, to-scale
        comparison figures using the clustermap.js library.
        
        positional arguments:
          files                 Gene cluster GenBank files
        
        optional arguments:
          -h, --help            show this help message and exit
        
        Alignment options:
          -i IDENTITY, --identity IDENTITY
                                Minimum alignment sequence identity
        
        Output options:
          -f, --force           Overwrite previous output file
          -o OUTPUT, --output OUTPUT
                                Save alignments to file
          -dl DELIMITER, --delimiter DELIMITER
                                Character to delimit output by
          -dc DECIMALS, --decimals DECIMALS
                                Number of decimal places in output
          -hl, --hide_link_headers
                                Hide alignment column headers
          -ha, --hide_aln_headers
                                Hide alignment cluster name headers
        
        Example usage
        -------------
        Align clusters, plot results and print scores to screen:
          $ clinker files/*.gbk
        
        Cameron Gilchrist, 2020
        ```
        
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
