Metadata-Version: 2.1
Name: clinker
Version: 0.0.18
Summary: UNKNOWN
Home-page: https://github.com/gamcil/clinker
Author: Cameron Gilchrist
License: UNKNOWN
Description: # clinker
        [![DOI](https://zenodo.org/badge/193022148.svg)](https://zenodo.org/badge/latestdoi/193022148)
        
        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.
        
        ![clinker visualisation demo](images/demo.gif)
        
        ## Installation
        clinker can be installed directly through pip:
        
        `pip install clinker`
        
        By cloning the source code from GitHub:
        
        ```
        git clone https://github.com/gamcil/clinker.git
        cd clinker
        pip install .
        ```
        
        Or, through conda:
        
        ```
        conda create -n clinker -c conda-forge -c bioconda clinker-py
        conda activate clinker
        ```
        
        ## Citation
        If you found clinker useful, please cite:
        ```
        clinker & clustermap.js: Automatic generation of gene cluster comparison figures.
        Gilchrist, C.L.M., Chooi, Y.-H., 2020.
        Bioinformatics. doi: https://doi.org/10.1093/bioinformatics/btab007
        ```
        
        ## Usage
        Running clinker can be as simple as:
        
        `clinker clusters/*.gbk`
        
        This will read in all GenBank files inside the folder, align them, and print
        the alignments to the terminal. To generate the visualisation, use the `-p/--plot`
        argument: 
        
        `clinker clusters/*.gbk -p <optional: file name to save static HTML>`
        
        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:
          -na, --no_align       Do not align clusters
          -i IDENTITY, --identity IDENTITY
                                Minimum alignment sequence identity
          -j JOBS, --jobs JOBS  Number of alignments to run in parallel (0 to use the
                                number of CPUs)
        
        Output options:
          -s SESSION, --session SESSION
                                Path to clinker session
          -ji JSON_INDENT, --json_indent JSON_INDENT
                                Number of spaces to indent JSON
          -f, --force           Overwrite previous output file
          -o OUTPUT, --output OUTPUT
                                Save alignments to file
          -p [PLOT], --plot [PLOT]
                                Plot cluster alignments using clustermap.js. If a path
                                is given, clinker will generate a portable HTML file
                                at that path. Otherwise, the plot will be served
                                dynamically using Python's HTTP server.
          -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
        
        Visualisation options:
          -ufo, --use_file_order
                                Display clusters in order of input files
        
        Example usage
        -------------
        Align clusters, plot results and print scores to screen:
          $ clinker files/*.gbk -p
        
        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
