Metadata-Version: 2.1
Name: groupBug
Version: 0.3
Summary: Clustering heatmap tool for kraken-style reports
Home-page: https://gitlab.com/ModernisingMedicalMicrobiology/groupBug
Author: ['Nick Sanderson']
Author-email: nicholas.sanderson@ndm.ox.ac.uk
License: MIT
Description: [![coverage report](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/badges/master/coverage.svg)](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/commits/master)
        [![pipeline status](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/badges/master/pipeline.svg)](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/commits/master)
        [![PyPI version](https://badge.fury.io/py/groupBug.svg)](https://badge.fury.io/py/groupBug)
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1405068.svg)](https://doi.org/10.5281/zenodo.1405068)
        
        # groupBug
        
        Clustering heatmap tool for kraken-style reports. Takes kraken style reports in text file format from eithr Kraken or Centrifuge (use centrifuge-kreport.pl). Produces a clustermap using seaborn of top species (default) using z scores for the heatmap and euclidean centroid clustering for the dendrograms.
        
        This work was inspired by the excellent hclust script available for metaphlan analysis, see here https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2#rst-header-create-a-heatmap-with-hclust2. And Pavian see here, https://github.com/fbreitwieser/pavian.
        
        This work was funded by NIHR Biomedical Research Centre at Oxford University Hospitals NHS Foundation Trust and the University of Oxford.
        
        ## Installation 
        
        From github
        ```
        git clone https://gitlab.com/ModernisingMedicalMicrobiology/groupBug
        cd groupBug
        sudo python3 setup.py install
        ```
        From pip3
        ```
        sudo pip3 install groupBug
        ```
        From pip3 if you don't have admin rights
        ```
        pip3 install --user groupBug
        ```
        
        # Requirements
        
        Written in python3 only and Currently dependant on the following packages:
        
        pandas
        ete3
        matplotlib
        seaborn
        six
        coverage
        nose
        
        
        An X display server is needed if the -sv/--saveName parameter is not used.
        
        ## Usage
        
        Command line options are as follows.
        ```
        usage: groupBug.py [-h] -k KRAKEN_REPORTS [KRAKEN_REPORTS ...] [-d DOMAIN]
                           [-t TAXIDS [TAXIDS ...]] [-sv SAVENAME] [-n TOPNUM]
                           [-suf SUF]
        
        cluster heatmap and information from kraken reports
        
        optional arguments:
          -h, --help            show this help message and exit
          -k KRAKEN_REPORTS [KRAKEN_REPORTS ...], --kraken_reports KRAKEN_REPORTS [KRAKEN_REPORTS ...]
                                list of kraken style report files
          -d DOMAIN, --domain DOMAIN
                                Domain of life to display, bacteria, viruses etc
          -t TAXIDS [TAXIDS ...], --taxids TAXIDS [TAXIDS ...]
                                list of taxids to specifically count
          -sv SAVENAME, --saveName SAVENAME
                                file name to save plot as
          -n TOPNUM, --topNum TOPNUM
                                Number of discrete species to display
          -suf SUF, --suf SUF   suffix to delete from sample name
        ```
        
        For example, use this command to display the top bacterial species.
        ```
        groupBug.py -k kreports/* 
        ```
        
        This will prodcuce a chart like this.
        ![](plots/PJI_ONT_zscores.pdf_bacteria_z_score_columns.png)
        
        The file names are used as sample labels along the x axis. To remove suffixes, use the -suf options like such.
        
        ```
        groupBug.py -k reports/* -suf _kreport_score_150.txt
        ```
        
        This will prodcuce a chart like this.
        ![](plots/PJI_ONT_zscores_shortname.png_bacteria_z_score_columns.png)
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
