{ "info": { "author": "['Nick Sanderson']", "author_email": "nicholas.sanderson@ndm.ox.ac.uk", "bugtrack_url": null, "classifiers": [], "description": "[![coverage report](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/badges/master/coverage.svg)](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/commits/master)\n[![pipeline status](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/badges/master/pipeline.svg)](https://gitlab.com/ModernisingMedicalMicrobiology/groupBug/commits/master)\n[![PyPI version](https://badge.fury.io/py/groupBug.svg)](https://badge.fury.io/py/groupBug)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1405068.svg)](https://doi.org/10.5281/zenodo.1405068)\n\n# groupBug\n\nClustering 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.\n\nThis 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.\n\nThis work was funded by NIHR Biomedical Research Centre at Oxford University Hospitals NHS Foundation Trust and the University of Oxford.\n\n## Installation \n\nFrom github\n```\ngit clone https://gitlab.com/ModernisingMedicalMicrobiology/groupBug\ncd groupBug\nsudo python3 setup.py install\n```\nFrom pip3\n```\nsudo pip3 install groupBug\n```\nFrom pip3 if you don't have admin rights\n```\npip3 install --user groupBug\n```\n\n# Requirements\n\nWritten in python3 only and Currently dependant on the following packages:\n\npandas\nete3\nmatplotlib\nseaborn\nsix\ncoverage\nnose\n\n\nAn X display server is needed if the -sv/--saveName parameter is not used.\n\n## Usage\n\nCommand line options are as follows.\n```\nusage: groupBug.py [-h] -k KRAKEN_REPORTS [KRAKEN_REPORTS ...] [-d DOMAIN]\n [-t TAXIDS [TAXIDS ...]] [-sv SAVENAME] [-n TOPNUM]\n [-suf SUF]\n\ncluster heatmap and information from kraken reports\n\noptional arguments:\n -h, --help show this help message and exit\n -k KRAKEN_REPORTS [KRAKEN_REPORTS ...], --kraken_reports KRAKEN_REPORTS [KRAKEN_REPORTS ...]\n list of kraken style report files\n -d DOMAIN, --domain DOMAIN\n Domain of life to display, bacteria, viruses etc\n -t TAXIDS [TAXIDS ...], --taxids TAXIDS [TAXIDS ...]\n list of taxids to specifically count\n -sv SAVENAME, --saveName SAVENAME\n file name to save plot as\n -n TOPNUM, --topNum TOPNUM\n Number of discrete species to display\n -suf SUF, --suf SUF suffix to delete from sample name\n```\n\nFor example, use this command to display the top bacterial species.\n```\ngroupBug.py -k kreports/* \n```\n\nThis will prodcuce a chart like this.\n![](plots/PJI_ONT_zscores.pdf_bacteria_z_score_columns.png)\n\nThe file names are used as sample labels along the x axis. To remove suffixes, use the -suf options like such.\n\n```\ngroupBug.py -k reports/* -suf _kreport_score_150.txt\n```\n\nThis will prodcuce a chart like this.\n![](plots/PJI_ONT_zscores_shortname.png_bacteria_z_score_columns.png)\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://gitlab.com/ModernisingMedicalMicrobiology/groupBug", "keywords": "", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "groupBug", "package_url": "https://pypi.org/project/groupBug/", "platform": "", "project_url": "https://pypi.org/project/groupBug/", "project_urls": { "Homepage": "https://gitlab.com/ModernisingMedicalMicrobiology/groupBug" }, "release_url": "https://pypi.org/project/groupBug/0.3/", "requires_dist": [ "pandas", "ete3", "matplotlib", "seaborn", "six" ], "requires_python": "", "summary": "Clustering heatmap tool for kraken-style reports", "version": 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