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        "author": "Ola Tarkowska",
        "author_email": "olat@ebi.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "[![Build Status](https://travis-ci.org/EBI-Metagenomics/emg-toolkit.svg?branch=master)](https://travis-ci.org/EBI-Metagenomics/emg-toolkit) [![PyPi package](https://badge.fury.io/py/mg-toolkit.svg)](https://badge.fury.io/py/mg-toolkit) [![Downloads](http://pepy.tech/badge/mg-toolkit)](http://pepy.tech/project/mg-toolkit)\n\n\nMetagenomics toolkit enables scientists to download all of the sample\nmetadata for a given study or sequence to a single csv file.\n\n\nInstall metagenomics toolkit\n============================\n\n    pip install -U mg-toolkit\n\n\nUsage\n=====\n\n    $ mg-toolkit -h\n    usage: mg-toolkit [-h] [-V] [-d]\n                      {original_metadata,sequence_search,bulk_download} ...\n\n    Metagenomics toolkit\n    --------------------\n\n    positional arguments:\n      {original_metadata,sequence_search,bulk_download}\n        original_metadata   Download original metadata.\n        sequence_search     Search non-redundant protein database using HMMER\n        bulk_download       Download result files in bulks for an entire study.\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      -V, --version         print version information\n      -d, --debug           print debugging information\n\n\nExamples\n========\n\nDownload metadata:\n\n    $ mg-toolkit original_metadata -a ERP001736\n\n\nSearch non-redundant protein database using HMMER and fetch metadata:\n\n    $ mg-toolkit sequence_search -seq test.fasta -db full evalue -incE 0.02\n\n    Databases:\n    - full - Full length sequences (default)\n    - all - All sequences\n    - partial - Partial sequences\n\n\nHow to bulk download result files for an entire study?\n\n    $ mg-toolkit bulk_download -h\n    usage: mg-toolkit bulk_download [-h] -a ACCESSION [-o OUTPUT_PATH]\n                                      [-p {1.0,2.0,3.0,4.0,4.1}]\n                                      [-g {sequence_data,functional_analysis,taxonomic_analysis,taxonomic_analysis_ssu,taxonomic_analysis_lsu,stats,non_coding_rna}]\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      -a ACCESSION, --accession ACCESSION\n                            Provide the study/project accession of your interest,\n                            e.g. ERP001736, SRP000319. The study must be publicly\n                            available in MGnify.\n      -o OUTPUT_PATH, --output_path OUTPUT_PATH\n                            Location of the output directory, where the\n                            downloadable files are written to. DEFAULT: CWD\n      -p {1.0,2.0,3.0,4.0,4.1}, --pipeline {1.0,2.0,3.0,4.0,4.1}\n                            Specify the version of the pipeline you are interested\n                            in. Lets say your study of interest has been analysed\n                            with multiple version, but you are only interested in\n                            a particular version then used this option to filter\n                            down the results by the version you interested in.\n                            DEFAULT: Downloads all versions\n      -g {sequence_data,functional_annotations,taxonomic_annotations,taxonomic_annot_ssu,taxonomic_annot_lsu,stats,non_coding_rna}, --result_group {sequence_data,functional_annotations,taxonomic_annotations,taxonomic_annot_ssu,taxonomic_annot_lsu,stats,non_coding_rna}\n                            Provide a single result group if needed. Supported\n                            result groups are: [sequence_data (all version),\n                            functional_annotations (all version),\n                            taxonomic_annotations (1.0-3.0), taxonomic_annot_ssu\n                            (>=4.0), taxonomic_annot_lsu (>=4.0), stats,\n                            non_coding_rna (>=4.0) DEFAULT: Downloads all result\n                            groups if not provided. (default: None).\n\nHow to download all files for a given study accession?\n\n    $ mg-toolkit -d bulk_download -a ERP009703\n\nHow to download results of a specific version for given study accession?\n\n    $ mg-toolkit -d bulk_download -a ERP009703 -v 4.0\n\nHow to download specific result file groups (e.g. functional annotations only) for given study accession?\n\n    $ mg-toolkit -d bulk_download -a ERP009703 -g functional_annotations\n\n",
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