Metadata-Version: 2.1
Name: mg-toolkit
Version: 0.8.0
Summary: Metagenomics toolkit.
Home-page: https://github.com/EBI-metagenomics/emg-toolkit
Author: EBI Microbiome Informatics Team
License: Apache Software License
Description: [![Build Status](https://travis-ci.com/EBI-Metagenomics/emg-toolkit.svg?branch=master)](https://travis-ci.com/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)
        
        
        Metagenomics toolkit enables scientists to download all of the sample
        metadata for a given study or sequence to a single csv file.
        
        
        Install metagenomics toolkit
        ============================
        
            pip install -U mg-toolkit
        
        
        Usage
        =====
        
            $ mg-toolkit -h
            usage: mg-toolkit [-h] [-V] [-d]
                              {original_metadata,sequence_search,bulk_download} ...
        
            Metagenomics toolkit
            --------------------
        
            positional arguments:
              {original_metadata,sequence_search,bulk_download}
                original_metadata   Download original metadata.
                sequence_search     Search non-redundant protein database using HMMER
                bulk_download       Download result files in bulks for an entire study.
        
            optional arguments:
              -h, --help            show this help message and exit
              -V, --version         print version information
              -d, --debug           print debugging information
        
        
        Examples
        ========
        
        Download metadata:
        
            $ mg-toolkit original_metadata -a ERP001736
        
        
        Search non-redundant protein database using HMMER and fetch metadata:
        
            $ mg-toolkit sequence_search -seq test.fasta -db full evalue -incE 0.02
        
            Databases:
            - full - Full length sequences (default)
            - all - All sequences
            - partial - Partial sequences
        
        
        How to bulk download result files for an entire study?
        
            usage: mg-toolkit bulk_download [-h] -a ACCESSION [-o OUTPUT_PATH]
                                            [-p {1.0,2.0,3.0,4.0,4.1,5.0}]
                                            [-g {statistics,sequence_data,functional_analysis,taxonomic_analysis,taxonomic_analysis_ssu_rrna,taxonomic_analysis_lsu_rrna,non-coding_rnas,taxonomic_analysis_itsonedb,taxonomic_analysis_unite,taxonomic_analysis_motupathways_and_systems}]
        
            optional arguments:
            -h, --help            show this help message and exit
            -a ACCESSION, --accession ACCESSION
                                    Provide the study/project accession of your interest, e.g. ERP001736, SRP000319. The study must be publicly available in MGnify.
            -o OUTPUT_PATH, --output_path OUTPUT_PATH
                                    Location of the output directory, where the downloadable files are written to.
                                    DEFAULT: CWD
            -p {1.0,2.0,3.0,4.0,4.1,5.0}, --pipeline {1.0,2.0,3.0,4.0,4.1,5.0}
                                    Specify the version of the pipeline you are interested in.
                                    Lets say your study of interest has been analysed with
                                    multiple version, but you are only interested in a particular
                                    version then used this option to filter down the results by
                                    the version you interested in.
                                    DEFAULT: Downloads all versions
            -g {statistics,sequence_data,functional_analysis,taxonomic_analysis,taxonomic_analysis_ssu_rrna,taxonomic_analysis_lsu_rrna,non-coding_rnas,taxonomic_analysis_itsonedb,taxonomic_analysis_unite,taxonomic_analysis_motupathways_and_systems}, --result_group {statistics,sequence_data,functional_analysis,taxonomic_analysis,taxonomic_analysis_ssu_rrna,taxonomic_analysis_lsu_rrna,non-coding_rnas,taxonomic_analysis_itsonedb,taxonomic_analysis_unite,taxonomic_analysis_motupathways_and_systems}
                                    Provide a single result group if needed.
                                    Supported result groups are:
                                    - statistics
                                    - sequence_data (all versions)
                                    - functional_analysis (all versions)
                                    - taxonomic_analysis (1.0-3.0)
                                    - taxonomic_analysis_ssu_rrna (>=4.0)
                                    - taxonomic_analysis_lsu_rrna (>=4.0)
                                    - non-coding_rnas (>=4.0)
                                    - taxonomic_analysis_itsonedb (>= 5.0)
                                    - taxonomic_analysis_unite (>= 5.0)
                                    - taxonomic_analysis_motu  (>= 5.0)
                                    - pathways_and_systems (>= 5.0)
                                    DEFAULT: Downloads all result groups if not provided.
                                    (default: None).
        
        
        How to download all files for a given study accession?
        
            $ mg-toolkit -d bulk_download -a ERP009703
        
        How to download results of a specific version for given study accession?
        
            $ mg-toolkit -d bulk_download -a ERP009703 -v 4.0
        
        How to download specific result file groups (e.g. functional analysis only) for given study accession?
        
            $ mg-toolkit -d bulk_download -a ERP009703 -g functional_analysis
        
        
        Contributors
        ============
        
        Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
        
        <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
        <!-- prettier-ignore-start -->
        <!-- markdownlint-disable -->
        <table>
          <tr>
            <td align="center"><a href="https://github.com/olatarkowska"><img src="https://avatars3.githubusercontent.com/u/1065155?v=4" width="100px;" alt=""/><br /><sub><b>Ola Tarkowska</b></sub></a><br /><a href="https://github.com/EBI-Metagenomics/emg-toolkit/commits?author=olatarkowska" title="Code">💻</a><a href="https://github.com/EBI-Metagenomics/EMG-docs/commits/master?author=olatarkowska">📖</a></td>
            <td align="center"><a href="https://github.com/mscheremetjew"><img src="https://avatars3.githubusercontent.com/u/1681284?v=4" width="100px;" alt=""/><br /><sub><b>Maxim Scheremetjew</b></sub></a><br /><a href="https://github.com/EBI-Metagenomics/emg-toolkit/commits?author=mscheremetjew" title="Code">💻</a><a href="https://github.com/EBI-Metagenomics/EMG-docs/commits/master?author=mscheremetjew">📖</a></td>
            <td align="center"><a href="https://github.com/mberacochea"><img src="https://avatars3.githubusercontent.com/u/1123897?v=4" width="100px;" alt=""/><br /><sub><b>Martin Beracochea</b></sub></a><br /><a href="https://github.com/EBI-Metagenomics/emg-toolkit/commits?author=mberacochea" title="Code">💻</a></td>
          </tr>
        </table>
        
        <!-- markdownlint-enable -->
        <!-- prettier-ignore-end -->
        <!-- ALL-CONTRIBUTORS-LIST:END -->
        
        This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
        
        Contact
        =======
        
        If the documentation do not answer your questions, please [contact us](https://www.ebi.ac.uk/support/metagenomics).
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.5
Description-Content-Type: text/markdown
