Metadata-Version: 2.1
Name: mg-toolkit
Version: 0.4.1
Summary: Metagenomics toolkit
Home-page: https://github.com/EBI-metagenomics/emg-toolkit
Author: Ola Tarkowska
Author-email: olat@ebi.ac.uk
License: Apache Software License
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)
        
        
        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?
        
            $ mg-toolkit bulk_download -h
            usage: mg-toolkit bulk_download [-h] -a ACCESSION [-o OUTPUT_PATH]
                                              [-v {1.0,2.0,3.0,4.0,4.1}]
                                              [-g {sequence_data,functional_analysis,taxonomic_analysis,taxonomic_analysis_ssu,taxonomic_analysis_lsu,stats,non_coding_rna}]
              
            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
              -v {1.0,2.0,3.0,4.0,4.1}, --version {1.0,2.0,3.0,4.0,4.1}
                                    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 {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}
                                    Provide a single result group if needed. Supported
                                    result groups are: [sequence_data (all version),
                                    functional_annotations (all version),
                                    taxonomic_annotations (1.0-3.0), taxonomic_annot_ssu
                                    (>=4.0), taxonomic_annot_lsu (>=4.0), stats,
                                    non_coding_rna (>=4.0) 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 annotations only) for given study accession?
            
            $ mg-toolkit -d bulk_download -a ERP009703 -g functional_annotations
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
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
Description-Content-Type: text/markdown
