Metadata-Version: 2.1
Name: mg-toolkit
Version: 0.3.0
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
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
Requires-Dist: requests
Requires-Dist: xmltodict
Requires-Dist: pandas

[![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} ...

    Metagenomics toolkit
    --------------------

    positional arguments:
      {original_metadata,sequence_search}
        original_metadata   Download original metadata
        sequence_search     Search non-redundant protein database using HMMER

    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


