mg-toolkit 0.2.3

Metagenomics toolkit

[](https://travis-ci.org/EBI-Metagenomics/emg-toolkit) [](https://badge.fury.io/py/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 -s test.fasta -b partial

Databases:
- full - Full length sequences (default)
- all - All sequences
- partial - Partial sequences