mg-toolkit 0.6.2

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,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]
[-p {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
-p {1.0,2.0,3.0,4.0,4.1}, --pipeline {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