tomblaze / emg-toolkit

MGnify API 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):

Ola Tarkowska 💻📖

Maxim Scheremetjew 💻📖

Martin Beracochea 💻

This project follows the all-contributors specification. Contributions of any kind welcome!

Contact

If the documentation do not answer your questions, please contact us.