Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.
pip install -U mg-toolkit
$ 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
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
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!
If the documentation do not answer your questions, please contact us.