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Metagenomics toolkit

Project description

Build Status PyPi package Downloads

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

Project details


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