mg-toolkit 0.2.6

Metagenomics 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 -seq test.fasta -db full evalue --incE 0.02

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