Metagenomics toolkit
Project description
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
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