pymibig 1.2.7

A small tool to download, match and save sequences from MIBiG.

pyMIBiG

A small tool to download, match and save sequences from MIBiG.

pyMIBiG can search by "organism name", "compound / product" and / or "biosynthetic class" as intersections of every argument added. Which means that the more arguments you add more restrictive your search becomes. It uses the available MIBiG download files which have less information then those returned when using their web search. So, for very specific queries, that yield fewer results, you will be better using the web interface.

Usage

Download the available package of pyMIBiG and execute pymibig -<target> where target is the term you wanto to search in MIBiG database.

You can also install it using pip. In a virtual environment execute:

pip install pymibig

By default pyMIBiG will fetch all cluster data and information of a given target.

You may change that using optional aguments passed along with the <target>:

usage: pyMIBiG [-h] [-o ORGANISM] [-p PRODUCT] [-b BIOSYNT] [-c {complete,incomplete,unknown,all}]
               [-i {maximum,minimal,all}]

A small tool to download, match and save targeted sequences from MIBiG.

options:
  -h, --help            show this help message and exit
  -o ORGANISM, --organism ORGANISM
                        Organism name to query in database.
  -p PRODUCT, --product PRODUCT
                        Compound to query in database.
  -b BIOSYNT, --biosynt BIOSYNT
                        Biosynthetic class to query in database.
  -c {complete,incomplete,unknown,all}, --completeness {complete,incomplete,unknown,all}
                        Loci completeness.
  -i {maximum,minimal,all}, --information {maximum,minimal,all}
                        Minimal annotation.

You have to use at least one of the following arguments: organism, product or biosynt. The others are optional.

On first execution pyMIBiG will download the database files from MIBiG and save locally, so an internet connection will be needed, after that it can be used offline.

As for this release pyMIBiG will download from MIBiG Version 3.1 (October 7th, 2022) the:

• Metadata in compressed format, including several JSON files;
• Nucleotide sequences of the biosynthetic gene clusters in compressed format, including several GBK files;
• Amino acid sequence translations of all genes from MIBiG entries are also available in a single compressed FASTa file.

License

pyMiBiG is distributed under the terms of the LGPL 3.0 license.