We have just released a Python 3 wrapper for the GATB-Core library: pyGATB.
The current release of pyGATB gives access to the following GATB-Core components:
- Bank: the class that enables to load Fasta and Fastaq files
- Sequence: the class that holds a sequence (ID, letters, quality)
- Graph: the class that holds the De Bruijn graph
- Node: the class that makes graph’s nodes
Using that API you can start prototyping algorithms:
- read a sequence file (Bank): FastA, FastQ (plain text or gzipped)
- or read a set of files (still using the same Bank!)
- convert that Bank to a De Bruijn graph (Graph)
- navigate through the Graph (Node)
all of that directly using the Python 3 Programming Language.
pyGATB is an open-source project hosted on Github.
View pyGATB in action.
Read the documentation.