/PlastomeBurstAndAlign

Extract and align coding regions, introns and intergenic spacers across a set of plastomes

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

PlastomeBurstAndAlign

Extract and align coding regions, introns and intergenic spacers across a set of plastomes

Installation

# Alignment software
apt install mafft  # Debian

# Other dependencies
pip install biopython
pip install coloredlogs
pip install ipdb

Testing

cd benchmarking
# CDS
python test_script_cds.py
# INT
python test_script_int.py
# IGS
python test_script_igs.py

Exemplary usage

See this document

Generating more test data

See this document