iRep.py and bPTR.py

These scripts are described in:

“In situ replication rates for uncultivated bacteria in microbial communities” - Christopher T. Brown, Matthew R. Olm, Brian C. Thomas, Jillian F. Banfield

http://dx.doi.org/10.1101/057992

Scripts require python3 and the following packages: lmfit numpy scipy pandas seaborn matplotlib cPickle

Example usage:

iRep

./bin/iRep.py -f sample_data/l_gasseri.fna -s sample_data/l_gasseri*sam -o test.iRep

bPTR

./bin/bPTR.py -f sample_data/l_gasseri.fna -s sample_data/l_gasseri*sam -o test.bPTR.tsv -plot test.bPTR.pdf -m coverage

GC Skew

./bin/gc_skew.py -f sample_data/l_gasseri.fna

Example output is provided in sample_output.