Dimer "forces" are defined in the following paper:
Greenbaum BD, Cocco S, Levine AJ, Monasson R. Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses. Proc Natl Acad Sci USA. 2014 Apr 1;111(13):5054-9.
Build the image from Dockerfile:
docker build . -t DimerForces
The build is based on debian:trixie
pip install .
possibly with the --user option.
Old way calling setup.py directly, deprecated, requires wheel to be installed:
python3 setup.py build && python3 setup.py install
- Dimer force calculation in scanning window:
compute_sliding_window_force.py [-h] [-L WINDOW] [-c CONTIG] [-d DIMER] [-e END] [-s START] fasta_infile
Arguments CONTIG to use, START, END and WINDOW length are optional. DIMER defaults to CG.
Output: contig_id, start, #(valid dimers), dimer force.
- Dimer force calculation for a subsequence with given coordinates:
compute_force_from_regions.py [-h] [-d DIMER] [-L MIN_LENGTH] [-s] fasta_infile coordinate_file
Input file format for coordinate_file:
contig start end OTHER_OPTIONAL_COLUMNS
If -s is specified, strand (+/-) is needed as well:
contig start end strand OTHER_OPTIONAL_COLUMNS
Regions shorter than MIN_LENGTH are removed.
Output: the same as input plus an extra column with the force.