A set of tools to calculate the "force" acting on the maximum length of complementary segments in a given transcript, dinucleotide motif, and sequence complexity

docker pull TODO

Alternatively, build the image from Dockerfile:

docker build . -t forces

The build is based on debian:bullseye and it requires the forces.tgz source tarball.

g++ -O3 -o fasta_xds calculate_xds.cpp 
g++ -O3 -o window_scan scan_window.cpp

Install the built executables into PATH

python3 setup.py build && python3 setup.py install

• Complexity calculation:

python get_complexity.py "YOUR SEQUENCE HERE"

• Double stranded force calculation in scanning window (of given window_length, sliding from start position by shift_size until end position is reached on a given chromosome. The human genome assembly has to be provided as a fasta file. Output is provided per line for each window):

window_scan fasta_file_with_genome chromosome start stop shiftsize window_length outputfilename

• Double stranded force calculation per each individual sequence provided in a fastafile:

fasta_xds fastafilename

• CpG 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.

• CpG force calculation for 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.