Tool for chromatin 3D structure reconstruction from 3C experimental data. Improvement of ShRec3D.
usage: sample_generator.py [-h] [-r RADIUS] [-pog PERCENT_OF_GAPS]
[-p POINTS_AMOUNT]
Generates sample Hi-C experimental data
optional arguments:
-h, --help show this help message and exit
-r RADIUS, --radius RADIUS
radius between each point (+/- radius divaded by 4)
-pog PERCENT_OF_GAPS, --percent-of-gaps PERCENT_OF_GAPS
percent of gaps introduced to distance matrix (0..1)
-p POINTS_AMOUNT, --points POINTS_AMOUNT
amount of points in sample model
usage: ga_main.py [-h] [-p POPULATION_SIZE] [-g GENERATIONS]
[-m MUTATION_RATE]
[--cg [CHECK_GENERATIONS [CHECK_GENERATIONS ...]]]
PATH
Generates sample Hi-C experimental data
positional arguments:
PATH path to sample folder
optional arguments:
-h, --help show this help message and exit
-p POPULATION_SIZE, --population POPULATION_SIZE
size of population for GA
-g GENERATIONS, --generations GENERATIONS
number of generations for GA
-m MUTATION_RATE, --mutation-rate MUTATION_RATE
mutation rate (0..1
--cg [CHECK_GENERATIONS [CHECK_GENERATIONS ...]]
generations on which FULL error is calculated
docker build -t skkap/mdsga:latest .
sudo docker run --name m1 -d -e SAMPLE_PATH='../samples/200_0.95_10_1/' -e TRIES='3' -v /raidz/skkap/docker/result:/app/result skkap/mdsga /app/docker-entry.sh
sudo docker run --name m2 -d -e SAMPLE_PATH='../samples/200_0.95_10_2/' -e TRIES='3' -v /raidz/skkap/docker/result:/app/result skkap/mdsga /app/docker-entry.sh
sudo docker run --name m3 -d -e SAMPLE_PATH='../samples/200_0.95_10_3/' -e TRIES='3' -v /raidz/skkap/docker/result:/app/result skkap/mdsga /app/docker-entry.sh