Assignments for job application at KI.
Tested on Ubuntu xenial distribution. Kia was developed using bedtools (v2.29.2)
For easiest install, create virtual environment (conda, venv etc) for python 3.6
# Example install
$ conda create -n kia python=3.6
$ conda activate kia
# Retrieve application
$ git clone https://github.com/karlnyr/KI-assignment.git
$ cd KI-assignment
$ pip install .
# Instal bedtools
$ sudo apt-get install -y bedtools
# Call kia
$ kia
Usage: kia [OPTIONS] COMMAND [ARGS]...
ki-assignment
Options:
--debug Run in test mode, will not create files
--help Show this message and exit.
Commands:
calcSummary Compose a report for input files, of BED format.
featureOverlap Calculates the number of overlapping sequences in BED...
plotCoverage Plots both normalized and non-normalized coverage data...Kia include three different commands, and are easily accessed like so:
$ kia plotCoverage
Usage: kia plotCoverage [OPTIONS]
Plots both normalized and non-normalized coverage data gathered from
sambamba depth. Red line in output indicates 100X coverage.
Options:
-i, --input-file PATH Input coverage file from the software sambamba depth
(https://lomereiter.github.io/sambamba/)
-o, --out-path PATH Specify out directory path, default = current
directory.
-p, --prefix TEXT Specify prefix on output, default = file_name
--bins INTEGER Specify size of bins for histogram, default=50 NOTE:
Increasing number drastically will increase
computation time
--dryrun Will test functionality of plot_coverage, will not
save a figure in the end
-h, --help Show this message and exit.