hicreppy
cmdoret
This is a python reimplementation of hicrep's algorithm with added support for sparse matrices (in .cool format).
hicrep measures similarity between Hi-C samples by computing a stratum-adjusted correlation coefficient (SCC). In this implementation, the SCC is computed separately for each chromosome and the chromosome length-weighted average of SCCs is computed.
hicrep is published at:
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li, 2017, Genome Research, doi: 10.1101/gr.220640.117
The original implementation, in R can be found at https://github.com/MonkeyLB/hicrep
Installation
You can install the package using pip:
pip install --user hicreppyUsage
To find the optimal value for smoothing parameter h, you can use the htrain subcommand:
Usage: hicreppy htrain [OPTIONS] COOL1 COOL2
Find the optimal value for smoothing parameter h. The optimal h-value is
printed to stdout. Run informations are printed to stderr.
Options:
-r, --h-max INTEGER Maximum value of the smoothing parameter h to
explore. All consecutive integer values from 0 to
this value will be tested. [default: 10]
-m, --max-dist INTEGER Maximum distance at which to compute the SCC, in
basepairs. [default: 100000]
-b, --blacklist TEXT Exclude those chromosomes in the analysis. List of
comma-separated chromosome names.
-w, --whitelist TEXT Only include those chromosomes in the analysis. List
of comma-separated chromosome names.
--help Show this message and exit.
To compute the SCC between two matrices, use the scc subcommand. The optimal h value obtained with htrain should be provided to the flag -v:
Usage: hicreppy scc [OPTIONS] COOL1 COOL2
Compute the stratum-adjusted correlation coefficient for input matrices
Options:
-v, --h-value INTEGER Value of the smoothing parameter h to use. Should
be an integer value >= 0. [default: 10]
-m, --max-dist INTEGER Maximum distance at which to compute the SCC, in
basepairs. [default: 100000]
-s, --subsample INTEGER Subsample contacts from both matrices to target
value. Leave to 0 to disable subsampling.
[default: 0]
-b, --blacklist TEXT Exclude those chromosomes in the analysis. List of
comma-separated chromosome names.
-w, --whitelist TEXT Only include those chromosomes in the analysis.
List of comma-separated chromosome names.
--help Show this message and exit.
When running multiple pairwise comparisons, compute the optimal h value once between two highly similar samples and reuse the h value for all scc commands
Contributing
All contributions are welcome. We use the numpy standard for docstrings when documenting functions.
The code formatting standard we use is black, with --line-length=79 to follow PEP8 recommendations. We use pytest with the pytest-doctest and pytest-pylint plugins as our testing framework. Ideally, new functions should have associated unit tests, placed in the tests folder.
To test the code, you can run:
pytest --doctest-modules --pylint --pylint-error-types=EF --pylint-rcfile=.pylintrc hicreppy tests
