Detect loops (and other patterns) in Hi-C contact maps.
Project description
Chromosight
Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.
Installation
Stable version with pip:
pip3 install --user chromosight
Stable version with conda:
conda install -c bioconda -c conda-forge chromosight
or, if you want to get the latest development version:
pip3 install --user -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight
Usage
chromosight
has 3 subcommands: detect
, quantify
and generate-config
. To get the list and description of those subcommands, you can always run:
chromosight --help
Pattern detection is done using the detect
subcommand. The generate-config subcommand is used to create a new type of pattern that can then be fed to detect
using the --custom-kernel
option. The quantify
subcommand is used to compute pattern matching scores for a list of 2D coordinates on a Hi-C matrix.
Get started
To get a first look at a chromosight run, you can run chromosight test
, which will download a test dataset from the github repository and run chromosight detect
on it.
Important options
--min-dist
: Minimum distance from which to detect patterns.--max-dist
: Maximum distance from which to detect patterns. Increasing also increases runtime and memory use.--pearson
: Decrease to allow a greater number of pattern detected (with potentially more false positives).--perc-undetected
: Proportion of empty pixels allowed in a window for detection.
Example
To detect all chromosome loops with sizes between 2kb and 200kb using 8 parallel threads:
chromosight detect --threads 8 --min-dist 20000 --max-dist 200000 hic_data.cool out_dir
Input
Input Hi-C contact maps should be in cool format. The cool format is an efficient and compact format for Hi-C data based on HDF5. It is maintained by the Mirny lab and documented here: https://mirnylab.github.io/cooler/
Most other Hi-C data formats (hic, homer, hic-pro), can be converted to cool using hicexplorer's hicConvertFormat. Bedgraph2 format can be converted directly using cooler with the command cooler load -f bg2 <chrom.sizes>:<binsize> in.bg2.gz out.cool
. For more informations, see the cooler documentation
Output
Two files are generated in the output directory (replace pattern by the pattern used, e.g. loops or borders):
pattern_out.txt
: List of genomic coordinates, bin ids and correlation scores for the pattern identifiedpattern_out.json
: JSON file containing the windows (of the same size as the kernel used) around the patterns from pattern.txt
Alternatively, one can set the --win-fmt=npy
option to dump windows into a npy file instead of JSON. This format can easily be loaded into a 3D array using numpy's np.load
function.
Options
Pattern exploration and detection
Explore and detect patterns (loops, borders, centromeres, etc.) in Hi-C contact
maps with pattern matching.
Usage:
chromosight detect [--kernel-config=FILE] [--pattern=loops] [--pearson=auto]
[--iterations=auto] [--resize-kernel] [--win-fmt={json,npy}]
[--subsample=no] [--inter] [--smooth-trend] [--n-mads=5]
[--min-dist=0] [--max-dist=auto] [--no-plotting]
[--min-separation=auto] [--threads=1] [--dump=DIR]
[--perc-undetected=auto] <contact_map> [<output>]
chromosight generate-config <prefix> [--preset loops] [--click contact_map] [--win-size=auto] [--n-mads=INT]
chromosight quantify [--inter] [--pattern=loops] [--subsample=no] [--win-fmt=json]
[--n-mads=5] [--win-size=auto] <bed2d> <contact_map> <output>
chromosight test
detect:
performs pattern detection on a Hi-C contact map using kernel convolution
generate-config:
Generate pre-filled config files to use for `chromosight detect`.
A config consists of a JSON file describing analysis parameters for the
detection and path pointing to kernel matrices files. Those matrices
files are tsv files with numeric values ordered in a square dense matrix
to use for convolution.
quantify:
Given a list of pairs of positions and a contact map, computes the
correlation coefficients between those positions and the kernel of the
selected pattern.
test:
Download example data and run the program on it.
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 nose2
as our testing framework. Ideally, new functions should have associated unit tests, placed in the tests
folder.
To test the code, you can run:
nose2 -s tests/
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