cooler 0.6.4

Sparse binary format for genomic interaction matrices

A cool place to store your Hi-C

Cooler is a support library for a sparse, compressed, binary persistent storage format for Hi-C contact matrices, called cool, which is based on HDF5.

Cooler aims to provide the following functionality:

• Generate contact matrices from contact lists at arbitrary resolutions.

• Store contact matrices efficiently in cool format based on the widely used HDF5 container format.

• Perform out-of-core genome wide contact matrix normalization (a.k.a. balancing)

• Perform fast range queries on a contact matrix.

• Convert contact matrices between formats.

• Provide a clean and well-documented Python API to work with Hi-C data.

To get started:

• Documentation is available here.

• Walkthrough with a Jupyter notebook.

• cool files from published Hi-C data sets are available at ftp://cooler.csail.mit.edu/coolers.

Installation

Requirements:

• Python 2.7/3.4+

• libhdf5 and Python packages numpy, scipy, pandas, h5py. We highly recommend using the conda package manager to install scientific packages like these. To get it, you can either install the full Anaconda Python distribution or just the standalone conda package manager.

Install from PyPI using pip.

$ pip install cooler

See the docs for more information.

Command line interface

The cooler library includes utilities for creating and querying cool files and for performing contact matrix balancing on a cool file of any resolution.

$ cooler makebins $CHROMSIZES_FILE $BINSIZE > bins.10kb.bed
$ cooler cload bins.10kb.bed $CONTACTS_FILE out.cool
$ cooler balance -p 10 out.cool
$ cooler dump -b -t pixels --header --join -r chr3:10,000,000-12,000,000 -r2 chr17 out.cool | head

chrom1  start1  end1    chrom2  start2  end2    count   balanced
chr3    10000000        10010000        chr17   0       10000   1       0.810766
chr3    10000000        10010000        chr17   520000  530000  1       1.2055
chr3    10000000        10010000        chr17   640000  650000  1       0.587372
chr3    10000000        10010000        chr17   900000  910000  1       1.02558
chr3    10000000        10010000        chr17   1030000 1040000 1       0.718195
chr3    10000000        10010000        chr17   1320000 1330000 1       0.803212
chr3    10000000        10010000        chr17   1500000 1510000 1       0.925146
chr3    10000000        10010000        chr17   1750000 1760000 1       0.950326
chr3    10000000        10010000        chr17   1800000 1810000 1       0.745982

See also:

• CLI Reference.

• Jupyter Notebook walkthrough.

Python API

The cooler library provides a thin wrapper over the excellent h5py Python interface to HDF5. It supports creation of cooler files and the following types of range queries on the data:

• Tabular selections are retrieved as Pandas DataFrames and Series.

• Matrix selections are retrieved as NumPy arrays or SciPy sparse matrices.

• Metadata is retrieved as a json-serializable Python dictionary.

• Range queries can be supplied using either integer bin indexes or genomic coordinate intervals.

>>> import cooler
>>> import matplotlib.pyplot as plt
>>> c = cooler.Cooler('bigDataset.cool')
>>> resolution = c.info['bin-size']
>>> mat = c.matrix(balance=True).fetch('chr5:10,000,000-15,000,000')
>>> plt.matshow(np.log10(mat), cmap='YlOrRd')

>>> import multiprocessing as mp
>>> import h5py
>>> pool = mp.Pool(8)
>>> f = h5py.File('bigDataset.cool', 'r')
>>> weights, stats = cooler.ice.iterative_correction(f, map=pool.map, ignore_diags=3, min_nnz=10)

See also:

• API Reference.

• Jupyter Notebook walkthrough.

Schema

The cool format implements a simple schema that stores a contact matrix in a sparse representation, crucial for developing robust tools for use on increasingly high resolution Hi-C data sets, including streaming and out-of-core algorithms.

The data tables in a cool file are stored in a columnar representation as HDF5 groups of 1D array datasets of equal length. The contact matrix itself is stored as a single table containing only the nonzero upper triangle pixels.

Contributing

Pull requests are welcome. The current requirements for testing are nose and mock.

For development, clone and install in “editable” (i.e. development) mode with the -e option. This way you can also pull changes on the fly.

$ git clone https://github.com/mirnylab/cooler.git
$ cd cooler
$ pip install -e .

License

BSD (New)