bandhic 0.2.0

A memory-efficient Python package for managing and analyzing Hi-C data down to sub-kilobase resolution

BandHiC

BandHiC is a Python package for efficient storage, manipulation, and analysis of Hi-C matrices using a banded matrix representation.

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Overview

Given that most informative chromatin contacts occur within a limited genomic distance (typically within 2 Mb), BandHiC adopts a banded storage scheme that stores only a configurable diagonal bandwidth of the dense Hi-C contact matrices. This design can reduce memory usage by up to 99% compared to dense matrices, while still supporting fast random access and user-friendly indexing operations. In addition, BandHiC supports flexible masking mechanisms to efficiently handle missing values, outliers, and unmappable genomic regions. It also provides a suite of vectorized operations optimized with NumPy, making it both scalable and practical for ultra-high-resolution Hi-C data analysis.

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Features

1. Memory-efficient data structure for Hi-C matrices
   • Optimized for large-scale chromatin interaction data
   • Support random accessing
2. NumPy-like API for ease of adoption
   • Familiar interface to reduce learning curve
3. Full NumPy compatibility
   • Seamless interoperability with NumPy operations
4. Efficient masking mechanisms
   • Handle missing values, outliers, and unmappable regions
5. Efficient vectorized operations optimized with NumPy
   • Enabling scalable analysis of ultra-high-resolution Hi-C datasets
6. Reduction functions with diagonal-axis support
   • Supports mean, max, sum, etc.
7. Input support for .hic (straw) and .cool (cooler) formats
   • Builds banded matrices directly from standard Hi-C files
8. Implementation of TopDom algorithm and KR normalization
   • Banded-matrix-optimized Hi-C analysis methods

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Useful links

For full tutorials and API reference, please refer to:

• Documentation (PDF)
• Website (online docs)

If you have any questions, please contact us:

• [e-mail]

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Data structure

BandHiC.band_hic_matrix is the core class implemented in the BandHiC package. This figure shows how to convert a dense symmetric matrix $A\in R^{n\times n}$ into a band_hic_matrix object $B$ consisting of a data matrix $D\in R^{n\times k}$, an element-wise mask matrix $M\in R^{n\times k}$, a row/column mask matrix $X\in R^{n\times 1}$, and a default value $d$ for out-of-band entries. Diagonal elements from $A$ are reorganized into columns of $D$; $M$ marks missing or outlier entries; $X$ indicates masked rows or columns. band_hic_matrix retains only the diagonals within a user-defined bandwidth $k$, yielding a compact representation $D$. This ensures that each column in $D$ corresponds to a fixed diagonal of $A$, such that the mapping $\ A[i,\ j]=D[i,j-i]$ holds for $|i-j|<k$.

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🔧 Installation

Core dependencies (required)

BandHiC could be installed in a linux-like system and requires the following dependencies.

1. python >= 3.11
2. numpy >= 2.3
3. pandas >= 2.3
4. scipy >= 1.16
5. cooler >= 0.10
6. hic-straw >= 1.3
7. joblib >= 1.2
8. numba >= 0.59

There are two recommended ways to install BandHiC:

Option 1: Install via pip

If you already have Python ≥ 3.11 installed:

$ pip install bandhic

If the installation fails due to dependency issues, please manually install the dependencies and then rerun the above command.

Option 2: Install from source code with conda

1. Clone the repository

$ git clone https://github.com/xdwwb/BandHiC-Master.git
$ cd BandHiC-Master

2. Create the environment and activate it

$ conda env create -f environment.yml
$ conda activate bandhic

3. Install BandHiC

$ pip install .

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Optional dependency for .hic file support: hic-straw

Support for reading .hic format Hi-C data relies on the third-party package hic-straw, which is not installed automatically with BandHiC.

If you do not need to read .hic files, you can ignore this dependency and use BandHiC normally.

If you do need .hic support, please install hic-straw manually using one of the following methods.

Method 1: Install via pip

pip install hic-straw

Note that hic-straw includes native C/C++ extensions. Installation via pip may require a compatible compiler toolchain and system libraries (e.g. libcurl development headers).

Method 2: Install via Conda

conda install -c bioconda hic-straw

Using Conda provides prebuilt binaries on many platforms and avoids local compilation issues.

Upstream installation guide

For detailed, system-specific installation instructions, please refer to the official straw repository maintained by the Aiden Lab:

https://github.com/aidenlab/straw

🚀 Quick Start

Prerequisites

BandHiC can serve as an alternative to the NumPy package when managing and manipulating Hi-C matrices, aiming to address the issue of excessive memory usage caused by storing dense matrices using NumPy’s ndarray. At the same time, BandHiC supports masking operations similar to NumPy’s ma.MaskedArray module, with enhancements tailored for Hi-C data.

Users can leverage their experience with NumPy when using the BandHiC package, so it is recommended that users have some basic knowledge of NumPy. A link to NumPy is provided below: https://numpy.org

Import bandhic package

>>> import bandhic as bh

Initialize a band_hic_matrix object

Initialize from a SciPy coo_matrix object:

>>> from scipy.sparse import coo_matrix
>>> coo = coo_matrix(([1, 2, 3], ([0, 1, 2],[0, 1, 2])), shape=(3,3))
>>> mat1 = bh.band_hic_matrix(coo, diag_num=2)

Initialize from a tuple (data, (row_indices, column_indices)):

>>> mat2 = bh.band_hic_matrix(([4, 5, 6], ([0, 1, 2],[2, 1, 0])), diag_num=1)

Initialize from a full dense array, only upper-triangular part is stored, lower part is symmetrized:

>>> arr = np.arange(16).reshape(4,4)
>>> mat3 = bh.band_hic_matrix(arr, diag_num=3)

Load or save a band_hic_matrix object

>>> bh.save_npz('./sample.npz', mat)
>>> mat = bh.load_npz('./sample.npz')

Load from .hic file:

>>> mat = bh.straw_chr('sample.hic', 
                        'chr1', 
                        resolution=10000, 
                        diag_num=200
                        )

Load from .mcool file:

>>> mat = bh.cooler_chr('sample.mcool', 
                        'chr1', 
                        diag_num=200
                        resolution=10000, 
                        )

Construct a band_hic_matrix object

Create a band_hic_matrix object filled with zeros.

>>> mat1 = bh.zeros((5, 5), diag_num=3, dtype=float)

Create a band_hic_matrix object filled with ones.

>>> mat2 = bh.ones((5, 5), diag_num=3, dtype=float)

Create a band_hic_matrix object filled as an identity matrix.

>>> mat3 = bh.eye((5, 5), diag_num=3, dtype=float)

Create a band_hic_matrix object filled with a specified value.

>>> mat4 = bh.full((5, 5), fill_value=0.1, diag_num=3, dtype=float)

Create a band_hic_matrix object matching another matrix, filled with zeros.

>>> mat5 = bh.zeros_like(mat1, diag_num=3, dtype=float)

Create a band_hic_matrix object matching another matrix, filled with ones.

>>> mat6 = bh.ones_like(mat1, diag_num=3, dtype=float)

Create a band_hic_matrix object matching another matrix, filled as an identity matrix.

>>> mat7 = bh.eye_like(mat1, diag_num=3, dtype=float)

Create a band_hic_matrix object matching another matrix, filled with a specified value.

>>> mat8 = bh.full_like(mat1, fill_value=0.1 diag_num=3, dtype=float)

Indexing on band_hic_matrix

First, we create a band_hic_matrix object:

>>> mat = bh.band_hic_matrix(np.arange(16).reshape(4,4), diag_num=2)

Single-element access (scalar)

>>> mat[1, 2]
6

Masked element returns masked

>>> mat2 = bh.band_hic_matrix(np.eye(4), dtype=int, diag_num=2, mask=([0],[1]))
>>> mat2[0, 1]
masked

Square submatrix via two-slice indexing returns band_hic_matrix

>>> sub = mat[1:3, 1:3]
>>> isinstance(sub, bh.band_hic_matrix)
True

Single-axis slice returns band_hic_matrix for square region

>>> sub2 = mat[0:2]  # equivalent to mat[0:2, 0:2]
>>> isinstance(sub2, bh.band_hic_matrix)
True

Fancy indexing returns ndarray or MaskedArray

>>> arr = mat[[0,2,3], [1,2,0]]
>>> isinstance(arr, np.ndarray)
True

Add mask to some entries

>>> mat.add_mask([0,1],[1,2])
>>> masked_arr = mat[[0,1], [1,2]]
>>> isinstance(masked_arr, np.ma.MaskedArray)
True

Boolean indexing with band_hic_matrix

>>> mat3 = bh.band_hic_matrix(np.eye(4), diag_num=2, mask=([0,1],[1,2]))
>>> bool_mask = mat3 > 0  # Create a boolean mask
>>> result = mat3[bool_mask]  # Use boolean mask for indexing
>>> isinstance(result, np.ma.MaskedArray)
True
>>> result
masked_array(data=[1.0, 1.0, 1.0, 1.0],
            mask=[False, False, False, False],
    fill_value=0.0)

Masking

Add item-wise mask:

>>> mat.add_mask([0, 1], [1, 2])

Add row/column mask:

>>> mask = np.array([True, False, False])
>>> mat.add_mask_row_col(mask)

Remove mask for specified indices.

>>> mat.unmask(( [0],[1] ))

Remove all item-wise mask and row/column mask.

>>> mat.unmask()

Remove all item-wise mask and row/column mask.

>>> mat.clear_mask()

Drop all item-wise mask but preserve all row/column mask.

>>> mat.drop_mask()

Drop all row/column mask.

>>> mat.drop_mask_row_col()

Access masked band_hic_matrix will obtain np.ma.MaskedArray object:

>>> mat.add_mask([0, 1], [1, 2])
>>> masked_arr = mat[[0,1], [1,2]]
>>> isinstance(masked_arr, np.ma.MaskedArray)
True

Universal functions(ufunc)

Universal functions that BandHiC support:

Function	Description	Function	Description
absolute	Absolute value	add	Element-wise addition
arccos	Inverse cosine	arccosh	Inverse hyperbolic cosine
arcsin	Inverse sine	arcsinh	Inverse hyperbolic sine
arctan	Inverse tangent	arctan2	Arctangent of y/x with quadrant
arctanh	Inverse hyperbolic tangent	bitwise_and	Element-wise bitwise AND
bitwise_or	Element-wise bitwise OR	bitwise_xor	Element-wise bitwise XOR
cbrt	Cube root	conj	Complex conjugate
conjugate	Alias for conj	cos	Cosine function
cosh	Hyperbolic cosine	deg2rad	Degrees to radians
degrees	Radians to degrees	divide	Element-wise division
divmod	Quotient and remainder	equal	Element-wise equality test
exp	Exponential	exp2	Base-2 exponential
expm1	exp(x) - 1	fabs	Absolute value (float)
float_power	Floating-point power	floor_divide	Integer division (floor)
fmod	Modulo operation	gcd	Greatest common divisor
greater	Element-wise greater-than test	greater_equal	Greater-than or equal test
heaviside	Heaviside step function	hypot	Euclidean norm
invert	Bitwise inversion	lcm	Least common multiple
left_shift	Bitwise left shift	less	Element-wise less-than test
less_equal	Less-than or equal test	log	Natural logarithm
log1p	log(1 + x)	log2	Base-2 logarithm
log10	Base-10 logarithm	logaddexp	log(exp(x) + exp(y))
logaddexp2	Base-2 version of logaddexp	logical_and	Element-wise logical AND
logical_or	Element-wise logical OR	logical_xor	Element-wise logical XOR
maximum	Element-wise maximum	minimum	Element-wise minimum
mod	Remainder (modulo)	multiply	Element-wise multiplication
negative	Element-wise negation	not_equal	Element-wise inequality test
positive	Returns input unchanged	power	Raise to power
rad2deg	Radians to degrees	radians	Degrees to radians
reciprocal	Element-wise reciprocal	remainder	Modulo remainder
right_shift	Bitwise right shift	rint	Round to nearest integer
sign	Sign of input	sin	Sine function
sinh	Hyperbolic sine	sqrt	Square root
square	Square of input	subtract	Element-wise subtraction
tan	Tangent function	tanh	Hyperbolic tangent
true_divide	Division that returns float

BandHiC supports these universal functions, and they can be used in the following four ways:

1. As methods of the band_hic_matrix object:

# When two band_hic_matrix objects are involved, their shape and diag_num must match
>>> mat3 = mat1.add(mat2)
>>> mat4 = mat1.less(mat2)
>>> mat5 = mat1.negative()

2. As functions of the BandHiC package

>>> mat3 = bh.add(mat1, mat2)
>>> mat4 = bh.less(mat1, mat2)
>>> mat5 = bh.negative(mat1)

3. Using mathematical operators:

>>> mat3 = mat1 + mat2
>>> mat4 = mat1 < mat2
>>> mat5 = - mat1

4. Calling NumPy's universal functions:

>>> mat3 = np.add(mat1, mat2)
>>> mat4 = np.less(mat1, mat2)
>>> mat5 = np.negative(mat1)

Array reduction and other Functions

Function	Description
sum	Compute the sum of all elements along the specified axis
prod	Compute the product of all elements along the specified axis
min	Return the minimum value along the specified axis
max	Return the maximum value along the specified axis
mean	Compute the arithmetic mean along the specified axis
var	Compute the variance (average squared deviation)
std	Compute the standard deviation (square root of variance)
ptp	Compute the range (max - min) of values along the axis
all	Return True if all elements evaluate to True
any	Return True if any element evaluates to True
clip	Limit values to a specified min and max range

BandHiC supports these functions, and they can be used in the following three ways:

1. As methods of the band_hic_matrix object:

Compute the sum of all elements including out-of-band values filled with default_value.

>>> result0 = mat1.sum()

Compute the sum of all elements along the row axis

>>> result1 = mat1.sum(axis=0)
>>> result1 = mat1.sum(axis='row')

Compute the sum of all elements along the diag axis

>>> result2 = mat1.sum(axis='diag')

2. Calling BandHiC's functions:

>>> result0 = bh.sum(mat1)
>>> result1 = bh.sum(mat1, axis=0)
>>> result2 = bh.sum(mat1, axis='diag')

3. Calling NumPy's functions:

>>> result0 = np.sum(mat1)
>>> result1 = np.sum(mat1, axis=0)
>>> result2 = np.sum(mat1, axis='diag')

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📝 License

MIT License © 2025 Weibing Wang