lib5c.writers.hic module

Module for writing contact matrices to text files formatted in the style of Rao et al.’s GEO submission.

lib5c.writers.hic.write_rao_matrix(matrix, resolution, outfile)[source]

Function for writing matrices to text files formatted in the style of Rao et al.’s GEO submission.

See https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525 for more details.

Parameters

  • matrix (np.ndarray) – The matrix to write to file.

  • resolution (int) – The resolution of the matrix, in base pairs.

  • outfile (str) – String reference to the file to write to.

Notes

To write matrices for all chromosomes in one call, try:

write_rao_matrix(counts_dict, 40000, {chrom: ‘outdir/%s.matrix’ % chrom

for chrom in counts_dict})

Examples

>>> import numpy as np
>>> from lib5c.writers.hic import write_rao_matrix
>>> from lib5c.parsers.hic import load_range_from_contact_matrix
>>> matrix = np.arange(16).reshape((4, 4))
>>> matrix += matrix.T
>>> write_rao_matrix(matrix, 10000, 'test/rao_matrix_written.matrix')
>>> grange = {'chrom': 'chr1', 'start': 0, 'end': 40000}
>>> parsed_matrix, _ = load_range_from_contact_matrix(
...     'test/rao_matrix_written.matrix', grange)
>>> np.all(matrix == parsed_matrix)
True