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