epiout.hic
Module Contents
Classes
Read chromotain contacts information from Hi-C data from hic files. |
Functions
Import optional dependency hic-straw if installed in env, |
- epiout.hic.import_hicstraw()
- Import optional dependency hic-straw if installed in env,
otherwise raise an error.
- class epiout.hic.HicReader(hic_file_paths: List[str], chrom_sizes: str, normalization='NONE', binsize=5000, bin_vicinity=200, batch_size=500000)
Read chromotain contacts information from Hi-C data from hic files.
- Parameters
hic_file_paths – List of hic file paths.
chrom_sizes – Chromosome sizes file path.
normalization – Normalization method for Hi-C data (default=None). Valid normalization methods defined in hic-straw package.
binsize – Bin size for Hi-C data (default=5_000).
bin_vicinity – Number of bins to consider around the diagonal (default=200) so defaults consider 1 Mb vicinity.
batch_size – Batch size for reading Hi-C data (default=500_000). Too large may cause memory issues and too small may cause performance issues.
- static _read_chrom_sizes(chrom_sizes)
Read chromosome sizes from file.
- Returns
Dictionary of chromosome sizes.
- static match_chrom(chrom, chroms)
Match chromosome name with the chromosome names in the hic file.
- Parameters
chrom – Chromosome name.
chroms – Chromosome names in the hic file.
- Returns
Matched chromosome name.
- _read_contacts(self, chrom)
Read contacts from hic file for given chromosome.
- Parameters
chrom – Chromosome name.
- Yields
Contact matrix for given chromosome as numpy array
- contact_scores(self, chrom)
Calculate contact scores for given chromosome.
- Parameters
chrom – Chromosome name.
- Returns
Contact scores as numpy array.