lib5c.contrib.pybigwig.bigwig module¶
Module for interfacing with the external pyBigWig
Python package, which
enables reading and searching genomic features from .bigwig
files.
-
class
lib5c.contrib.pybigwig.bigwig.
BigWig
(filename)[source]¶ Bases:
object
Wrapper class around pyBigWig, mostly to expose our own query() function.
-
bw
¶ The underlying pyBigWig object.
Type: pyBigWig object
-
query
(grange, stat='max', num_bins=None, exact=True)[source]¶ Signature rework/wrapper around pyBigWig’s stats() and intervals().
Parameters: - grange (Dict[str, Any]) –
The genomic range to query. Should have at least the following structure:
{ 'chrom': str, 'start': int, 'end': int }
- num_bins (Optional[int]) – Pass an integer to split grange into num_bins bins of equal width, and return a summary statistic for each bin. Pass None to return all bigwig features in grange without binning.
- stat (str) – The summary statistic to use if num_bins is not None.
- exact (bool) – Pass True to ignore bigwig zoom levels when computing summary statistics and return the exact answer instead.
Returns: A list of bed features with ‘value’ keys representing the results of the query.
Return type: List[Dict[str, Any]]
- grange (Dict[str, Any]) –
-