lib5c.contrib.pybigwig.bigwig module¶
Module for interfacing with the external pyBigWig
Python package, which
enables reading and searching genomic features from .bigwig
files.
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class
lib5c.contrib.pybigwig.bigwig.
BigWig
(filename)[source]¶ Bases:
object
Wrapper class around pyBigWig, mostly to expose our own query() function.
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bw
¶ The underlying pyBigWig object.
- Type
pyBigWig object
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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]]
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