lib5c.contrib.interlap.util module

Module containing utilities for interfacing with InterLap objects from the external interlap Python package, which provides efficient binary interval search for finding overlapping genomic features.

lib5c.contrib.interlap.util.features_to_interlaps(features, chroms=None)

Converts feature dicts to InterLap objects.

Parameters

• features (dict of list of dict) –

  The keys of the outer dict should be chromosome names as strings. The values of the outer dict represent lists of features found on that chromosome. The inner dicts represent individual genomic features, with at least the following keys:

  {
      'chrom': str,
      'start': int,
      'end'  : int
  }
  

  See lib5c.parsers.load_features() for more information.

• chroms (list of str, optional) – To create InterLap objects for only specified chromosomes, pass a list of their names. Pass None to create InterLap objects for all chromosomes.

Returns

The keys are chromosome names as strings, the values are InterLap objects containing all features on the chromosome. The original feature dicts are saved in the data element of each interval in the InterLap.

Return type

dict of InterLap

lib5c.contrib.interlap.util.query_interlap(interlap, query_feature)

Searches an InterLap object to find features that overlap a given query feature.

Parameters

• interlap (InterLap) – The InterLap object to search. Each interval in the InterLap object must have a data element, see lib5c.contrib.interlap.util.features_to_interlaps().

• query_feature (dict) –

  Dict representing the genomic region in which to search for overlapping features. Must have at least the following keys:

  {
      'chrom': str,
      'start': int,
      'end'  : int
  }
  

Returns

Each dict in the list represents a feature found in the InterLap object that overlaps the query feature.

Return type

list of dict