lib5c.util.annotationmap module¶

Module containing utilities for constructing annotatiomaps.

Annotatiomaps record the number of BED features of a certain type present at a given linear bin as specified by a pixelmap.

lib5c.util.annotationmap.main()[source]¶

lib5c.util.annotationmap.make_annotationmaps(pixelmap, directory='./annotations', add_wildcard=True)[source]¶

Gets a dict of annotationmaps, one for every BED file in a specified directory.

Parameters

pixelmap (pixelmap) – The pixelmap to use to generate the annotationmap. See lib5c.parsers.bed.get_pixelmap().
directory (str) – The directory to look in for BED files describing the annotations.
add_wildcard (bool) – Pass True to add a ‘wildcard’ annotation that has 100 hits in every bin. Useful for doing “unsided” enrichments later.

Returns

The keys of the outer dict are annotation names as parsed from the names of the BED files in directory. The values are annotationmaps. See lib5c.util.annotationmap.get_single_annotatiomap().

Return type

dict of dict of lists

lib5c.util.annotationmap.make_single_annotationmap(annotation, pixelmap)[source]¶

Generates an annotationmap given an annotation and a pixelmap.

Parameters

annotation (dict of lists of dicts) –
The keys are chromosome names. The values are lists of features for that chromosome. The features are represented as dicts with the following structure:
```
{
    'chrom': str
    'start': int,
    'end'  : int,
}
```
See lib5c.parsers.bed.load_features().
pixelmap (pixelmap) – The pixelmap to use to generate the annotationmap. See lib5c.parsers.bed.get_pixelmap().

Returns

The keys of the dictionary are region names. The values are lists, where the i th entry represents the number of intersections between the annotation and the i th bin of that region.

Return type

dict of lists