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.
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
- pixelmap (pixelmap) – The pixelmap to use to generate the annotationmap. See
-
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 thei
th bin of that region.Return type: dict of lists
- annotation (dict of lists of dicts) –