lib5c.util.bedgraph module¶
Module containing utilities for manipulating bedgraph files.
-
lib5c.util.bedgraph.
in_boundaries
(peak, chrom, boundaries)[source]¶ Checks to see if a given feature on a given chromosome is within the boundaries.
- Parameters
peak (dict) –
The feature to check. This dict should have the following structure:
{ 'start': int, 'end': int }
See lib5c.parsers.bed.load_features().
chrom (str) – The chromosome this feature is on.
boundaries (dict of dicts) –
Information about the region boundaries. The outer keys are region names as strings. The values are dicts describing the boundaries of that region with the following structure:
{ 'chrom': str, 'start': int, 'end': int }
- Returns
True if the feature is in one of the regions, False otherwise.
- Return type
bool
-
lib5c.util.bedgraph.
reduce_bedgraph
(bedfile, pixelmap)[source]¶ Reduces a bedgraph file by excluding peaks that fall outside of the regions described by a pixelmap.
- Parameters
bedfile (str) – String reference to the bedgraph file to reduce.
pixelmap (dict of lists of dicts) –
The keys of the outer dict are region names. The values are lists, where the
i
th entry represents thei
th bin in that region. Bins are represented as dicts with at least the following structure:{ 'chrom': string, 'start': int, 'end' : int }
See
lib5c.parsers.primers.get_pixelmap()
.
- Returns
The keys are chromosome names. The values are lists of peaks for that chromosome. The peaks are represented as dicts with at least the following keys:
{ 'start': int, 'end' : int }
- Return type
dict of lists of dicts