lib5c.util.bedgraph module

Module containing utilities for manipulating bedgraph files.

lib5c.util.bedgraph.in_boundaries(peak, chrom, boundaries)

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.main()

lib5c.util.bedgraph.reduce_bedgraph(bedfile, pixelmap)

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 the i 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