lib5c.util.slicing module

Module containing utility functions related to matrix and primermap slicing.

lib5c.util.slicing.convert_grange_to_slice(grange, regional_primermap)[source]

Finds the slice of a regional primermap/pixelmap that covers a given grange.

Parameters

  • grange (dict) – The genomic range the slice should cover. Should have keys ‘chrom’, ‘start’, ‘end’.

  • regional_primermap (list of dict) – The primermap whose indices should make up the slice.

Returns

The slice.

Return type

slice

Examples

>>> regional_primermap = [{'chrom': 'chr1', 'start': 100, 'end': 200},
...                       {'chrom': 'chr1', 'start': 300, 'end': 400},
...                       {'chrom': 'chr1', 'start': 500, 'end': 600}]
>>> grange = {'chrom': 'chr1', 'start': 350, 'end': 550}
>>> convert_grange_to_slice(grange, regional_primermap)
slice(1, 3, None)
>>> grange = {'chrom': 'chr1', 'start': 300, 'end': 600}
>>> convert_grange_to_slice(grange, regional_primermap)
slice(1, 3, None)
lib5c.util.slicing.convert_slice_to_grange(s, regional_pixelmap)[source]

Converts an index-based slice into a dict describing the genomic range covered by the slice.

Parameters

  • s (slice) – The slice.

  • regional_pixelmap (list of dict) – The pixelmap or primermap being indexed into by the slice.

Returns

The genomic range covered by the slice, as a dict with ‘chrom’, ‘start’, and ‘end’ keys.

Return type

dict

Examples

>>> regional_pixelmap = [{'chrom': 'chr1', 'start': 100, 'end': 200},
...                      {'chrom': 'chr1', 'start': 300, 'end': 400},
...                      {'chrom': 'chr1', 'start': 500, 'end': 600}]
>>> (convert_slice_to_grange(slice(1, 3), regional_pixelmap) ==
...  {'chrom': 'chr1', 'start': 300, 'end': 600})
True
lib5c.util.slicing.slice_matrix_by_grange(matrix, regional_primermap_x, grange_x, grange_y=None, regional_primermap_y=None)[source]

Convenience function for slicing matrices.

Parameters

  • matrix (np.ndarray) – The matrix to slice.

  • regional_primermap_x (list of dict) – The primermap describing the column indices of matrix.

  • grange_x (dict) – The genomic range to slice the x-axis of the matrix with (columns).

  • grange_y (dict, optional) – The genomic range to slice the y-axis of the matrix with (rows). Pass None to assume that the two ranges are equal.

  • regional_primermap_y (list of dict, optional) – The primermap describing the row indices of matrix. If matrix is symmetric, pass None.

Returns

The np.ndarray is the sliced matrix. The two dicts are the x- and y-axis ranges actually represented by the matrix slice.

Return type

np.ndarray, dict, dict