lib5c.util.primers module

Module containing utilities for manipulating 5C primer information.

lib5c.util.primers.aggregate_primermap(primermap, region_order=None)

Aggregates a primermap into a single list.

Parameters:

• primermap (Dict[str, List[Dict[str, Any]]]) – Primermap to aggregate. See lib5c.parsers.primers.get_primermap().
• region_order (Optional[List[str]]) – Order in which regions should be concatenated. If None, the regions will be concatenated in order of increasing genomic coordinate. See lib5c.util.primers.determine_region_order().

Returns:

The dicts represent primers in the same format as the inner dicts of the passed primermap; however, they exist as a single flat list instead of within an outer dict structure. The regions are arranged within this list in contiguous blocks, arranged in the order specified by the region_order kwarg.

Return type:

List[Dict[str, Any]]

Notes

This function returns a list of references to the original primermap, under the assumption that primer dicts are rarely modified. To avoid this, pass a copy of the primermap instead of the original primermap.

lib5c.util.primers.determine_region_order(primermap)

Orders regions in a primermap by genomic coordinate.

Parameters:primermap (Dict[str, List[Dict[str, Any]]]) – Primermap containing information about the regions to be ordered. See lib5c.parsers.primers.get_primermap(). Returns:List of ordered region names. Return type:List[str]

lib5c.util.primers.guess_bin_step(regional_pixelmap)

Guesses the bin step from a regional pixelmap.

Parameters:regional_pixelmap (List[Dict[str, Any]]) – Ordered list of bins for a single region. Returns:The guessed bin step for this pixelmap. Return type:int

lib5c.util.primers.natural_sort_key(s)

Function to enable natural sorting of alphanumeric strings.

Parameters:s (str) – String being sorted. Returns:This list is an alternative represenation of the input string that will sort in natural order. Return type:List[Union[int, str]]

Notes

Function written by SO user http://stackoverflow.com/users/15055/claudiu and provided in answer http://stackoverflow.com/a/16090640.