lib5c.parsers.primer_names module

Module providing helper functions for working with primer naming conventions, necessary for parsing certain primerfiles.

lib5c.parsers.primer_names.dblalt_primer_parser(name)

The double alternating primer name parser.

Parameters

name (str) – The name of the primer found in the appropriate column of the primer bedfile.

Returns

This dict has the following structure:

{
    'region': str,
    'number': int,
    'orientation': "3'" or "5'",
    'name': str
}

These fields are parsed from the primer name.

Return type

dict

Notes

You can write other name parsers to accommodate different primer naming conventions.

lib5c.parsers.primer_names.default_bin_parser(name)

The default bin name parser.

Parameters

name (str) – The name of the bin found in the appropriate column of the bin bedfile.

Returns

This dict has the following structure:

{
    'region': str,
    'index': int
}

These fields are parsed from the bin name.

Return type

dict

Notes

You can write other name parsers to accommodate different bin naming conventions.

lib5c.parsers.primer_names.default_primer_parser(name)

The default primer name parser.

Parameters

name (str) – The name of the primer found in the appropriate column of the primer bedfile.

Returns

This dict has the following structure:

{
    'region': str,
    'number': int,
    'name': str
}

These fields are parsed from the primer name.

Return type

dict

Notes

You can write other name parsers to accommodate different primer naming conventions.

lib5c.parsers.primer_names.guess_primer_name_parser(name)

Guesses the appropriate primer or bin name parser to use by looping through a list of possible parsers and testing if they work on a given primer name.

Parameters

name (str) – The name of a primer to use for testing.

Returns

The parser thought to be appropriate for this kind of primer name.

Return type

function