Library

Barcode design via the library is done in three steps. First obtain the full set of permutations with the all_barcodes function:

>>> from barcode import all_barcodes, filter_distance, filter_stretches
>>>
>>> # Generate all barcodes of length 2.
>>> all_barcodes(2)
['AA', 'AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA',
'TC', 'TG', 'TT']

The resulting list can be filtered with the filter_distance and filter_stretches functions:

>>> # Filter all barcodes of length 3 for a minimal edit distance of 3.
>>> filter_distance(all_barcodes(3), 3)
['AAA', 'CCC', 'GGG', 'TTT']
>>>
>>> # Filter all barcodes of lenght 2 for mononucleotide stretches of length
>>> # longer than 1.
>>> filter_stretches(all_barcodes(2), 1)
['AC', 'AG', 'AT', 'CA', 'CG', 'CT', 'GA', 'GC', 'GT', 'TA', 'TC', 'TG']

For the best result, apply the filter_stretches function before applying the filter_distance function:

>>> # Make a set of barcodes of length 3, having no mononucleotide stretches
>>> # and a minimum edit distance of 3.
>>> filter_distance(filter_stretches(all_barcodes(3), 1), 3)
['ACA', 'CGC', 'GAG']