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- dimer_groups(width)
- dimer_groups(width) -- For every possible word of width "width" with at most one ambiguity code,
assemble the REGULAR EXPRESSIONS of form word-gap-(word'), where (word')
is the reverse complement of word, and the gap is the text string '.{a,b}'
where 'a' and 'b' vary between 0-16 such that b > a. Intended to represent
all possible variable gap motifs that are symmetric.
- dimer_words(width)
- dimer_words(width) -- For every possible word of width "width" with at most one ambiguity code,
assemble the words of form word-gap-(word'), where (word') is the reverse
complement of word, and gap is a string of "N"s ranging in length from
0 to 12.
- expt()
- gapped_words(width)
- gapped_words(width) -- For every pair returned from uniq_syl_pairs (see documentation for that function)
assemble into words with spacings 0-12. So (AA, GT) --> AAGT, AANGT, AANNGT, ...
- permute(letters, depth, seqs=[''], curdepth=0)
- permute(letters, depth, seqs=[''],curdepth=0) -- Generate all possible sequences from the alphabet
"letters" of length "depth" (sorry about the
variable names). For example, "permute('ACGT',4)"
generates all 256 possible 4-letter DNA sequences.
- restricted_permute(base_letters, extra_letters, depth, seqs=[''])
- restricted_permute(base_letters, extra_letters, depth, seqs = ['']) -- [Utility function] Like permute()
above, but allows at most one letter
from "extra_letters" into the
permutations. Used for including
ambiguity codes.
- uniq_syl_pairs(width)
- uniq_syl_pairs(width) -- Generates all possible (left,right) sequences, allowing at most one
ambiguous letter (S, W, R, or Y) in either left or right. uniq_syl_pairs(4)
returns 836,160 tuples, beginning ('AAAA', 'AAAA'), ('AAAA', 'AAAC'),
('AAAA', 'AAAG'), ('AAAA', 'AAAT'), ('AAAA', 'AAAS'), ...
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