It is a very simple script but several things I want to mention:
1. what is the fast string concatenation method in python?
in the first function, we tend to write something like:
out_seq = ' '
for base in reversed(seq):
out_seq += seq_dict[base]
but it turned out to be very slow. Read this post for more details http://www.skymind.com/~ocrow/python_string/
the list comprehension is the fastest and most elegant way to concatenate a string.
2. for more complicated IUPAC ambiguity codes, read this post:
http://pythonforbiologists.com/index.php/how-to-count-non-dna-bases-in-a-sequence-using-python/
Nucleotide Code: Base: ---------------- ----- A.................Adenine C.................Cytosine G.................Guanine T (or U)..........Thymine (or Uracil) R.................A or G Y.................C or T S.................G or C W.................A or T K.................G or T M.................A or C B.................C or G or T D.................A or G or T H.................A or C or T V.................A or C or G N.................any base . or -............gap
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