@John: No, ranges in Python are half-open, i.e. The 7 isn't included and you end up with start - stop = 6 options from start to stop - 1. – user395760 Mar 15 '11 at 18:11 1 random.randint(1, 6) might be more clear. – nmichaels Mar 15 '11 at 18:15. Python dice simulator, why it is running without stopping? Hot Network Questions Scrum and interruptions Why the pitot tube is located near the nose? GitHub Gist: instantly share code, notes, and snippets.

(This is not why most people want to use khmer – see An assembly handbook for khmer - rough draft for that.)

khmer ktables are a simple C++ library for counting k-mers in DNAsequences. There’s a complete Python wrapping and it should be prettydarned fast; it’s intended for genome-scale k-mer counting.

‘ktable’s are a table of 4**k counters. khmer then maps each k-merinto this table with a simple (and reversible) hash function.

Right now, only the Python interface is documented here. The C++interface is essentially identical; if you need to use it and wantit documented, drop me a line.

Counting Speed and Memory Usage¶

On the 5 mb Shewanella oneidensis genome, khmer takes less than a secondto count all k-mers, for any k between 6 and 12. At 13 it craps outbecause the table goes over my default stack size limit.

Approximate memory usage can be calculated by finding the size of alonglong on your machine and then multiplying that by 4**k.For a 12bp wordsize, this works out to 16384*1024; on an Intel-basedprocessor running Linux, longlong is 8 bytes, so memory usageis approximately 128 mb.

Python interface¶

Essentially everything requires a ktable.

These commands will create a new ktable of size 4**L, suitablefor counting L-mers.

Each ktable object has a few accessor functions:

• ktable.ksize() will return L.
• ktable.max_hash() will return the max hash value in the table, 4**L - 1.
• ktable.n_entries() will return the number of table entries, 4**L.

The forward and reverse hashing functions are directly accessible:

• hashval=ktable.forward_hash(kmer) will return the hash value

  of the given kmer.

• kmer=ktable.reverse_hash(hashval) will return the kmer that hashes

  to the given hashval.

There are also some counting functions:

• ktable.count(kmer) will increment the count associated with the given kmerby one.
• ktable.consume(sequence) will run through the sequence and counteach kmer present.
• n=ktable.get(kmer hashval) will return the count associated with thegiven kmer string or the given hashval, whichever is passed in.
• ktable.set(kmer hashval,count) set the count for the given kmerstring or hashval.

In all of the cases above, ‘kmer’ is an L-length string, ‘hashval’ isa non-negative integer, and ‘sequence’ is a DNA sequence containing ONLYA/C/G/T.

Note: ‘N’ is not a legal DNA character as far as khmer is concerned!

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And, finally, there are some set operations:

• ktable.clear() empties the ktable.
• ktable.update(other) adds all of the entries in other intoktable. The wordsize must be the same for both ktables.
• intersection=ktable.intersect(other) returns a ktable whereonly nonzero entries in both ktables are kept. The count for achentry is the sum of the counts in ktable and other.

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An Example¶

This short code example will count all 6-mers present in the givenDNA sequence, and then print them all out along with their prevalence.

Released:

Encodes and decodes files in .crap format. This allows one to execute the file in any languge, immediately upon import.

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