Line segments, overlap, and bits

[George Sakkis]

On Mar 26, 5:28 pm, Sean Davis <seand... at gmail.com> wrote:
> I am working with genomic data.  Basically, it consists of many tuples
> of (start,end) on a line.  I would like to convert these tuples of
> (start,end) to a string of bits where a bit is 1 if it is covered by
> any of the regions described by the (start,end) tuples and 0 if it is
> not.  I then want to do set operations on multiple bit strings (AND,
> OR, NOT, etc.).  Any suggestions on how to (1) set up the bit string
> and (2) operate on 1 or more of them?  Java has a BitSet class that
> keeps this kind of thing pretty clean and high-level, but I haven't
> seen anything like it for python.
>
> Thanks,
> Sean

Have you looked at Pypi [1] ? From a quick search, there are at least
four potentially relevant packages: BitPacket, BitVector, BitBuffer,
BitBucket.

George


[1] http://pypi.python.org/pypi?%3Aaction=search&term=bit&submit=search