Issue #42 new
Wilmer Garzon
created an issue

Hi Friends,

I have a problem and I would like if your help me. I have many intervals and I need join all in one sequence, but I need solve the overlap and gaps. Example:

I1:[3,8] = A T C G G G I2:[2,6] = G A C G A I3:[9,11] = T A C Result = G A N N N G G T A C

Any idea....

Thanks.

Comments (2)

  1. Anonymous

    I'm pretty sure there's nothing in bxpython that is a direct solution. But it seems like a simple thing to solve. The straightforward algorithm would be create an array of L zeros (where L is the full sequence length) interpret that as 4 bits per entry, one bit for A, one for C, etc. scan each of your intervals and set the corresponding bits then scan the array and report the contents using the IUPAC 15-letter code

    There also may be some SNP tool that does something close to what you want.

    Bob H

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