Graph Data Structures

[Nathan Harmston]

Hi,

It seems that by just going through the problem writing out a better
explanation for the reply I have figured out a solution and the
problem isnt as difficult as I thought it would be.

What is a wontok?

Thanks

Nathan

PS --> the start of my reply:

class Interval(object):
     _id = "gene1"
      _start = 50
     _end = 200
     _strand = 1

class Sequence(object):
    _sequence = "atgtcgtgagagagagttgtgag................."

> Only vaguely. You use several terms which appear to be from your trade
> jargon

Sequence is a string made from a restricted alphabet (A,T,G,C...).
Sequences can be aligned:          1     ATGCTGCAT
                                                      2     TAGCTGTTA
                                                                  -------
                                                                 2        5

I m trying to represent this as a graph Interval(id=1, start=2, end=6,
strand=1) ---edge------Interval(id=2, start=2, end=6, strand=1)

The problem is I was planning on storing the sequences in a dictionary
{id:Seq}, however each dictionary would represent a different source
of sequences. File1, File2....... (
STORE THE SOURCES AS A DICT AND HAVE SOURCE IN INTERVAL ASWELL