Graph Data Structures

[John Machin]

Nathan Harmston wrote:
> 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.

Often happens.

>
> What is a wontok?

It's Melanesian Pidgin (from the English "one talk") meaning a person
who speaks the same language as you, a member of your clan, ... the
context being that [at least in Papua New Guinea] there are relatively
many languages each with relatively not many speakers :-)

>
> 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 sure they can be, but appearances can be deceptive when you mix
tabs and spaces -- or whatever caused the above 4 lines to be not
vertically aligned but staggered diagonally like a flight of ducks
heading equatorwards for winter.

Sometimes a line of code (e.g. str1[2:6] == str2[2:6]) is worth a
thousand pictures :-)

>
> 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

Mapping what keys to what values?

> AND HAVE SOURCE IN INTERVAL ASWELL

So you had a data modelling problem. These are often better solved as a
separate step before you think about implementation details like
dictionaries.

Good luck with your project.

Cheers,
John