Nathan Harmston wrote: > Hi, > > The idea is that I m going to use it to build graphs for sequence > alignment (at the moment), I read a discussion on the corebio > (reimplementation of biopython) group about using intervals to > represent sequence slices. The idea being that, my graph may contain > millions of alignments and storing the sequence (the actual ATGC) is > not required. > > class Node(object): > pass > > class Interval(Node): > _id = "gene1" > _start = 50 > _end = 200 > _strand = 1
What is the point of subclassing Node if it's just a dummy? > > class Sequence(object): > _sequence = "atgtcgtgagagagagttgtgag................." > > So one interval on one sequence would align to another interval from > another sequence, but I want changes I make to the interval to be > reflected in the representation later. If I reverse complement it i > want the interval to store this information but the Sequence only > shows this later on when I call use it calling repr or str. > > Do you get what I mean. Only vaguely. You use several terms which appear to be from your trade jargon as they are not understandable when interpreted in either the context of Python-speak or ordinary English e.g. "sequence", "alignment", "ATGC", "reverse complement", "interval". Two options: (a) communicate understandably (b) wait till your wontoks are back from holidays. -- http://mail.python.org/mailman/listinfo/python-list