[BioPython] calculate F-Statistics from SNP data

[Giovanni Marco Dall'Olio]

On Thu, Oct 23, 2008 at 11:57 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Oct 23, 2008, Giovanni Marco Dall'Olio wrote:
> > On Wed, Oct 22, Peter wrote:
> >> On Wed, Oct 22, Giovanni Marco Dall'Olio wrote:
> >> >
> >> > Iterators are more difficult to implement in Ped files, because in
> this
> >> > format every line of the file is an individual, so to write an
> iterator
> >> > which iterates by population we will need to read at list the first
> row
> >> > of every line of all the file.
> >>
> >> It sounds like for Ped files it would make more sense to iterate over
> >> the individuals.  The mental picture I have in mind is a big
> >> spreadsheet, individuals as rows (lines), populations (and other
> >> information) as columns.  By having the parser iterate over the
> >> individuals one by one, the user could then "simplify" each individual
> >> as they are read in, recording in memory just the interesting data.
> >> This way the whole dataset need not be kept in memory.
> >
> > This makes sense.
> > Basically, we should write a (Ped/GenePop)Iterator function, which should
> > read the file one line at a time, check if it a has correct syntax and is
> > not a comment, and then use 'yield' to create a Record object. Am I
> right?
>
> Yes :)
>
> Python functions written with "yield" are called  "generator functions",
> see:
> http://www.python.org/dev/peps/pep-0255/
>

So, how should we modify the current GenePop parser to make it work as an
iterator?
Now it has a 'Scanner' and 'Consumer' methods. Should I remove them and
write a RecordIterator instead?
-
http://github.com/dalloliogm/biopython---popgen/tree/master/src/PopGen/Gio/Ped/__init__.py
Can you explain me more or less how the 'Consumer' object works? It is
mandatory to use it when creating biopython objects?

p.s. do you like the doctest to show how to use the parser?


> Peter
>



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