[Biopython-dev] Sequences and simple plots

Peter biopython at maubp.freeserve.co.uk
Thu Sep 25 19:39:49 UTC 2008

On Thu, Sep 25, 2008 at 7:34 PM, Jared Flatow <jflatow at northwestern.edu> wrote:
> Hi Peter,
> Good ideas for some useful examples! (though I can't actually find them in
> the cookbook...)

They are in CVS only at the moment - I can send you the PDF of the
current tutorial if you like off list.  We don't normally update the
tutorial on the website except as part of making a new release - this
avoid the tutorial talking about unreleased code.

> Anyway I hope you don't mind but while I was looking, I added another
> example for SeqIO input/output that uses the new format method:
> http://biopython.org/wiki/SeqIO
> I tend to prefer this type of method to SeqIO.write, though I don't think it
> appears anywhere in the documentation

The format method should be in the Tutorial as of Biopython 1.48 (see
the final section of Chapters 4 and 5).

Personally I think for your new example using "with" just confuses
things, but otherwise mentioning the format() method in this context
makes sense.  I would probably make it explicit that this with ONLY
work for sequential file formats - which is why I prefer to encourage
the SeqIO.write() method giving all the records at once (possibly as
an iterator).


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