[BioPython] Sequence numbering. Moving on...

[Andrew Dalke]

Thomas.Sicheritz@molbio.uu.se said:
>Again - for practical reasons, why not an additional
>return_seqReverse method ?
>    MySlice(7,30).return_seqReverse().translate()

Does this mean it returns a new (reversed) sequence, or that it
does the reverse and returns itself?

For the former, that means the object doesn't do anything in
your example, since the final result it thrown away.  For
the latter, consistency with Python's existing behaviour.

Seen any foolish hobgoblins around? [*]

>BTW - I don't think I have an account on a
>bioperl/biopython/bioxml/biojava/whatever machine
>- but I'd like to look into your line_lexer, is it available via
>FTP ?
>
>If I am able to understand your parser, I can try to add rules for
>SWISSPROT.

Take a look at
   ftp://ftp.ks.uiuc.edu/pub/group/dalke/line_lexer.tar.gz
The code isn't well documented, and I did it in one evening to
see if the idea of building the parse tree off of Python's
parser worked.  It did.  Then I tried to see if I could make
it support a simple file format.  It did.  It does not work for
more complicated formats, though swissprot shouldn't be a problem.
That's where an NFA should be used instead.

In other words, beware!

						Andrew
						dalke@acm.org
[*]
Ooops! Given a thread in the python newsgroup, I should explain
the culture bias that this is a reference to a quote by Ralph
Waldo Emerson's "Self Reliance": "A foolish consistancy is the
hobgoblin of little minds."
  Aren't I polite ;)

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