[BioPython] Transcription

[Martin MOKREJŠ]

Michael Fahy wrote:
> It would have helped me avoid some confusion if the Tutorial had mentioned
> the difference between sequences from the coding strand and from the
> template strand and the fact that the transcribe function in BioPython
> expects a sequence from the coding strand.  My biology colleagues here seem
> to prefer thinking of transcribing the sequence from the template strand.
> It's not a big deal now that we understand what the intent is, but it caused
> some misunderstanding at first.

Yes, I read the discussion last week, it is fooling for me as well, I don't
think I need the transcribe() as I would probably always do seq.tostring().replace('tT', 'uU')
and not search a special function in the code. But what I would do look for
is a function doing reverse_complement() and replace('tT', 'uU') while
allowing me to optionally pass in intron or probably even more conveniently
exon positions. Sure one can do it himself.

Definitely, the Transcribe API docs are bad as for the Translate which
is really really bad. One one wondered what translate_to_stop really
does as one would hope that it starts as well on the very first AUG
being in the correct frame, maybe does 3-frame or even six-frame translation
... who know what the undocumented function does. ;-))

Well, doing http://www.google.com/search?hl=en&q=site%3Abiopython.org+translate_to_stop&btnG=Google+Search
gave few hits, one in tutorial and one can see it only translates to the stop
and doesn't care about start and frames. Definitely, no other docs exist
except the Tutorial and Cookbook as shown in the Google output. Very bad
I think.

Maybe someone would really fix the Transcribe?
http://www.google.com/search?num=100&hl=en&q=%22from+Bio+import+Transcribe%22&btnG=Search&lr=lang_en

Similarly, the Translate points me to the original thread years ago:
http://209.85.135.104/search?q=cache:MU0IHhkMV9YJ:portal.open-bio.org/pipermail/biopython/2005-May.txt+%22from+Bio+import+Translate%22&hl=en&ct=clnk&cd=6&lr=lang_cs|lang_en|lang_de|lang_sk

Martin


> 
> -----Original Message-----
> From: biopython-bounces at lists.open-bio.org
> [mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Peter
> Sent: Monday, July 16, 2007 9:26 AM
> To: Martin MOKREJŠ
> Cc: BioPython at lists.open-bio.org
> Subject: Re: [BioPython] Transcription
> 
> Martin MOKREJŠ wrote:
>> BTW, someone who has the rights should include this example in the docs.
>> The relevant section is empty:
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc68
> 
> Or remove it? We cover transcription and translation earlier:
> 
> Section 2.2  Working with sequences
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc8
> 
> The source to the tutorial is a TeX (or LaTeX?) file in CVS, which 
> generates the HTML and PDF tutorial. I can update the CVS files, but I 
> don't think I can update the file on the webpage...
> 
> Peter
> 
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