[BioPython] Transcription

[Martin MOKREJŠ]

Peter,

Peter wrote:
> 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

But is is buried in the text, it is more helpful to have a chapter item
like this. Moreover, I ended up going through my thrash and picking up
the email on this thread last from week. Now I have

from Bio.Seq import translate
...
print ''.join(('>', _record.id, ' ', _description, ' ', _start.strip(), '..', _stop.strip(), '\n', translate(_record.seq.tostring()[int(_start)-1:int(_stop)])))


but following the Tutorial would have been better as one could choose
different translator.

For example, now I wanted to look again into the docs to show you what's in,
I did search on the main webpage but searching for 'translate' gave nothing,
so I ticked also some additional set like the discussion but nothing came.
I went to Documentation section, picked up API documentation as that is the
fastest http://biopython.org/DIST/docs/api/public/trees.html , found the
Bio.Translate.Translator . Again, the generated docs are bad:
http://biopython.org/DIST/docs/api/public/Bio.Translate.Translator-class.html

and

>>> help(Translate)

is not much helpful ither:

<quote>
Help on module Bio.Translate in Bio:

NAME
    Bio.Translate

FILE
    /usr/lib/python2.4/site-packages/Bio/Translate.py

CLASSES
    Translator
    
    class Translator
     |  Methods defined here:
     |  
     |  __init__(self, table)
     |  
     |  back_translate(self, seq)
     |  
     |  translate(self, seq, stop_symbol='*')
     |  
     |  translate_to_stop(self, seq)

DATA
    ambiguous_dna_by_id = {1: <Bio.Translate.Translator instance>, 2: <Bio...
    ambiguous_dna_by_name = {'Alternative Yeast Nuclear': <Bio.Translate.T...
    ambiguous_rna_by_id = {1: <Bio.Translate.Translator instance>, 2: <Bio...
    ambiguous_rna_by_name = {'Alternative Yeast Nuclear': <Bio.Translate.T...
    key = 15
    unambiguous_dna_by_id = {1: <Bio.Translate.Translator instance>, 2: <B...
    unambiguous_dna_by_name = {'Alternative Yeast Nuclear': <Bio.Translate...
    unambiguous_rna_by_id = {1: <Bio.Translate.Translator instance>, 2: <B...
    unambiguous_rna_by_name = {'Alternative Yeast Nuclear': <Bio.Translate...
    value = <Bio.Data.CodonTable.AmbiguousCodonTable instance>
</quote>


I think the classes should be documented at least in the source code.
That's one of the very nice python features, of course not unique only to it.

Regards,
Martin