[BioPython] restrichtion map like "remap"

[Frederic Sohm]

Hi,

I don't know for the emboss support but for Restriction map you can use the 
module Restriction :

Python 2.4.2 (#1, Sep 28 2005, 17:53:13) 
[GCC 3.4.3 (Mandrakelinux 10.2 3.4.3-7mdk)] on linux2
Type "copyright", "credits" or "license()" for more information.

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IDLE 1.1.2      
>>> from Bio.Restriction import Analysis, AllEnzymes, CommOnly
>>> from Bio.Seq import Seq
>>> pbr = Seq('TTCT --- cut pBR322 sequence ---')
>>> restmap = Analysis(AllEnzymes, pbr, False)
>>> # False means the sequence is circular
>>> # Nothing or True the sequence is linear.
>>> restmap.print_that(None, 'restriction map of pBR322 \n\n')

restriction map of pBR322

AccII      :  348, 704, 819, 948, 975, 980, 1041, 1107, 1236, 1246, 1391, 
1417,
               1539, 1636, 2006, 2075, 2180, 2521, 3102, 3432, 3925, 4257.
--- cut all the enzymes and their sites ---

   Enzymes which do not cut the sequence.

AatI      Acc65I    AcvI      AflII     AgeI      AhlI      ApaI      AsiAI     
--- cut the enzymes absent from the sequence ---

>>> # to use only commercially available enzymes do that :
>>> restmap = Analysis(CommOnly, pbr, False)
--- results cut ---


You can format the results as map by doing :

>>> restmap.print_as('map')
>>> restmap.print_that()
...


Hope that helps. unfortunately there is no support for translation frames with 
this module. For more details on how to use it see the manual provided in the 
doc, cookbook style : here :
http://www.biopython.org/docs/cookbook/Restriction.html

best regards

Fred

Le Samedi 22 Octobre 2005 12:43, Hans Meier a écrit :
> Dear friends,
>
> there's a feature in Biopython I can't find
> or it is missing.
>
> It's a function like "remap" from emboss
> or "map" from gcg. So you input a sequence
> in raw- or fasta-format and you get a map
> of your sequence including (optionally)
> restriction sites, translation in all six frames ...
> You can also format the output by telling
> how many bases per line, marginwitdth etc. etc.
>
> Is there nothing similiar within Biopython?
> Any other suggestions (except using Emboss :)
>
>
> Thanks a lot, Harald
>
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-- 
Frédéric Sohm
Equipe INRA U1126 "Morphogenèse du système nerveux des Chordés"
UPR 2197 DEPSN, CNRS
Institut de Neurosciences A. Fessard
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91 198 GIF-SUR-YVETTE
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