[Biopython-dev] [Bug 2965] New: Updating Bio.Restriction with latest REBASE data

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2965

           Summary: Updating Bio.Restriction with latest REBASE data
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


The Bio/Restriction/Restriction_Dictionary.py file hasn't been updated since
2004.

The latest REBASE restriction digest files seem to be from Nov 29 2009,
ftp://ftp.neb.com/pub/rebase/

This bug is to update Restriction_Dictionary.py to use the Nov 2009 data. I
have tried and failed as described below:

----------------------------------------------------------------------------

I manually downloading these files to the Scripts/Restriction directory:
ftp://ftp.neb.com/pub/rebase/emboss_e.912
ftp://ftp.neb.com/pub/rebase/emboss_r.912
ftp://ftp.neb.com/pub/rebase/emboss_s.912

And then ran ranacompiler.py which generated a new Restriction_Dictionary.py

As an aside, module sre is deprecate, re is suggested instead. Other
interesting output:

WARNING : HaeIV cut twice with different overhang length each time.            
        Unable to deal with this behaviour.             
        This enzyme will not be included in the database. Sorry.
        Checking : Anyway, HaeIV is not commercially available.


WARNING : TaqII has two different sites.


The new database contains 753 enzymes.

So far so good, but using the new Restriction_Dictionary.py the unit tests
fail:

$ python test_Restriction.py
Traceback (most recent call last):
  File "test_Restriction.py", line 6, in <module>
    from Bio.Restriction import *
  File
"/Users/myusername/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Restriction/__init__.py",
line 61, in <module>
    from Bio.Restriction.Restriction import *
  File
"/Users/myusername/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Restriction/Restriction.py",
line 2358, in <module>
    newenz = T(k, bases, enzymedict[k])
  File
"/Users/myusername/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Restriction/Restriction.py",
line 216, in __init__
    cls.compsite = re.compile(cls.compsite)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/re.py",
line 188, in compile
    return _compile(pattern, flags)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/re.py",
line 241, in _compile
    raise error, v # invalid expression
sre_constants.error: bad character in group name


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