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bugzilla-daemon | 1 Mar 2008 04:04

[Bug 2464] New: from Bio import db doesn't work?

http://bugzilla.open-bio.org/show_bug.cgi?id=2464

           Summary: from Bio import db doesn't work?
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: blocker
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: patrikd <at> gmail.com

Just trying to run an example straight out of the BioPython cookbook:

ncbi_dict = GenBank.NCBIDictionary("nucleotide", "genbank")

Traceback (most recent call last):
  File "<pyshell#86>", line 1, in <module>
    ncbi_dict = GenBank.NCBIDictionary("nucleotide", "genbank")
  File "C:\Program Files\Python25\lib\site-packages\Bio\GenBank\__init__.py",
line 1283, in __init__
    from Bio import db
ImportError: cannot import name db

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bugzilla-daemon | 1 Mar 2008 09:54

[Bug 2464] from Bio import db doesn't work?

http://bugzilla.open-bio.org/show_bug.cgi?id=2464

mdehoon <at> ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |DUPLICATE

------- Comment #1 from mdehoon <at> ims.u-tokyo.ac.jp  2008-03-01 03:54 EST -------
Duplicate of Bug #2393, which was fixed in CVS.

*** This bug has been marked as a duplicate of bug 2393 ***

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bugzilla-daemon | 1 Mar 2008 09:54

[Bug 2393] Bio.GenBank.NCBIDictionary fails with release 1.44

http://bugzilla.open-bio.org/show_bug.cgi?id=2393

mdehoon <at> ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |patrikd <at> gmail.com

------- Comment #13 from mdehoon <at> ims.u-tokyo.ac.jp  2008-03-01 03:54 EST -------
*** Bug 2464 has been marked as a duplicate of this bug. ***

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Michiel de Hoon | 1 Mar 2008 09:52
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Re: deprecation?

Dear Gregorio,

Thanks for letting us know.
Could you show us what exactly you are trying to do in your script?
This function was deprecated because there were several functions in Biopython doing nearly the same
thing, and we're trying to converge on one function. 
So probably, the best thing would be to avoid using Bio\config\DBRegistry.py.

--Michiel.

Gregorio Fernandez <gregorio <at> umh.es> wrote: Dear  Sir,
I had this messasge in one of my scripts. Can I have this feature 
available?

C:\Python25\lib\site-packages\Bio\config\DBRegistry.py:149: 
DeprecationWarning:
Concurrent behavior has been deprecated, as this functionality needs 
Bio.MultiPr
oc, which itself has been deprecated. If you need the concurrent 
behavior, pleas
e let the Biopython developers know by sending an email to 
biopython-dev <at> biopyth
on.org to avoid permanent removal of this feature.
 DeprecationWarning)

Thanks
Gregorio

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bugzilla-daemon | 3 Mar 2008 22:53

[Bug 2437] comparing alphabet references causes assert to fail when it should pass

http://bugzilla.open-bio.org/show_bug.cgi?id=2437

------- Comment #2 from biopython-bugzilla <at> maubp.freeserve.co.uk  2008-03-03 16:53 EST -------
Defining __eq__ and __ne__ methods for the Alphabet class would probably work,
but we would also have to do this for the AlphabetEncoder "decorator" class. 
I'm a little wary of this...

    def __ne__(self, other) :
        """Check if this alphabet object <> another alphabet"""
        return not self == other

    def __eq__(self, other) :
        """Check if this alphabet object == another alphabet"""
        #TODO - what exactly do we want to check here?
        if id(self) == id(other) :
            return True
        if not isinstance(other, Alphabet) \
        and not isinstance(other, AlphabetEncoder):
            raise ValueError("Comparing an alphabet to a non-alphabet")
        if self.__class__ <> other.__class__ :
            return False
        if self.size <> other.size :
            return False
        if self.letters <> other.letters :
            return False
        if dir(self) <> dir(other) :
            return False
        for attr in ["gap_char", "stop_symbol"] :
            if hasattr(self, attr) <> hasattr(other, attr) :
                return False
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Michiel de Hoon | 6 Mar 2008 16:24
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New Biopython release

Hi everybody,

Let's make a new release (1.45). I'm thinking of Friday 21st, which gives us about two weeks. The current
Biopython release (1.44) has a nasty bug that causes an error with one of the Bio.GenBank examples in the
tutorial. This bug has since been fixed in CVS.

If you have any code that is ready to be submitted to CVS, now would be a good time to do so. If your code is not yet
ready from prime time, please don't submit it to CVS until after the release to avoid any last-minute problems.

Biopython 1.44 had a large number of deprecations, but I feel it is too soon to remove them from the release
completely. Bio.Blast.blast and Bio.Blast.blasturl have been deprecated for several releases now, so
if there are no objections I think we should remove them. Bio.Kabat has been deprecated since release
1.43. Since it has few (if any) users, I think we should remove it too.

Also, please have a look at the Biopython bugs that are still open to see if there's anything we can do about them.

--Michiel.

       
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bugzilla-daemon | 8 Mar 2008 21:25

[Bug 2437] comparing alphabet references causes assert to fail when it should pass

http://bugzilla.open-bio.org/show_bug.cgi?id=2437

------- Comment #3 from biopython-bugzilla <at> maubp.freeserve.co.uk  2008-03-08 15:25 EST -------
Changing Bio/Translate.py line 14+ and 36+ from this:

        assert seq.alphabet == self.table.nucleotide_alphabet, \
        ...

to this:

        #Allow different instances of the same class to be used:
        assert seq.alphabet.__class__ == \
               self.table.nucleotide_alphabet.__class__, \
        ...

seems to resolve the original bug report.  I'd like to check this doesn't
affect any of the unit tests under Linux - Windows looks OK.

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bugzilla-daemon | 10 Mar 2008 11:12

[Bug 1999] new frame translation method

http://bugzilla.open-bio.org/show_bug.cgi?id=1999

------- Comment #2 from mdehoon <at> ims.u-tokyo.ac.jp  2008-03-10 06:12 EST -------
Since SeqUtils.frameTranslations and SeqUtils.six_frame_translations are so
similar, I think we should keep only one of these functions. Preferably named
"six_frame_translations", for backward compatibility.
Also, I think we should not require the seqO argument to be a Seq object.
If this function is to replace the existing SeqUtils.six_frame_translations, we
should make to sure to keep all the existing functionality of that function. I
believe current the GC content calculation is missing in
SeqUtils.frameTranslations.

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Peter | 12 Mar 2008 01:37
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Re: Biopython to begin transition to Subversion

Hi Chris,

I haven't heard anything about the CVS to SVN move recently.  Did
anyone resolve the multiple password prompt niggle?

On another point, is the test SVN repository intended to be writable
(for those of us with developer access)?  I really should try running
some things like "svn diff" and committing sample changes to get a
feel for how it compares to CVN.

Peter
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Sebastian Bassi | 12 Mar 2008 15:52
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BLAST XML to HTML

Is there a Biopython module to convert a VLAST XML output to HTML?
Like this one from BioJAVA:
http://www.biojava.org/wiki/BioJava:CookBook:Blast:XML
If there is no such a module, could this be included into Biopython if
I provide the code?

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Gmane