Biopython Developers List

bugzilla-daemon | 8 Jun 2005 20:11

[Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so...

http://bugzilla.open-bio.org/show_bug.cgi?id=1812

misiek <at> genesilico.pl changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
           Severity|normal                      |enhancement

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bugzilla-daemon | 8 Jun 2005 20:14

[Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so...

http://bugzilla.open-bio.org/show_bug.cgi?id=1812

misiek <at> genesilico.pl changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
  BugsThisDependsOn|                            |1813

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bugzilla-daemon | 8 Jun 2005 20:04

[Bug 1812] New: Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so...

http://bugzilla.open-bio.org/show_bug.cgi?id=1812

           Summary: Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so...
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: misiek <at> genesilico.pl

Writing a structure with Bio.PDB.PDBIO means a loss of all header information
(essentially all anything that's not ATOM,HETATM,TER,END,MODEL,CONECT).

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bugzilla-daemon | 13 Jun 2005 22:24

[Bug 1816] New: Error when importing GenBank file into BioSQL database

http://bugzilla.open-bio.org/show_bug.cgi?id=1816

           Summary: Error when importing GenBank file into BioSQL database
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: scresawn <at> ufl.edu

When importing a GenBank file with accession number AY243312 into a BioSQL
database, I get an error.  (See below.)  Importing the file was done according
to the documentation at http://biopython.org/docs/biosql/python_biosql_basic.html
I'm using python-2.3.4 and biopython-1.40b.  The biosql-schema was checked out
today (6/13/05) from cvs.
The error follows:

>>> db.load(iterator)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "BioSQL/BioSeqDatabase.py", line 414, in load
    db_loader.load_seqrecord(cur_record)
  File "BioSQL/Loader.py", line 43, in load_seqrecord
    self._load_reference(reference, rank, bioentry_id)
  File "BioSQL/Loader.py", line 324, in _load_reference
    (reference.pubmed_id,))

(Continue reading)

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Michiel De Hoon | 17 Jun 2005 21:42

[BioPython] Re; Rethinking Seq objects

Dear biopythoneers,

A couple of weeks ago there was a discussion on the Biopython mailing lists
about the Seq and MutableSeq classes in Bio.Seq. Whereas opinions were
divided on most of my proposals (which I therefore did not implement), most
people agreed that there was a need for a more user-friendly way to
transcribe and translate sequences.

So I added a transcribe, back_transcribe, and translate function to Bio.Seq.
I wrote these as functions rather than a method so that it can take both Seq
objects and Python string objects as input. These functions work
approximately the same as the corresponding methods in Bio.Transcribe and
Bio.Translate.

The example in the Biopython tutorial would look like this:

Using strings:

>>> my_seq = 'GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA'
>>> transcribe(my_seq)
'GCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGA'
>>> back_transcribe(_)
'GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA'
>>> translate(my_seq)
'AIVMGR*KGAR'
>>> translate(my_seq,table="Vertebrate Mitochondrial")
'AIVMGRWKGAR'
>>> translate(my_seq,table=1)
'AIVMGR*KGAR'
>>> translate(my_seq,table=2)

(Continue reading)

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bugzilla-daemon | 22 Jun 2005 14:26

[Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so...

http://bugzilla.open-bio.org/show_bug.cgi?id=1812

Bug 1812 depends on bug 1813, which changed state.

Bug 1813 Summary: Bio.PDB doesn't understand SEQRES...
http://bugzilla.open-bio.org/show_bug.cgi?id=1813

           What    |Old Value                   |New Value
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |WONTFIX

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bugzilla-daemon | 22 Jun 2005 14:24

[Bug 1812] Bio.PDB.PDBIO Doesn't write HEADER, SEQRES and so...

http://bugzilla.open-bio.org/show_bug.cgi?id=1812

thamelry <at> binf.ku.dk changed:

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

------- Additional Comments From thamelry <at> binf.ku.dk  2005-06-22 08:24 -------

This is not a bug but a feature request.

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