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Michiel de Hoon | 1 Mar 2009 13:17
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ScanProsite

ScanProsite is a web tool to scan protein sequences against the PROSITE database (see
http://www.expasy.org/tools/scanprosite/). Biopython contains code in Bio.Prosite to interact
with ScanProsite. However, this code needs to be updated, as it does not work with the current ScanProsite
web pages: Neither accessing ScanProsite nor extracting the hits from the HTML page works.

This problem is relatively easy to solve, since ExPASy nowadays allows programmatic access to
ScanProsite (see http://www.expasy.org/tools/scanprosite/ScanPrositeREST.html). This returns
the Prosite hits in XML format, which can be parsed easily in Python.

The only issue now is how this should be presented to the user. The current (broken) way to access Prosite
looks like this:

>>> from Bio import ExPASy
>>> handle = ExPASy.scanprosite1(seq=mysequence)
to get a handle to the raw HTML output, and

>>> from Bio import Prosite
>>> hits = Prosite.scan_sequence_expasy(seq=mysequence)
which returns the hits as a Python list.

One possibility is to have a ScanProsite module under Bio.Prosite or Bio.ExPASy for interaction with
ScanProsite. Something like this:
>>> from Bio.ExPASy import ScanProsite
>>> handle = ScanProsite.search(seq=mysequence)
>>> hits = ScanProsite.read(handle)

Another option is to have a scan function in the Bio.Prosite module that accesses the ScanProsite web tool
and parses the results:
>>> from Bio import Prosite
>>> hits = Prosite.scan(seq=mysequence)
(Continue reading)

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bugzilla-daemon | 1 Mar 2009 18:00

[Bug 2495] parse element symbols for ATOM/HETATM records (Bio.PDB.PDBParser)

http://bugzilla.open-bio.org/show_bug.cgi?id=2495

------- Comment #1 from barry_finzel <at> yahoo.com  2009-03-01 12:00 EST -------
IO.save should also write these element types on an output PDB file

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bugzilla-daemon | 1 Mar 2009 18:06

[Bug 2292] Bio.PDBIO writes TER records without any required fields

http://bugzilla.open-bio.org/show_bug.cgi?id=2292

barry_finzel <at> yahoo.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |barry_finzel <at> yahoo.com

------- Comment #2 from barry_finzel <at> yahoo.com  2009-03-01 12:06 EST -------
IO.save is also writing TER cards at the end of chains, rather than at the end
of polypeptide chains.
TER cards should never follow HETATM  atom records.  

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bugzilla-daemon | 1 Mar 2009 18:22

[Bug 2774] New: Bio.PDBIO.save doesn't write the required END record

http://bugzilla.open-bio.org/show_bug.cgi?id=2774

           Summary: Bio.PDBIO.save doesn't write the required END record
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: barry_finzel <at> yahoo.com

According to the PDB format specification
(http://www.wwpdb.org/documentation/format32/sect1.html)
All PDB files must be terminated with a record containing just "END\n".

Easy to fix in PDBIO.save()

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Peter | 2 Mar 2009 11:26
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Re: ScanProsite

On Sun, Mar 1, 2009 at 12:17 PM, Michiel de Hoon <mjldehoon <at> yahoo.com> wrote:
> ScanProsite is a web tool to scan protein sequences against the PROSITE
> database (see http://www.expasy.org/tools/scanprosite/). Biopython contains
> code in Bio.Prosite to interact with ScanProsite. However, this code needs to
> be updated, as it does not work with the current ScanProsite web pages:
> Neither accessing ScanProsite nor extracting the hits from the HTML page works.
>
> This problem is relatively easy to solve, since ExPASy nowadays allows
> programmatic access to ScanProsite
> (see http://www.expasy.org/tools/scanprosite/ScanPrositeREST.html). This
> returns the Prosite hits in XML format, which can be parsed easily in Python.
>
> The only issue now is how this should be presented to the user. ...
> ...
> This is more straightforward, but on the other hand people may want to save the
> XML search results in an XML file, and for that purpose we'd need a function that
> does the parsing only.
>
> Any opinions?

I would definitely have two functions, one returning a handle to the
XML, and one for parsing XML from a handle.  This would be more
consistent with Bio.Entrez and other parsers, and more flexible.  For
example, the user can opt to save the XML to disk, and they can also
use our parser on files or the remote site - plus of course they can
use any other XML parser they may prefer.

I like your suggestion to have a REST XML based module under
Bio.ExPASy, which means we can deprecate the HTML based Bio.Prosite
module and in the process make the top level list of modules in
(Continue reading)

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bugzilla-daemon | 2 Mar 2009 16:22

[Bug 2776] New: Bio.pairwise2 returns non-optimal alignment in at least some cases

http://bugzilla.open-bio.org/show_bug.cgi?id=2776

           Summary: Bio.pairwise2 returns non-optimal alignment in at least
                    some cases
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: klaus.kopec <at> tuebingen.mpg.de

At least in some cases, Bio.pairwise2 returns an alignment that is not the one
with the highest score for the input parameters. This occurs in localXX and
globalXX.

Yet, I only encountered the problem with large mismatch values (which I use as
I need mismatch free alignments).

simple example (the bug also occured for longer sequences):
>>> sequence1 = 'GKG'
>>> sequence2 = 'GWG'
>>> A = pairwise2.align.globalms(sequence1, sequence2, 5, -100, -5, -5)[0]
>>> A[0]
'GKG--'
>>> A[1]
'--GWG'
(Continue reading)

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bugzilla-daemon | 4 Mar 2009 13:41

[Bug 2777] New: [Solution is one line change!] Entity sorting altered by detach_child() calls

http://bugzilla.open-bio.org/show_bug.cgi?id=2777

           Summary: [Solution is one line change!] Entity sorting altered by
                    detach_child() calls
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: trivial
          Priority: P1
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: klaus.kopec <at> tuebingen.mpg.de

detach_child(self, id) in Bio.PDB.Entity changes the order of self.child_list.

This bug is caused by line 71, where self.child_list is set to
self.child_dict.values() which are values of an unordered(!) dict:
self.child_list=self.child_dict.values()

Solution: Replace line 71 by:
self.child_list.remove(child)

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bugzilla-daemon | 4 Mar 2009 13:48

[Bug 2777] [Solution is one line change!] Entity sorting altered by detach_child() calls

http://bugzilla.open-bio.org/show_bug.cgi?id=2777

------- Comment #1 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-03-04 07:48 EST -------
Have you got a short example to demonstrate the original problem?

It would be useful to evaluate your change, and could be made into a unit test
too.

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bugzilla-daemon | 4 Mar 2009 14:58

[Bug 2777] [Solution is one line change!] Entity sorting altered by detach_child() calls

http://bugzilla.open-bio.org/show_bug.cgi?id=2777

------- Comment #2 from klaus.kopec <at> tuebingen.mpg.de  2009-03-04 08:58 EST -------
Created an attachment (id=1253)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1253&action=view)
example PDB file that can be used to see the bug

## Python Code to see the bug:
import os
from Bio.PDB.PDBParser import PDBParser
p=PDBParser(PERMISSIVE=1)
filename=os.path.expanduser("entity_detach_order_bug_example.pdb")
s=p.get_structure('Entity.py bug example: detach changes order', filename)

print 'order before detach:'
for r in s[0]['A'].child_list:
    print r.id

detach_me = s[0]['A'].child_list[-1] ## this is independent of the chosen entry
in the list
s[0]['A'].detach_child(detach_me.id)

print 'order after detach:'
for r in s[0]['A'].child_list:
    print r.id

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bugzilla-daemon | 4 Mar 2009 15:18

[Bug 2777] [Solution is one line change!] Entity sorting altered by detach_child() calls

http://bugzilla.open-bio.org/show_bug.cgi?id=2777

------- Comment #3 from klaus.kopec <at> tuebingen.mpg.de  2009-03-04 09:18 EST -------
the output of the code in my Comment #2 is:
order before detach:
('H_PCA', 1, ' ')
(' ', 2, ' ')
(' ', 3, ' ')
(' ', 4, ' ')
order after detach:
(' ', 2, ' ')
(' ', 3, ' ')
('H_PCA', 1, ' ')

I forgot to mention, that the line "self.child_list.sort(self._sort)" needs to
be commented out as well for the fix to work (as hetatms are otherwise sorted
to the end).

hmmm... it just came to me, that this probably breaks the Parser for some other
PDB files, where residues are unsorted.

These changes do not break any existing unit tests for the PDB module, so maybe
it's still a step in the right direction.

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Gmane