From mjldehoon at yahoo.com  Sat Jan  5 03:41:25 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 5 Jan 2008 00:41:25 -0800 (PST)
Subject: [Biopython-dev] Bio.Ais
Message-ID: <140129.37367.qm@web62402.mail.re1.yahoo.com>

Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in <module>
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
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From mjldehoon at yahoo.com  Fri Jan 11 06:16:45 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 11 Jan 2008 03:16:45 -0800 (PST)
Subject: [Biopython-dev] Bio.Ais
In-Reply-To: <140129.37367.qm@web62402.mail.re1.yahoo.com>
Message-ID: <426295.9925.qm@web62415.mail.re1.yahoo.com>

Looking at this again, currently we have no documentation for Bio.Ais, no maintainer, and no apparent users (at least, I couldn't find any in the mailing list archives). Would anybody mind very much if I mark this module as deprecated?
Just to find out if there are any users of this code out there.

--Michiel.

Michiel de Hoon <mjldehoon at yahoo.com> wrote: Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in 
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
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From josh at globalherald.net  Sun Jan 13 03:03:56 2008
From: josh at globalherald.net (Josh)
Date: Sun, 13 Jan 2008 03:03:56 -0500 (EST)
Subject: [Biopython-dev] Fetching PubMed Entries with Recent Python
Message-ID: <alpine.LRH.1.00.0801130256360.14131@home-av-server.home-av>


Howdy,

Has anyone used a recent Python (2.4 or above) with recent Entrez-PubMed 
DTD's or WSDL's to fetch PubMed entries?

I've spent several hours on two methods.  First, I tried using ZSI with 
the PubMed WSDL's.  That resulted in a gargantuan PubMed Types .py file 
with several errors.

I then found Andrew Dalke's EUtils python module.  When I tried to use it 
the first time, as outlined in the README, it complained about missing 
modules.  The DTD modules weren't installed under the EUtils dir under 
site-packages, and it was missing some pubmed DTD's, so I fixed those two 
problems and ended up with a validation exception.

At some point I'll probably have to spend the hours to fix all the 
problems with EUtils, but I wanted to ping everyone to see if anyone has 
done this yet.  I'm using the Python 2.4.3 included with CentOS 5.1.

Cheers,
-Josh


From biopython at maubp.freeserve.co.uk  Tue Jan 15 09:09:47 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Jan 2008 14:09:47 +0000
Subject: [Biopython-dev] [BioPython] [Biopython] Blast problem
In-Reply-To: <4ac065b80801150526q79215288k7e6a0e633d83f1c4@mail.gmail.com>
References: <4ac065b80801150526q79215288k7e6a0e633d83f1c4@mail.gmail.com>
Message-ID: <320fb6e00801150609y16c77bdch927dd6d9689996a5@mail.gmail.com>

Hi Joost,

> Iam having a problem with the hsp.match function in the Bio-Python Blast
> module. A few weeks ago the hsp.match returned me the following:
>
> ATGGCA++TGG
>
> But now it gives me:
>
> ATGGCA TGG
>
> I can't see the number of gaps anymore, anyone a solution for this?

Are you using the online version of blast with Biopython?  Perhaps the
NCBI changed something.  Are you parsing the XML output or the plain
text?  Can you provide any more information (e.g. which version of
Biopython).

Thanks

Peter

From bugzilla-daemon at portal.open-bio.org  Tue Jan 15 17:41:12 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 15 Jan 2008 17:41:12 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801152241.m0FMfCJN001996@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375


tiagoantao at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|tiagoantao at gmail.com        |biopython-dev at biopython.org
             Status|ASSIGNED                    |NEW




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From bugzilla-daemon at portal.open-bio.org  Tue Jan 15 17:46:30 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 15 Jan 2008 17:46:30 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801152246.m0FMkU9S002237@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #14 from tiagoantao at gmail.com  2008-01-15 17:46 EST -------
(In reply to comment #13)
> Style wise, I would use os.path functions rather than doing this yourself with
> os.sep, and also I'm not personally so keen on the import style (I should try
> and find a style reference to back this up though!).

Regarding the import style, I was probably not on my best days. Agree and
changed.

> I doubt Michael has been following this bug (since it is assigned to you Tiago
> none of these comments are being posted to the dev mailing list), but it would
> be nice to have his (or anyone else's) opinion on this (both style, and how
> best to fix the unit test).

I have remove the assignment, so everybody should be seeing this.

I think the coalescent code should be more or less on track for the next
release (whenever Michiel decides to do it).


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From bugzilla-daemon at portal.open-bio.org  Tue Jan 15 20:33:29 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 15 Jan 2008 20:33:29 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801160133.m0G1XTBd010079@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #15 from mdehoon at ims.u-tokyo.ac.jp  2008-01-15 20:33 EST -------
Indeed I was not following this bug.
To me the patch for setup.py looks fine. Feel free to commit it.

The solution in Bio/PopGen/SimCoal/__init__.py to find builtin_tpl_dir is not
so beautiful, but on the other hand I don't see a better way to do it. In
essence, this is an oversight in the Python testing framework. It makes sense
to test from the build directory instead of from the installation directory (we
want to test before we install). Unless I missed something in the
documentation, the current testing framework does not really take that into
account. Anyway, I think the current solution is the best we can do.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan 18 07:16:50 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 18 Jan 2008 07:16:50 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801181216.m0ICGone018126@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #16 from tiagoantao at gmail.com  2008-01-18 07:16 EST -------
(In reply to comment #15)
> To me the patch for setup.py looks fine. Feel free to commit it.

I have committed it. I have tested it on 2 machines, but considering that my
setup is highly biased towards my needs, please test it.

PS - I have an attachment on this bug with a (rather big) addition to the
manual (pic included). If you want to have a look I would be most thankful.

Tiago


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From mjldehoon at yahoo.com  Fri Jan 18 07:20:38 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Jan 2008 04:20:38 -0800 (PST)
Subject: [Biopython-dev] Bio.Ais
In-Reply-To: <426295.9925.qm@web62415.mail.re1.yahoo.com>
Message-ID: <565042.83375.qm@web62414.mail.re1.yahoo.com>

Since no users came forward, I deprecated Bio.Ais and removed the corresponding test_ais.py. I added a statement in the DeprecationWarning that this module is on the nomination to be removed (in some future Biopython release), if no users come forward.

--Michiel.

Michiel de Hoon <mjldehoon at yahoo.com> wrote: Looking at this again, currently we have no documentation for Bio.Ais, no maintainer, and no apparent users (at least, I couldn't find any in the mailing list archives). Would anybody mind very much if I mark this module as deprecated?
Just to find out if there are any users of this code out there.

--Michiel.

Michiel de Hoon  wrote: Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in 
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
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From mjldehoon at yahoo.com  Fri Jan 18 07:32:25 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Jan 2008 04:32:25 -0800 (PST)
Subject: [Biopython-dev] LocusLink, anybody?
Message-ID: <397687.73819.qm@web62408.mail.re1.yahoo.com>

When I was making an inventory of Biopython code involved in accessing NCBI's databases, I came across the Bio.LocusLink module, containing a paser for NCBI's LocusLink. The website for LocusLink is http://www.ncbi.nlm.nih.gov/LocusLink/.

However, this website says:
"LocusLink is superceded by Entrez Gene...."
As far as I can tell, LocusLink is no longer used, making Bio.LocusLink superfluous. Did I miss something? Does anybody see a reason for keeping Bio.LocusLink?

--Michiel

       
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From bugzilla-daemon at portal.open-bio.org  Fri Jan 18 07:43:54 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 18 Jan 2008 07:43:54 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801181243.m0IChsbC019332@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #17 from biopython-bugzilla at maubp.freeserve.co.uk  2008-01-18 07:43 EST -------
Apeart from test_PopGen_FDist and test_PopGen_SimCoal where I don't have the
tools installed, the PopGen unit tests pass, and it seems to install fine too.

I've skimmed over the tutorial diff, but have not tried the examples (I don't
have SimCoal installed, nor time right now to try it).

Regarding the figure, using a PNG image is probably best as we want to produce
both HTML and PDF output.  You can make the file about half the size by saving
it as a greyscale PNG image (and cropping the bottom margin a little more).

Otherwise it looks fine.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan 18 07:46:42 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 18 Jan 2008 07:46:42 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801181246.m0ICkgao019590@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #18 from tiagoantao at gmail.com  2008-01-18 07:46 EST -------
(In reply to comment #17)
> Regarding the figure, using a PNG image is probably best as we want to produce
> both HTML and PDF output.  You can make the file about half the size by saving
> it as a greyscale PNG image (and cropping the bottom margin a little more).
> 
> Otherwise it looks fine.

I will make the changes to the image as you say, and if nobody opposes I will
commit the changes myself.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 23 08:03:09 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 23 Jan 2008 08:03:09 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801231303.m0ND39pm022177@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #19 from biopython-bugzilla at maubp.freeserve.co.uk  2008-01-23 08:03 EST -------
I'd previously only tried this on Linux.  I've now also tested this on Windows
now (compiling from source), and it seems to install the data files as
expected, and the unit tests look fine.

Once the documentation is checked in, I think this bug can be marked as fixed.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 23 08:22:13 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 23 Jan 2008 08:22:13 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801231322.m0NDMDBI023110@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #20 from tiagoantao at gmail.com  2008-01-23 08:22 EST -------
(In reply to comment #19)
> Once the documentation is checked in, I think this bug can be marked as fixed.

I checked it in a couple of days ago. Please have a final "helicopter" look at
it just to see if there are any gross problems with it. The Tutorial is now
precisely 100 pages long, BTW.


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 28 14:12:33 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 28 Jan 2008 14:12:33 -0500
Subject: [Biopython-dev] [Bug 2437] New: comparing alphabet references
	causes assert to fail when it should pass
Message-ID: <bug-2437-42@http.bugzilla.open-bio.org/>

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

           Summary: comparing alphabet references causes assert to fail when
                    it should pass
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: rjalves at igc.gulbenkian.pt


/var/lib/python-support/python2.4/Bio/Translate.py in translate_to_stop(self,
seq)
    34     def translate_to_stop(self, seq):
    35         # This doesn't have a stop encoding
---> 36         assert seq.alphabet == self.table.nucleotide_alphabet, \
    37                "cannot translate from given alphabet (have %s, need %s)"
%\
    38                (seq.alphabet, self.table.nucleotide_alphabet)

AssertionError: cannot translate from given alphabet (have IUPACAmbiguousDNA(),
need IUPACAmbiguousDNA())


What I did:

from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio import Translate
from Bio import Seq

a=Seq.Seq("ATCGGATGA...ATGCAGT",alphabet=IUPACAmbiguousDNA())
b=Translate.ambiguous_dna_by_id[11]

b.translate_to_stop(a) ... error pops out

The only way around I was able to find is:

b.table.nucleotide_alphabet=a.alphabet


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 28 14:34:12 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 28 Jan 2008 14:34:12 -0500
Subject: [Biopython-dev] [Bug 2437] comparing alphabet references causes
	assert to fail when it should pass
In-Reply-To: <bug-2437-42@http.bugzilla.open-bio.org/>
Message-ID: <200801281934.m0SJYCnT017522@portal.open-bio.org>

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





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-01-28 14:34 EST -------
This code snippet shows the same issue:

from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA

alpha1 = IUPACAmbiguousDNA()
alpha2 = IUPACAmbiguousDNA()

assert type(alpha1) == type(alpha2)
assert dir(alpha1) == dir(alpha2)
assert alpha1.letters == alpha2.letters

assert alpha1 == alpha2 #fails, different instances of same class

We could update the Alphabet class to define an equality check, and/or modify
Bio.Translate to use a less harsh assertion.


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From marcin.cieslik at gmail.com  Thu Jan 31 02:05:26 2008
From: marcin.cieslik at gmail.com (=?UTF-8?B?TWFyY2luIENpZcWbbGlr?=)
Date: Thu, 31 Jan 2008 02:05:26 -0500
Subject: [Biopython-dev] Atomic / Residue contacts for Bio.PDB
Message-ID: <47A17336.2090503@gmail.com>

Hello,
I've written several classes to work with the ccp4 ncont program. They
use the AbstractPropertyMap, AbstractAtomPropertyMap classes to map
contacts between atoms and residues. I'd like to contribute this code.

it consists of
* one 'private' function which runs ncat and parses output into
{full_atom_id_in_biopython_tuple : (other_full_id, distance)
				 : (yet another atom, distance)
....
}

and classes:
class _AbstractAtomContacts(AbstractAtomPropertyMap):
	class WaterAtomContacts(_AbstractAtomContacts):
	class CrystalAtomContacts(_AbstractAtomContacts):

class _AbstractContacts(AbstractPropertyMap):
	class CrystalContacts(_AbstractContacts):
	class WaterContacts(_AbstractContacts):

the ncat calling function is called only by _AbstractAtomContacts, the
results are stored in the .xtra dict. Specific contact classes are just
'definitions' of settings for ncat e.g CrystalContacts searches contacts
between symmetry mates only, in 27 unit cells, ommiting all waters etc.

One negative side of this code is that ncat and the mmdb library (and as
a consequence ccp4 6.0.2) do not support PDB v3 files. Luckily RCSB
provides a python PDB translator script 3.1 <--> 2.3.

Marcin

From mjldehoon at yahoo.com  Thu Jan 31 05:18:54 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 31 Jan 2008 02:18:54 -0800 (PST)
Subject: [Biopython-dev] Atomic / Residue contacts for Bio.PDB
In-Reply-To: <47A17336.2090503@gmail.com>
Message-ID: <709883.8309.qm@web62410.mail.re1.yahoo.com>

Dear Marcin,

For contributions to Bio.PDB, it's best to ask Thomas Hamelryck directly. See http://www.binf.ku.dk/User:Thomas_Hamelryck. I'm not sure if he is still actively reading this mailing list.

--Michiel.

Marcin Cie??lik <marcin.cieslik at gmail.com> wrote: Hello,
I've written several classes to work with the ccp4 ncont program. They
use the AbstractPropertyMap, AbstractAtomPropertyMap classes to map
contacts between atoms and residues. I'd like to contribute this code.

it consists of
* one 'private' function which runs ncat and parses output into
{full_atom_id_in_biopython_tuple : (other_full_id, distance)
     : (yet another atom, distance)
....
}

and classes:
class _AbstractAtomContacts(AbstractAtomPropertyMap):
 class WaterAtomContacts(_AbstractAtomContacts):
 class CrystalAtomContacts(_AbstractAtomContacts):

class _AbstractContacts(AbstractPropertyMap):
 class CrystalContacts(_AbstractContacts):
 class WaterContacts(_AbstractContacts):

the ncat calling function is called only by _AbstractAtomContacts, the
results are stored in the .xtra dict. Specific contact classes are just
'definitions' of settings for ncat e.g CrystalContacts searches contacts
between symmetry mates only, in 27 unit cells, ommiting all waters etc.

One negative side of this code is that ncat and the mmdb library (and as
a consequence ccp4 6.0.2) do not support PDB v3 files. Luckily RCSB
provides a python PDB translator script 3.1 <--> 2.3.

Marcin
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From thamelry at binf.ku.dk  Thu Jan 31 05:35:58 2008
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Thu, 31 Jan 2008 11:35:58 +0100
Subject: [Biopython-dev] Atomic / Residue contacts for Bio.PDB
In-Reply-To: <709883.8309.qm@web62410.mail.re1.yahoo.com>
References: <47A17336.2090503@gmail.com>
	<709883.8309.qm@web62410.mail.re1.yahoo.com>
Message-ID: <2d7c25310801310235h29a076f8m517e94df7169faba@mail.gmail.com>

On Jan 31, 2008 11:18 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> Dear Marcin,
>
> For contributions to Bio.PDB, it's best to ask Thomas Hamelryck directly.
> See http://www.binf.ku.dk/User:Thomas_Hamelryck. I'm not sure if he is
> still actively reading this mailing list.
>

I am in fact, just really busy these days.

Marcin, you can add the code to Bio.PDB - it looks like a nice addition. Can
someone give Marcin access to CVS?
Remember that you need to provide tests for your contribution!

Cheers,

-Thomas

From mjldehoon at yahoo.com  Sat Jan  5 08:41:25 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 5 Jan 2008 00:41:25 -0800 (PST)
Subject: [Biopython-dev] Bio.Ais
Message-ID: <140129.37367.qm@web62402.mail.re1.yahoo.com>

Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in <module>
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
---------------------------------
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From mjldehoon at yahoo.com  Fri Jan 11 11:16:45 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 11 Jan 2008 03:16:45 -0800 (PST)
Subject: [Biopython-dev] Bio.Ais
In-Reply-To: <140129.37367.qm@web62402.mail.re1.yahoo.com>
Message-ID: <426295.9925.qm@web62415.mail.re1.yahoo.com>

Looking at this again, currently we have no documentation for Bio.Ais, no maintainer, and no apparent users (at least, I couldn't find any in the mailing list archives). Would anybody mind very much if I mark this module as deprecated?
Just to find out if there are any users of this code out there.

--Michiel.

Michiel de Hoon <mjldehoon at yahoo.com> wrote: Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in 
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
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From josh at globalherald.net  Sun Jan 13 08:03:56 2008
From: josh at globalherald.net (Josh)
Date: Sun, 13 Jan 2008 03:03:56 -0500 (EST)
Subject: [Biopython-dev] Fetching PubMed Entries with Recent Python
Message-ID: <alpine.LRH.1.00.0801130256360.14131@home-av-server.home-av>


Howdy,

Has anyone used a recent Python (2.4 or above) with recent Entrez-PubMed 
DTD's or WSDL's to fetch PubMed entries?

I've spent several hours on two methods.  First, I tried using ZSI with 
the PubMed WSDL's.  That resulted in a gargantuan PubMed Types .py file 
with several errors.

I then found Andrew Dalke's EUtils python module.  When I tried to use it 
the first time, as outlined in the README, it complained about missing 
modules.  The DTD modules weren't installed under the EUtils dir under 
site-packages, and it was missing some pubmed DTD's, so I fixed those two 
problems and ended up with a validation exception.

At some point I'll probably have to spend the hours to fix all the 
problems with EUtils, but I wanted to ping everyone to see if anyone has 
done this yet.  I'm using the Python 2.4.3 included with CentOS 5.1.

Cheers,
-Josh



From biopython at maubp.freeserve.co.uk  Tue Jan 15 14:09:47 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Jan 2008 14:09:47 +0000
Subject: [Biopython-dev] [BioPython] [Biopython] Blast problem
In-Reply-To: <4ac065b80801150526q79215288k7e6a0e633d83f1c4@mail.gmail.com>
References: <4ac065b80801150526q79215288k7e6a0e633d83f1c4@mail.gmail.com>
Message-ID: <320fb6e00801150609y16c77bdch927dd6d9689996a5@mail.gmail.com>

Hi Joost,

> Iam having a problem with the hsp.match function in the Bio-Python Blast
> module. A few weeks ago the hsp.match returned me the following:
>
> ATGGCA++TGG
>
> But now it gives me:
>
> ATGGCA TGG
>
> I can't see the number of gaps anymore, anyone a solution for this?

Are you using the online version of blast with Biopython?  Perhaps the
NCBI changed something.  Are you parsing the XML output or the plain
text?  Can you provide any more information (e.g. which version of
Biopython).

Thanks

Peter


From bugzilla-daemon at portal.open-bio.org  Tue Jan 15 22:41:12 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 15 Jan 2008 17:41:12 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801152241.m0FMfCJN001996@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375


tiagoantao at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|tiagoantao at gmail.com        |biopython-dev at biopython.org
             Status|ASSIGNED                    |NEW




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From bugzilla-daemon at portal.open-bio.org  Tue Jan 15 22:46:30 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 15 Jan 2008 17:46:30 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801152246.m0FMkU9S002237@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #14 from tiagoantao at gmail.com  2008-01-15 17:46 EST -------
(In reply to comment #13)
> Style wise, I would use os.path functions rather than doing this yourself with
> os.sep, and also I'm not personally so keen on the import style (I should try
> and find a style reference to back this up though!).

Regarding the import style, I was probably not on my best days. Agree and
changed.

> I doubt Michael has been following this bug (since it is assigned to you Tiago
> none of these comments are being posted to the dev mailing list), but it would
> be nice to have his (or anyone else's) opinion on this (both style, and how
> best to fix the unit test).

I have remove the assignment, so everybody should be seeing this.

I think the coalescent code should be more or less on track for the next
release (whenever Michiel decides to do it).


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 16 01:33:29 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 15 Jan 2008 20:33:29 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801160133.m0G1XTBd010079@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #15 from mdehoon at ims.u-tokyo.ac.jp  2008-01-15 20:33 EST -------
Indeed I was not following this bug.
To me the patch for setup.py looks fine. Feel free to commit it.

The solution in Bio/PopGen/SimCoal/__init__.py to find builtin_tpl_dir is not
so beautiful, but on the other hand I don't see a better way to do it. In
essence, this is an oversight in the Python testing framework. It makes sense
to test from the build directory instead of from the installation directory (we
want to test before we install). Unless I missed something in the
documentation, the current testing framework does not really take that into
account. Anyway, I think the current solution is the best we can do.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan 18 12:16:50 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 18 Jan 2008 07:16:50 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801181216.m0ICGone018126@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #16 from tiagoantao at gmail.com  2008-01-18 07:16 EST -------
(In reply to comment #15)
> To me the patch for setup.py looks fine. Feel free to commit it.

I have committed it. I have tested it on 2 machines, but considering that my
setup is highly biased towards my needs, please test it.

PS - I have an attachment on this bug with a (rather big) addition to the
manual (pic included). If you want to have a look I would be most thankful.

Tiago


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From mjldehoon at yahoo.com  Fri Jan 18 12:20:38 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Jan 2008 04:20:38 -0800 (PST)
Subject: [Biopython-dev] Bio.Ais
In-Reply-To: <426295.9925.qm@web62415.mail.re1.yahoo.com>
Message-ID: <565042.83375.qm@web62414.mail.re1.yahoo.com>

Since no users came forward, I deprecated Bio.Ais and removed the corresponding test_ais.py. I added a statement in the DeprecationWarning that this module is on the nomination to be removed (in some future Biopython release), if no users come forward.

--Michiel.

Michiel de Hoon <mjldehoon at yahoo.com> wrote: Looking at this again, currently we have no documentation for Bio.Ais, no maintainer, and no apparent users (at least, I couldn't find any in the mailing list archives). Would anybody mind very much if I mark this module as deprecated?
Just to find out if there are any users of this code out there.

--Michiel.

Michiel de Hoon  wrote: Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in 
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
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From mjldehoon at yahoo.com  Fri Jan 18 12:32:25 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Fri, 18 Jan 2008 04:32:25 -0800 (PST)
Subject: [Biopython-dev] LocusLink, anybody?
Message-ID: <397687.73819.qm@web62408.mail.re1.yahoo.com>

When I was making an inventory of Biopython code involved in accessing NCBI's databases, I came across the Bio.LocusLink module, containing a paser for NCBI's LocusLink. The website for LocusLink is http://www.ncbi.nlm.nih.gov/LocusLink/.

However, this website says:
"LocusLink is superceded by Entrez Gene...."
As far as I can tell, LocusLink is no longer used, making Bio.LocusLink superfluous. Did I miss something? Does anybody see a reason for keeping Bio.LocusLink?

--Michiel

       
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From bugzilla-daemon at portal.open-bio.org  Fri Jan 18 12:43:54 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 18 Jan 2008 07:43:54 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801181243.m0IChsbC019332@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #17 from biopython-bugzilla at maubp.freeserve.co.uk  2008-01-18 07:43 EST -------
Apeart from test_PopGen_FDist and test_PopGen_SimCoal where I don't have the
tools installed, the PopGen unit tests pass, and it seems to install fine too.

I've skimmed over the tutorial diff, but have not tried the examples (I don't
have SimCoal installed, nor time right now to try it).

Regarding the figure, using a PNG image is probably best as we want to produce
both HTML and PDF output.  You can make the file about half the size by saving
it as a greyscale PNG image (and cropping the bottom margin a little more).

Otherwise it looks fine.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan 18 12:46:42 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 18 Jan 2008 07:46:42 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801181246.m0ICkgao019590@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #18 from tiagoantao at gmail.com  2008-01-18 07:46 EST -------
(In reply to comment #17)
> Regarding the figure, using a PNG image is probably best as we want to produce
> both HTML and PDF output.  You can make the file about half the size by saving
> it as a greyscale PNG image (and cropping the bottom margin a little more).
> 
> Otherwise it looks fine.

I will make the changes to the image as you say, and if nobody opposes I will
commit the changes myself.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 23 13:03:09 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 23 Jan 2008 08:03:09 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801231303.m0ND39pm022177@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #19 from biopython-bugzilla at maubp.freeserve.co.uk  2008-01-23 08:03 EST -------
I'd previously only tried this on Linux.  I've now also tested this on Windows
now (compiling from source), and it seems to install the data files as
expected, and the unit tests look fine.

Once the documentation is checked in, I think this bug can be marked as fixed.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 23 13:22:13 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 23 Jan 2008 08:22:13 -0500
Subject: [Biopython-dev] [Bug 2375] Coalescent support through Simcoal2
In-Reply-To: <bug-2375-42@http.bugzilla.open-bio.org/>
Message-ID: <200801231322.m0NDMDBI023110@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2375





------- Comment #20 from tiagoantao at gmail.com  2008-01-23 08:22 EST -------
(In reply to comment #19)
> Once the documentation is checked in, I think this bug can be marked as fixed.

I checked it in a couple of days ago. Please have a final "helicopter" look at
it just to see if there are any gross problems with it. The Tutorial is now
precisely 100 pages long, BTW.


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 28 19:12:33 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 28 Jan 2008 14:12:33 -0500
Subject: [Biopython-dev] [Bug 2437] New: comparing alphabet references
	causes assert to fail when it should pass
Message-ID: <bug-2437-42@http.bugzilla.open-bio.org/>

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

           Summary: comparing alphabet references causes assert to fail when
                    it should pass
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: rjalves at igc.gulbenkian.pt


/var/lib/python-support/python2.4/Bio/Translate.py in translate_to_stop(self,
seq)
    34     def translate_to_stop(self, seq):
    35         # This doesn't have a stop encoding
---> 36         assert seq.alphabet == self.table.nucleotide_alphabet, \
    37                "cannot translate from given alphabet (have %s, need %s)"
%\
    38                (seq.alphabet, self.table.nucleotide_alphabet)

AssertionError: cannot translate from given alphabet (have IUPACAmbiguousDNA(),
need IUPACAmbiguousDNA())


What I did:

from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio import Translate
from Bio import Seq

a=Seq.Seq("ATCGGATGA...ATGCAGT",alphabet=IUPACAmbiguousDNA())
b=Translate.ambiguous_dna_by_id[11]

b.translate_to_stop(a) ... error pops out

The only way around I was able to find is:

b.table.nucleotide_alphabet=a.alphabet


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 28 19:34:12 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 28 Jan 2008 14:34:12 -0500
Subject: [Biopython-dev] [Bug 2437] comparing alphabet references causes
	assert to fail when it should pass
In-Reply-To: <bug-2437-42@http.bugzilla.open-bio.org/>
Message-ID: <200801281934.m0SJYCnT017522@portal.open-bio.org>

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





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-01-28 14:34 EST -------
This code snippet shows the same issue:

from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA

alpha1 = IUPACAmbiguousDNA()
alpha2 = IUPACAmbiguousDNA()

assert type(alpha1) == type(alpha2)
assert dir(alpha1) == dir(alpha2)
assert alpha1.letters == alpha2.letters

assert alpha1 == alpha2 #fails, different instances of same class

We could update the Alphabet class to define an equality check, and/or modify
Bio.Translate to use a less harsh assertion.


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From marcin.cieslik at gmail.com  Thu Jan 31 07:05:26 2008
From: marcin.cieslik at gmail.com (=?UTF-8?B?TWFyY2luIENpZcWbbGlr?=)
Date: Thu, 31 Jan 2008 02:05:26 -0500
Subject: [Biopython-dev] Atomic / Residue contacts for Bio.PDB
Message-ID: <47A17336.2090503@gmail.com>

Hello,
I've written several classes to work with the ccp4 ncont program. They
use the AbstractPropertyMap, AbstractAtomPropertyMap classes to map
contacts between atoms and residues. I'd like to contribute this code.

it consists of
* one 'private' function which runs ncat and parses output into
{full_atom_id_in_biopython_tuple : (other_full_id, distance)
				 : (yet another atom, distance)
....
}

and classes:
class _AbstractAtomContacts(AbstractAtomPropertyMap):
	class WaterAtomContacts(_AbstractAtomContacts):
	class CrystalAtomContacts(_AbstractAtomContacts):

class _AbstractContacts(AbstractPropertyMap):
	class CrystalContacts(_AbstractContacts):
	class WaterContacts(_AbstractContacts):

the ncat calling function is called only by _AbstractAtomContacts, the
results are stored in the .xtra dict. Specific contact classes are just
'definitions' of settings for ncat e.g CrystalContacts searches contacts
between symmetry mates only, in 27 unit cells, ommiting all waters etc.

One negative side of this code is that ncat and the mmdb library (and as
a consequence ccp4 6.0.2) do not support PDB v3 files. Luckily RCSB
provides a python PDB translator script 3.1 <--> 2.3.

Marcin


From mjldehoon at yahoo.com  Thu Jan 31 10:18:54 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 31 Jan 2008 02:18:54 -0800 (PST)
Subject: [Biopython-dev] Atomic / Residue contacts for Bio.PDB
In-Reply-To: <47A17336.2090503@gmail.com>
Message-ID: <709883.8309.qm@web62410.mail.re1.yahoo.com>

Dear Marcin,

For contributions to Bio.PDB, it's best to ask Thomas Hamelryck directly. See http://www.binf.ku.dk/User:Thomas_Hamelryck. I'm not sure if he is still actively reading this mailing list.

--Michiel.

Marcin Cie??lik <marcin.cieslik at gmail.com> wrote: Hello,
I've written several classes to work with the ccp4 ncont program. They
use the AbstractPropertyMap, AbstractAtomPropertyMap classes to map
contacts between atoms and residues. I'd like to contribute this code.

it consists of
* one 'private' function which runs ncat and parses output into
{full_atom_id_in_biopython_tuple : (other_full_id, distance)
     : (yet another atom, distance)
....
}

and classes:
class _AbstractAtomContacts(AbstractAtomPropertyMap):
 class WaterAtomContacts(_AbstractAtomContacts):
 class CrystalAtomContacts(_AbstractAtomContacts):

class _AbstractContacts(AbstractPropertyMap):
 class CrystalContacts(_AbstractContacts):
 class WaterContacts(_AbstractContacts):

the ncat calling function is called only by _AbstractAtomContacts, the
results are stored in the .xtra dict. Specific contact classes are just
'definitions' of settings for ncat e.g CrystalContacts searches contacts
between symmetry mates only, in 27 unit cells, ommiting all waters etc.

One negative side of this code is that ncat and the mmdb library (and as
a consequence ccp4 6.0.2) do not support PDB v3 files. Luckily RCSB
provides a python PDB translator script 3.1 <--> 2.3.

Marcin
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From thamelry at binf.ku.dk  Thu Jan 31 10:35:58 2008
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Thu, 31 Jan 2008 11:35:58 +0100
Subject: [Biopython-dev] Atomic / Residue contacts for Bio.PDB
In-Reply-To: <709883.8309.qm@web62410.mail.re1.yahoo.com>
References: <47A17336.2090503@gmail.com>
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On Jan 31, 2008 11:18 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> Dear Marcin,
>
> For contributions to Bio.PDB, it's best to ask Thomas Hamelryck directly.
> See http://www.binf.ku.dk/User:Thomas_Hamelryck. I'm not sure if he is
> still actively reading this mailing list.
>

I am in fact, just really busy these days.

Marcin, you can add the code to Bio.PDB - it looks like a nice addition. Can
someone give Marcin access to CVS?
Remember that you need to provide tests for your contribution!

Cheers,

-Thomas