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bugzilla-daemon | 3 Jun 2003 19:53

[Bug 1447] New: Testing new bugzilla installation

http://bugzilla.bioperl.org/show_bug.cgi?id=1447

           Summary: Testing new bugzilla installation
           Product: Biopython
           Version: 1.10
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: jchang <at> biopython.org

just ported it over from cvs.open-bio.org to portal

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Coleman, Michael | 6 Jun 2003 22:53

RE: blastpgp parsing buglet

Hi,

It looks like a further change is required on this.  The problem is that when blank lines following
'CONVERGED' (and perhaps in other cases) are not consumed, _scan_alignments will see them and its tests
will not work properly.

Mike

--- NCBIStandalone.py~  2003-05-08 13:36:06.000000000 -0500
+++ NCBIStandalone.py   2003-06-06 15:38:31.000000000 -0500
 <at>  <at>  -247,6 +247,7  <at>  <at> 
                 read_and_call_while(uhandle, consumer.noevent, blank=1)

         attempt_read_and_call(uhandle, consumer.converged, start='CONVERGED')
+       read_and_call_while(uhandle, consumer.noevent, blank=1)

         consumer.end_descriptions()

> -----Original Message-----
> From: Coleman, Michael 
> Sent: Thursday, May 08, 2003 1:45 PM
> To: biopython-dev <at> biopython.org
> Subject: blastpgp parsing buglet
> 
> 
> Parsing by NCBIStandalone.py fails for BLASTP 2.2.5 output.  
> This is the partial output that trips the problem:
> 
> gi|23099742|ref|NP_693208.1| ornithine aminotransferase 
> [Oceanob...   430   e-119
(Continue reading)

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Jeffrey Chang | 9 Jun 2003 04:11

Re: RE: blastpgp parsing buglet

Thanks very much for the patch.  I've committed it to the CVS tree.

Jeff

On Friday, June 6, 2003, at 01:53  PM, Coleman, Michael wrote:

> Hi,
>
> It looks like a further change is required on this.  The problem is 
> that when blank lines following 'CONVERGED' (and perhaps in other 
> cases) are not consumed, _scan_alignments will see them and its tests 
> will not work properly.
>
> Mike
>
>
>
>
>
>
>
>
> --- NCBIStandalone.py~  2003-05-08 13:36:06.000000000 -0500
> +++ NCBIStandalone.py   2003-06-06 15:38:31.000000000 -0500
>  <at>  <at>  -247,6 +247,7  <at>  <at> 
>                  read_and_call_while(uhandle, consumer.noevent, 
> blank=1)
>
>          attempt_read_and_call(uhandle, consumer.converged, 
> start='CONVERGED')
(Continue reading)

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Brad Chapman | 11 Jun 2003 00:09
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Re: [BioPython] performance problem in ParserSupport.EventGenerator._get_set_flags

[moving this to the dev list since it's got attachments 'n things]

Hi Andreas;
I want to preface this by saying that I know nearly next to nothing
about profiling. That doesn't mean I'm not interested in helping
speed things up, just that I don't have much experience in doing it.

> it seems that when I parse a large GenBank file, most of the time is
> spend in this function. Can anybody think of a more efficient way to do
> this? I don't fully understand the algorithm here. What values can be
> stored in this flags? Only 0 and 1? Is there a difference between value
> 0 and not having the key in the dict?

I don't know about the efficiency issues, but I can help at least
explain what I'm trying to do here. Basically, this code is meant to
sort of transition between the way Martel does things (with XML and
SAX events) and the way that Biopython does things (with Consumers
and Event generators). So, saying that, it's going to be inherently
not optimized since I am basically jamming two concepts together
with this EventGenerator glue. Also, I suck at optimization (I try
to focus more on code clarity), so there's that as well.

The idea is that the flags keep track of where you are at in the XML
and collect up that information before passing it on to the
appropriate event. Looking at my code, it looks like a couple of
things are especially bad, but the biggest culprit is probably the
characters function:

        def characters(self, content):
            """Extract the information.
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Michiel Jan Laurens de Hoon | 12 Jun 2003 06:44
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Bio.Cluster

Dear biopython developers,

I have added Bio.Cluster to the Biopython CVS. Bio.Cluster contains 
clustering techniques for gene expression data (hierarchical, k-means, 
and SOMs); most routines are written in C with a Python wrapper. This 
package also exists separately as Pycluster.

The Python and C source code is in Bio/Cluster; I have also added 
Bio.Cluster to setup.py.

In case you want to try this package, there is a manual at
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster.pdf
(replace "from Pycluster import *" by "from Bio.Cluster import *") and a 
sample data set at
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/demo.txt.
Please let me know if you find any problems with this package.

--Michiel.

--

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon
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Jeffrey Chang | 13 Jun 2003 07:11
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making new release

Hey developers,

It feels like time to make a new release.  There's been a bunch of new 
code and fixes, and the BLAST parser is sufficiently out of date.  :)  
Plus, Michiel is anxious to get his new clustering software available!  
Hmmm...  I just noticed that Andrew just checked in EUtils as well.

So, everybody working on the code in the CVS repository, please let me 
know where you are.  Specifically, I need to know whether the code is 
not ready to be released yet, and when it will be.

All the tests should pass.  On my system now, test_FSSP is failing.  It 
looks minor -- Iddo?

Jeff
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Andrew Dalke | 13 Jun 2003 07:19

Re: making new release

Yup, added EUtils so Brad can boast about it at BOSC.
I'm done until the end of this month (at a client's site
then at EuroPython).  Brad will make any extra changes
needed to get EUtils working in Biopython.  There are
also a few changes to make w.r.t updating EUtils for
the latest EUtils spec, but that'll have to wait.

So unless you want to wait another month, go ahead
with a new release.

					Andrew
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Brad Chapman | 13 Jun 2003 18:12
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Re: making new release

Hey Jeff;

> It feels like time to make a new release.  There's been a bunch of new 
> code and fixes, and the BLAST parser is sufficiently out of date.  :)  
> Plus, Michiel is anxious to get his new clustering software available!  
> Hmmm...  I just noticed that Andrew just checked in EUtils as well.

Definitely agree with making a release. I think a few more people 
other then me should hit on EUtils to make sure I fixed everything 
after Andrew checked it in. Just so I'm not soley responsible :-).

> So, everybody working on the code in the CVS repository, please let me 
> know where you are.  Specifically, I need to know whether the code is 
> not ready to be released yet, and when it will be.

The only thing I have (besides double checking EUtils) is the
speed-up stuff in GenBank. I hope that should be finished by the end
of the weekend. I also want to update (at least) the install
documentation so links and things point to the new website. That
should also be done by the end of the weekend.

> All the tests should pass.  On my system now, test_FSSP is failing.  It 
> looks minor -- Iddo?

KDTree and LocusLink are commented out in setup.py (which gives
import warnings in the test). Is there are a reason for this or
should we try to get those working as well?

test_GFF is also failing for me:
(Continue reading)

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katel@worldpath.net | 13 Jun 2003 21:09

Re: making new release


Original Message:
-----------------
From: Brad Chapman chapmanb <at> uga.edu
Date: Fri, 13 Jun 2003 12:12:35 -0400
To: biopython-dev <at> biopython.org
Subject: Re: [Biopython-dev] making new release

Hey Jeff;

  Since the last release I uploaded a humungous Locus test file.  That may
explain the problem?  What error does it give when the comments are removed?

KDTree and LocusLink are commented out in setup.py (which gives
import warnings in the test). Is there are a reason for this or
should we try to get those working as well?

test_GFF is also failing for me:

12:05pm Tests> python run_tests.py test_GFF.py
test_GFF ... FAIL

======================================================================
FAIL: test_GFF

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