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Jeffrey Chang | 1 Jul 2003 06:04

Re: [Bug 1462] New: building Bio.trie fails

Hi,

Thanks for the report.  I think this has been fixed in the CVS version 
of the triemodule.c file, at cvs.biopython.org.  Please let me know if 
it is still a problem.

Thanks,
Jeff

On Monday, June 30, 2003, at 01:36  PM, 
bugzilla-daemon <at> portal.open-bio.org wrote:

> http://bugzilla.bioperl.org/show_bug.cgi?id=1462
>
>            Summary: building Bio.trie fails
>            Product: Biopython
>            Version: 1.10
>           Platform: PC
>         OS/Version: Linux
>             Status: NEW
>           Severity: blocker
>           Priority: P2
>          Component: Main Distribution
>         AssignedTo: biopython-dev <at> biopython.org
>         ReportedBy: malex <at> purdue.edu
>
>
> building 'Bio.trie' extension
> gcc -DNDEBUG -DNDEBUG -g -O3 -Wall -Wstrict-prototypes 
> -fno-strict-aliasing
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Yves Bastide | 2 Jul 2003 19:03
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FormatIO and SwissProt

Hi,

FormatIO doesn't seem to handle SwissProt files well...

bionix:~/src/bio/biopython/Tests% python
Python 2.2.2 (#1, Feb 14 2003, 12:23:31)
[GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import SeqRecord
>>> sequence_iterator = SeqRecord.io.readFile(open("SwissProt/sp008"))
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File
"/.amd/archipel/export/archive/d08/symbiose/ybastide/src/bio/biopython/build/lib.linux-i686-2.2/Bio/FormatIO.py",
line 97, in readFile
     raise TypeError("Could not determine file type")
TypeError: Could not determine file type

[OK, there are two Swissprot parsers.  Erm, why */build/lib-*/Bio/FormatIO.py?
It's certainly not in my path :)]

 >>> sequence_iterator = SeqRecord.io.readFile(open("SwissProt/sp008"), format="swissprot/40")
 >>> sequence_iterator.next()
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File
"/.amd/archipel/export/archive/d08/symbiose/ybastide/src/bio/biopython/build/lib.linux-i686-2.2/Bio/FormatIO.py",
line 13, in next
     x = self.obj.next()
   File "/local/lib/python2.2/site-packages/Martel/IterParser.py", line 76, in iterateFile
(Continue reading)

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Jeffrey Chang | 3 Jul 2003 07:28

Re: FormatIO and SwissProt

On Wednesday, July 2, 2003, at 10:03  AM, Yves Bastide wrote:

> Hi,
>
> FormatIO doesn't seem to handle SwissProt files well...
>
> bionix:~/src/bio/biopython/Tests% python
> Python 2.2.2 (#1, Feb 14 2003, 12:23:31)
> [GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from Bio import SeqRecord
>>>> sequence_iterator = SeqRecord.io.readFile(open("SwissProt/sp008"))
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File  
> "/.amd/archipel/export/archive/d08/symbiose/ybastide/src/bio/ 
> biopython/build/lib.linux-i686-2.2/Bio/FormatIO.py", line 97, in  
> readFile
>     raise TypeError("Could not determine file type")
> TypeError: Could not determine file type
>
> [OK, there are two Swissprot parsers.  Erm, why  
> */build/lib-*/Bio/FormatIO.py?
> It's certainly not in my path :)]

Is this related to the patch you sent in?  This also fails on my  
system, but the path points to my usual python path (i.e. not  
../build...).

And yes, you've hit the problem right on the nose.  There are two
(Continue reading)

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Yves Bastide | 3 Jul 2003 11:43
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Re: FormatIO and SwissProt

Jeffrey Chang wrote:
> On Wednesday, July 2, 2003, at 10:03  AM, Yves Bastide wrote:
> 
>> Hi,
>>
>> FormatIO doesn't seem to handle SwissProt files well...
>>
>> bionix:~/src/bio/biopython/Tests% python
>> Python 2.2.2 (#1, Feb 14 2003, 12:23:31)
>> [GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>
>>>>> from Bio import SeqRecord
>>>>> sequence_iterator = SeqRecord.io.readFile(open("SwissProt/sp008"))
>>
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in ?
>>   File  "/.amd/archipel/export/archive/d08/symbiose/ybastide/src/bio/ 
>> biopython/build/lib.linux-i686-2.2/Bio/FormatIO.py", line 97, in  
>> readFile
>>     raise TypeError("Could not determine file type")
>> TypeError: Could not determine file type
>>
>> [OK, there are two Swissprot parsers.  Erm, why  
>> */build/lib-*/Bio/FormatIO.py?
>> It's certainly not in my path :)]
> 
> 
> Is this related to the patch you sent in?  This also fails on my  
> system, but the path points to my usual python path (i.e. not
(Continue reading)

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Jeffrey Chang | 4 Jul 2003 08:53

Re: FormatIO and SwissProt


On Thursday, July 3, 2003, at 02:43  AM, Yves Bastide wrote:

> Jeffrey Chang wrote:
>> On Wednesday, July 2, 2003, at 10:03  AM, Yves Bastide wrote:
[SwissProt in FormatIO fails on SwissProt file]

>> And yes, you've hit the problem right on the nose.  There are two  
>> Swiss-Prot parsers.  The FormatIO one is still considered 
>> experimental,  and is not maintained as well.  I'd recommend using 
>> the  Bio/SwissProt/SProt parser instead.
>
> There are three SP parsers: Bio/SwissProt/SProt and two for FormatIO 
> (../Bio/expressions/swissprot/sprot{38,40}.py)
>
> I'd like to use FormatIO because
>
> 1. It's cool to use the same code whether I'm accessing nr or sprot or 
> something else
>
> 2. Bio.SeqRecord: to insert into a database.  One can't get a 
> Bio.SeqRecord from SProt, I think

Yes, both are excellent points.  Andrew started the framework for 
Bio.expressions and started to populate it with some parsers.  However, 
he soon got busy with other things (like EUtils).  We really need 
someone to pick up work on this (hint, hint :), before we can really 
start pushing it for mainstream use.

> About GenBank:
(Continue reading)

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bugzilla-daemon | 15 Jul 2003 03:45

[Bug 1470] New: KDTree init error

http://bugzilla.bioperl.org/show_bug.cgi?id=1470

           Summary: KDTree init error
           Product: Biopython
           Version: 1.10
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: yuji <at> pachbell.harvard.edu

KDTree fail to initilize during loading of Numeric Python modules.

KDTree/__init__.py raise an module import error on line 4:

from RandomArray import *

Simply comment out this line seems to solve the problem.

System:  
  Python2.2
  Numberic Python 23.0

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Michiel Jan Laurens de Hoon | 18 Jul 2003 09:46
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Re: Bio.Cluster

I have added an option to do hierarchical clustering based on the 
distance matrix directly. The new version in in Biopython's CVS. To 
apply hierarchical clustering to the gene expression data, use

treecluster(my_matrix, ...)

or

treecluster(data=my_matrix, ...)

To do hierarchical clustering on the distance matrix directly, use

treecluster(distancematrix=my_distance_matrix, ...)

where my_distance_matrix is a 2D Numpy array which is symmetric and has 
zeros on the diagonal (though the code does not check for it). This 
works for pairwise single-, maximum-, and average-linkage, but not for 
pairwise centroid-linkage, for which you would need the original gene 
expression data.

I had to make some modifications in the Python <-> C interface for this, 
which tends to be error prone. If you find any bugs, please let me know.

--Michiel.

Iddo Friedberg wrote:

> Dear Michiel,
> 
> I just looked at the manual for Bio.Cluster (very well written, BTW). Is
(Continue reading)

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Iddo Friedberg | 18 Jul 2003 18:23

Re: Bio.Cluster

Thanks! That looks extremely useful.

One comment (just from reading your email, I haven't looked at this 
yet): if the data in the matrix is very sparse, then a NumPy array would 
seem redundant in the sense that most of it will be zeros, and the user 
wil be trying to pass a huge data structure, in which most of the data 
is superfluous. Or am I getting something wrong here?

Thanks!

Iddo

Michiel Jan Laurens de Hoon wrote:
> I have added an option to do hierarchical clustering based on the 
> distance matrix directly. The new version in in Biopython's CVS. To 
> apply hierarchical clustering to the gene expression data, use
> 
> treecluster(my_matrix, ...)
> 
> or
> 
> treecluster(data=my_matrix, ...)
> 
> To do hierarchical clustering on the distance matrix directly, use
> 
> treecluster(distancematrix=my_distance_matrix, ...)
> 
> where my_distance_matrix is a 2D Numpy array which is symmetric and has 
> zeros on the diagonal (though the code does not check for it). This 
> works for pairwise single-, maximum-, and average-linkage, but not for
(Continue reading)

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Bartek Wilczynski | 18 Jul 2003 18:45
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checker_function for the options in bio.application.abstractCommandline

Hello,

I think, there's something not exactly consistent about the parameter setting in
AbstractCommandline class. The problem i see is the following code in the
set_parameter method:

   if parameter.checker_function is not None:
      paramater.checker_function(value)

   parameter.value = value

if we put it together with the documentation of a checker_function:

    o checker_function -- a reference to a function that will determine
    if a given value is valid for this parameter.

it is at least confusing.

I'm not sure, whether the author meant checker_function to raise an exception when
the parameter is not valid, or he just forgot to put the value assignement into
another if-then statement with the result of checker_function as condition, but
I would really appreciate if someone made it more clear.

I would rather opt for the if-then statement, because it allows me to write
simple and self-explanatory checker functions like 

lambda x : isinstance(x,int)

and not to bother with raising the exception. the code in the set_parameter
could look then like:
(Continue reading)

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Iddo Friedberg | 18 Jul 2003 18:44

[Fwd: O'Reilly Life Science Informatics Conference: Call For Participation]


Hi all,

O'Reilly is holding another Bioinformatics conference. They have a slot
for a Biopython presentation. Free admission to speakers. Any takers?

Iddo

-------- Original Message --------
Subject: O'Reilly Life Science Informatics Conference: Call For
Participation
Date: Thu, 17 Jul 2003 16:27:01 -0700
From: O'Reilly Conferences <elists-admin <at> oreillynet.com>
To: idoerg

Call For Participation:
The 2004 O'Reilly Life Science Informatics Conference
February 9-12, 2004
Westin Horton Plaza, San Diego, CA, USA
http://conferences.oreilly.com/lsicon/

With two successful conferences focused on bioinformatics behind
us, O'Reilly & Associates is putting a new twist on the 2004
event: we're expanding its scope to reflect the evolutionary
changes happening in the field of life science informatics. If
you're a biologist, computer scientist, software engineer,
mathematician, or an expert in another related field, we invite
you to submit proposals to lead tutorial and conference sessions
at the 2004 O'Reilly Life Science Informatics Conference. Proposals
are due September 1, 2003.
(Continue reading)

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Gmane