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Brad Chapman | 2 Aug 2004 22:41
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[BioPython] Some Biopython news, plans, and grants

Hello everyone;
As some of you may have noticed, I've been relatively absent from
the Biopython lists over the last couple of months. This was due to
the unfortunate arrival of dissertation and defense time for me;
thankfully all of my painful finishing work is, well, finished and I
am happily in PhD land as of this upcoming Saturday.

What that means is that I'm going to make a concerted effort to go
through the mailing list and try and sort out problems and bugs that
have been posted that no one has been able to get to. I'd like this
to lead up to a semi-soonish release, and then we'll worry about
what goes from there.

For the upcoming release, I'll stay simple. The main things I'd 
like to do before release are:

-> Cleaning up bugs, problems from the mailing lists. This will take
a bit; there are a lot of things that need attention.

-> Move from using Numeric (Numpy, Numerical Python) to Numarray
(http://www.stsci.edu/resources/software_hardware/numarray). Since
development on this package is now entirely focused on Numarray, I
think it makes the most sense for us to migrate over.

That's it. Pretty simple. Besides a new release, another idea I'd
like to toss out there is trying to write a grant for the Python
Software Foundation to get money to "hire" someone to help with
Biopython documentation. The PSF is accepting proposals up until
October 1st:
(Continue reading)

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Thomas Hamelryck | 3 Aug 2004 15:22
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Re: [BioPython] Problem superimposing structures


Hi Sergio,

Sorry about the delay in replying.

>    I am trying to superimpose two crystal structures using the
> Bio.PDB.Superimposer, following the example in the biopython FAQ
> document where it explains how to do this.  For the purposes of testing, I
> am only using 5 atoms in the atoms lists.  Below I show the two atom lists
> and the error I get when I try to use the set_atoms method.
>
> >>> ebg_res1
>
> [<Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>]
>
> >>> ebh_res1
>
> [<Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>]
>
> >>> sup.set_atoms( ebg_res1, ebh_res1)
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> TypeError: unbound method set_atoms() must be called with Superimposer
> instance as first argument (got list instance instead)

You haven't sent in all the code. What is the sup variable? I suspect 
you erroneously assigned sup to the Superimposer class itself, and not to an 
instance of this class - hence the complaint about an unbound method.
(Continue reading)

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Peter Wilkinson | 3 Aug 2004 16:59
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[BioPython] Entrez module

I suddenly had an urge to query entrez with python ....

I have looked through the latest release ... but did not find an entrez module

is there an interface to Entrez hidden somewhere?

Peter

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython
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Peter Wilkinson | 3 Aug 2004 17:06
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Re: [BioPython] Entrez module

I just found the interface in Bio.WWW

Peter

At 10:59 AM 8/3/2004, Peter Wilkinson wrote:
>I suddenly had an urge to query entrez with python ....
>
>I have looked through the latest release ... but did not find an entrez module
>
>is there an interface to Entrez hidden somewhere?
>
>Peter
>
>_______________________________________________
>BioPython mailing list  -  BioPython <at> biopython.org
>http://biopython.org/mailman/listinfo/biopython

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython
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Brad Chapman | 3 Aug 2004 18:24
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Re: [BioPython] Entrez module

Hi Peter;

> >I suddenly had an urge to query entrez with python ....
> >
> >I have looked through the latest release ... but did not find an entrez 
> >module
[...]
> I just found the interface in Bio.WWW

The best way to query Entrez from programs is using the EUtils
interfaces at NCBI:

http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html

Biopython has a interface to EUtils in Bio.EUtils. There is a lot of
source code documentation within there. For instance, for an example
of retrieving PubMed information, Bio.EUtils.HistoryClient provides
some good code examples:

http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html

The only thing you have to do is adjust the imports to be from
Biopython, like from Bio.EUtils import HistoryClient (sorry, older
documentation from when EUtils was not within Biopython -- I updated
this).

If you have specific questions feel free to ask, but the EUtils
interfaces should definitely be more stable than the older stuff in
Bio.WWW.
(Continue reading)

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Peter Wilkinson | 3 Aug 2004 18:44
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Re: [BioPython] Entrez module

That is good to know. I will have a loot at the EUtils first.

Peter

At 12:24 PM 8/3/2004, Brad Chapman wrote:
>Hi Peter;
>
> > >I suddenly had an urge to query entrez with python ....
> > >
> > >I have looked through the latest release ... but did not find an entrez
> > >module
>[...]
> > I just found the interface in Bio.WWW
>
>The best way to query Entrez from programs is using the EUtils
>interfaces at NCBI:
>
>http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
>
>Biopython has a interface to EUtils in Bio.EUtils. There is a lot of
>source code documentation within there. For instance, for an example
>of retrieving PubMed information, Bio.EUtils.HistoryClient provides
>some good code examples:
>
>http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html
>
>The only thing you have to do is adjust the imports to be from
>Biopython, like from Bio.EUtils import HistoryClient (sorry, older
>documentation from when EUtils was not within Biopython -- I updated
>this).
(Continue reading)

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Peter Wilkinson | 3 Aug 2004 19:16
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Re: [BioPython] Some Biopython news, plans, and grants

I certainly would be interested in the documentation project, if you can 
find funding. I do like working on tutorials and documentation 
'solutions'... my own personal war on bad and thin documentation. Please 
add me to a list, and let me know what the time commitments would be.

With regards to numarray, i will be exploring this module for the use in 
microarray analysis as I need some structures (I think) that would be 
useful in  vectorising calculations. I am working on  some code that is 
structured after the RGlist and MAlist objects you find in Bioconductor's 
limma package. I am doing some large scale micrarra analysis (in the 
hundreds of arrays per project), and I find that R is not the tool for 
batch work, but it is a good tool for statistical analysis. Python + rpy or 
RSpython might = batch work. I am still exploring. It might turn out better 
to implement some new normalization algorithms directly in Python or in 
C++. R has memory management problems, and it is built for you to load all 
the data you want to work with at once ... this is limits batch processing.

I am hoping numarray can help.

Peter

At 04:41 PM 8/2/2004, Brad Chapman wrote:
>Hello everyone;
>As some of you may have noticed, I've been relatively absent from
>the Biopython lists over the last couple of months. This was due to
>the unfortunate arrival of dissertation and defense time for me;
>thankfully all of my painful finishing work is, well, finished and I
>am happily in PhD land as of this upcoming Saturday.
>
>What that means is that I'm going to make a concerted effort to go
(Continue reading)

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Peter Wilkinson | 3 Aug 2004 19:30
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[BioPython] BioEutils

This is my first attempt with this package ... on win32 with what I think 
is the latest Biopython.

I would like to look up records for image clones like:

clone = client.search("IMAGE:624360",db="nucleotide")

This would be the way I look for a clone in the nucleotide set using the 
search field on the root of the ncbi homepage.  I know that this clone is 
in nucleotide, but this query does not work here, I get a result of length = 0.

or by accession number if the clone has one:

clone = client.search("AA759046",db="nucleotide")

however I get the following error

Traceback (most recent call last):
   File "<pyshell#8>", line 1, in -toplevel-
     clone = client.search("AA759046",db="nucleotide")
   File "C:\Python23\lib\site-packages\Bio\EUtils\HistoryClient.py", line 
354, in search
     searchinfo = parse.parse_search(infile, self.webenv_ref)
   File "C:\Python23\lib\site-packages\Bio\EUtils\parse.py", line 201, in 
parse_search
     for ele in pom["TranslationStack"]:
   File "C:\Python23\lib\site-packages\Bio\EUtils\POM.py", line 355, in 
__getitem__
     raise IndexError, "no item matches"
IndexError: no item matches.
(Continue reading)

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Iddo Friedberg | 3 Aug 2004 19:33
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Re: [BioPython] Some Biopython news, plans, and grants

<CONCERTED_CHEERING>

DR. CHAPMAN!!

DR. CHAPMAN!!

DR. CHAPMAN!!

DR. CHAPMAN!!

</CONCERTED_CHEERING>

You will never be bumped off a flight again.

Iddo

=====
--
Iddo Friedberg                   
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA, 92037
USA 
T: (858) 646 3100 x3516
http://ffas.ljcrf.edu/~iddo

	
		
__________________________________
Do you Yahoo!?
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Peter Wilkinson | 3 Aug 2004 19:40
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Re: [BioPython] Entrez module

I dont seem to be getting any of the EUtils to work.

I have tried the dbIds client sample code:

 >>> result = client.search("dalke", retmax = 100)

Traceback (most recent call last):
   File "<pyshell#24>", line 1, in -toplevel-
     result = client.search("dalke", retmax = 100)
   File "C:\Python23\lib\site-packages\Bio\EUtils\DBIdsClient.py", line 
294, in search
     searchinfo = parse.parse_search(infile, [None])
   File "C:\Python23\lib\site-packages\Bio\EUtils\parse.py", line 219, in 
parse_search
     raise TypeError("Unknown OP code: %r" % (s,))
TypeError: Unknown OP code: u'GROUP'

NCBI changing things around so the EUtils packages breaks?

Peter

At 12:24 PM 8/3/2004, Brad Chapman wrote:
>Hi Peter;
>
> > >I suddenly had an urge to query entrez with python ....
> > >
> > >I have looked through the latest release ... but did not find an entrez
> > >module
>[...]
> > I just found the interface in Bio.WWW
(Continue reading)

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Gmane