Pablo Barrera González | 5 Sep 19:33 2002
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[BioPython] Read Astral file

Hello,

I have the astral-scopdom-seqres-all-1.59.fa file.

Here it's an example:
 >d1a3oa_ a.1.1.2 (A:) Hemoglobin, alpha-chain {Human (Homo sapiens)}
vlspadktnvkaawgkvgahageygaealermflsfpttkthfphfdlshgsaqvkghgk
kvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaahlpaeftpa
vhasldkflasvstvltskyr

I would like to read it, and work with the sequence, but I don't know if 
there's any class in biopython for doing this or I should write it myself.

I need the info of the SCOP classification (the "a.1.1.2"  part) and the 
sequence in order to by able to cluster the sequences with the same 
superfamily.

Thanks to everyone

--

-- 
---------------------------------------------------------------
Pablo Barrera Gonzalez 
Ingenieria en Telecomunicacion
Universidad Carlos III de Madrid
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Brad Chapman | 5 Sep 20:56 2002
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Re: [BioPython] Read Astral file

Hi Pablo;

> I have the astral-scopdom-seqres-all-1.59.fa file.
> 
> Here it's an example:
> >d1a3oa_ a.1.1.2 (A:) Hemoglobin, alpha-chain {Human (Homo sapiens)}
> vlspadktnvkaawgkvgahageygaealermflsfpttkthfphfdlshgsaqvkghgk
> kvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaahlpaeftpa
> vhasldkflasvstvltskyr
> 
> I would like to read it, and work with the sequence, but I don't know if 
> there's any class in biopython for doing this or I should write it myself.

I don't really know anything about these type of files, but from your
example they look just like Fasta formatted files in which case you can
use the Fasta parser in Biopython.

> I need the info of the SCOP classification (the "a.1.1.2"  part) and the 
> sequence in order to by able to cluster the sequences with the same 
> superfamily.

This should be pretty easy to do. All you'd need to do is something
like:

from Bio import Fasta
# set up the file
handle = open("astral-scopdom-seqres-all-1.59.fa", "r")
parser = Fasta.RecordParser()
iterator = Fasta.Iterator(handle, parser)

(Continue reading)

Patrick K. O'Brien | 6 Sep 17:34 2002

[BioPython] Python for bioinformatics articles

I'm working on a couple of articles for O'Reilly focusing on the use of
Python in bioinformatics, and I'd love some feedback from the folks on this
list. In particular, I'm looking for a few people who would like to provide
input and/or critique the articles before they get published.

The first article I've written is an introduction to Python for
bioinformatics. The next one will be a profile of the BioPython project. The
first article is finished, so if you'd like to critique it let me know asap
and I will send you a link to the article.

If you have an interest in this, please let me know. Thanks.

Pat

--
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Orbtech
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Culhane, Aedin | 16 Sep 14:09 2002
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[BioPython] (no subject)

Dear Biopython
I am trying to query and retrieve batches of sequences from Entrez using
NCBI.query, however I don't seem to be able to use displmax (to allow more
sequences than just 20) or mode (plain text).

Also NCBI seem to be changing pmfetch, pmsearch etc for newer utilities
http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi.  Are there plans
to update these modules for these?

Thanks a million
Aedin

-------------------------------
Aedín  Culhane, PhD
Biochemistry Department
University College Cork
Cork, Ireland
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Jeffrey Chang | 17 Sep 09:02 2002
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Re: [BioPython] (no subject)

Hi Aedin,

Does NCBI.query(XXX, dispmax=50) not work?

I'm not sure how to use the mode parameter -- I can't find it
documented on NCBI's website for the CGI script.
http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html

While it would be useful to migrate our code to the new utilities,
there's no plans to implement them in the near future.  I would be
interested in hearing from people who would like to do so, though!

Jeff

On Mon, Sep 16, 2002 at 01:09:40PM +0100, Culhane, Aedin wrote:
> Dear Biopython
> I am trying to query and retrieve batches of sequences from Entrez using
> NCBI.query, however I don't seem to be able to use displmax (to allow more
> sequences than just 20) or mode (plain text).
> 
> Also NCBI seem to be changing pmfetch, pmsearch etc for newer utilities
> http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi.  Are there plans
> to update these modules for these?
> 
> Thanks a million
> Aedin
> 
> -------------------------------
> Aedín  Culhane, PhD
> Biochemistry Department
(Continue reading)

Jason Stajich | 17 Sep 14:13 2002

Re: [BioPython] (no subject)

You ought to migrate to the new e-utils before the end of December as the
old style CGIs will go away on Jan 1, 2003 I believe.

-jason
On Tue, 17 Sep 2002, Jeffrey Chang wrote:

> Hi Aedin,
>
> Does NCBI.query(XXX, dispmax=50) not work?
>
> I'm not sure how to use the mode parameter -- I can't find it
> documented on NCBI's website for the CGI script.
> http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html
>
> While it would be useful to migrate our code to the new utilities,
> there's no plans to implement them in the near future.  I would be
> interested in hearing from people who would like to do so, though!
>
> Jeff
>
>
>
> On Mon, Sep 16, 2002 at 01:09:40PM +0100, Culhane, Aedin wrote:
> > Dear Biopython
> > I am trying to query and retrieve batches of sequences from Entrez using
> > NCBI.query, however I don't seem to be able to use displmax (to allow more
> > sequences than just 20) or mode (plain text).
> >
> > Also NCBI seem to be changing pmfetch, pmsearch etc for newer utilities
> > http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi.  Are there plans
(Continue reading)

Jeffrey Chang | 17 Sep 19:26 2002
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Re: [BioPython] (no subject)

That refers to the htbin-post CGI, no?  This function hits hitting
query.fcgi, which should be safe.

Hmmm...  We do have scripts that hit things like PmFetch, which will
be obsolete.  So I guess we will have to migrate.  I'll file a bug for
the database...

Jeff

On Tue, Sep 17, 2002 at 08:13:26AM -0400, Jason Stajich wrote:
> You ought to migrate to the new e-utils before the end of December as the
> old style CGIs will go away on Jan 1, 2003 I believe.
> 
> -jason
> On Tue, 17 Sep 2002, Jeffrey Chang wrote:
> 
> > Hi Aedin,
> >
> > Does NCBI.query(XXX, dispmax=50) not work?
> >
> > I'm not sure how to use the mode parameter -- I can't find it
> > documented on NCBI's website for the CGI script.
> > http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html
> >
> > While it would be useful to migrate our code to the new utilities,
> > there's no plans to implement them in the near future.  I would be
> > interested in hearing from people who would like to do so, though!
> >
> > Jeff
> >
(Continue reading)

Cath Lawrence | 19 Sep 04:59 2002
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[BioPython] Trees in BioPython?

Hi,

Is anyone working on phylogenetic trees?
Are these likely to turn up in BioPython soon?

(If not would you like ours?? In development, so not Real Soon.)

cheers
Cath
Cath Lawrence,                       Cath.Lawrence <at> anu.edu.au
Scientific Programmer,  Centre for Bioinformation Science,
John Curtin School of Medical Research
Australian National University,  Canberra ACT 0200
ph: Maths (02) 6125 2904;  JCSMR (02) 6125 0417;
mobile: 0421-902694   fax: (02) 61254712

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Michiel Jan Laurens de Hoon | 19 Sep 05:14 2002
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Re: [BioPython] Trees in BioPython?

Are you thinking about phylogenetic trees for sequences or for gene 
expression data? We have developed a Python extension module for the 
latter, you can find it at 
http://bonsai.ims.u-tokyo.ac.jp/%7Emdehoon/software/cluster/index.htm

--Michiel.

Cath Lawrence wrote:

> Hi,
>
> Is anyone working on phylogenetic trees?
> Are these likely to turn up in BioPython soon?
>
> (If not would you like ours?? In development, so not Real Soon.)

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BioPython mailing list  -  BioPython <at> biopython.org
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Re: [BioPython] Trees in BioPython?

hi

we have scripts for building the full ncbi tree from their dump files in the elm(http://elm.eu.org) project...

r.
On Thu, Sep 19, 2002 at 12:59:38PM +1000, Cath Lawrence wrote:
> Hi,
> 
> Is anyone working on phylogenetic trees?
> Are these likely to turn up in BioPython soon?
> 
> (If not would you like ours?? In development, so not Real Soon.)
> 
> cheers
> Cath
> Cath Lawrence,                       Cath.Lawrence <at> anu.edu.au
> Scientific Programmer,  Centre for Bioinformation Science,
> John Curtin School of Medical Research
> Australian National University,  Canberra ACT 0200
> ph: Maths (02) 6125 2904;  JCSMR (02) 6125 0417;
> mobile: 0421-902694   fax: (02) 61254712
> 
> _______________________________________________
> BioPython mailing list  -  BioPython <at> biopython.org
> http://biopython.org/mailman/listinfo/biopython
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