From mauriceling at acm.org  Thu Dec  8 12:16:40 2005
From: mauriceling at acm.org (Maurice Ling)
Date: Thu Dec  8 12:28:47 2005
Subject: [BioPython] problem with GenBank
Message-ID: <43986A78.6020704@acm.org>

Hi,

I'm using BioPython 1.41 with Python 2.4.1. I'm trying to use GenBank 
module,

Python 2.4.1 (#1, Sep 16 2005, 17:46:53)
[GCC 4.0.0 (Apple Computer, Inc. build 5026)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> from Bio import GenBank
 >>> GenBank.search_for('OCT4')

But this takes forever. Any idea?

Cheers
Maurice


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From idoerg at burnham.org  Thu Dec  8 12:55:05 2005
From: idoerg at burnham.org (Iddo Friedberg)
Date: Thu Dec  8 13:02:55 2005
Subject: [BioPython] problem with GenBank
In-Reply-To: <43986A78.6020704@acm.org>
References: <43986A78.6020704@acm.org>
Message-ID: <43987379.1000601@burnham.org>


Hi Maurice,

Try narrowing down your initial search space. For example:
GenBank.search_for('OCT4', database='protein')

or:

GenBank.search_for('OCT4', database='nucleotide')

This actualy completes, although slower.

I am puzzled by why this is so slow myself, expecially as other queries 
seem to complete in reasonable time. If anyone out there has any ideas, 
please share them with us.

./I

Maurice Ling wrote:

> Hi,
>
> I'm using BioPython 1.41 with Python 2.4.1. I'm trying to use GenBank 
> module,
>
> Python 2.4.1 (#1, Sep 16 2005, 17:46:53)
> [GCC 4.0.0 (Apple Computer, Inc. build 5026)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from Bio import GenBank
> >>> GenBank.search_for('OCT4')
>
> But this takes forever. Any idea?
>
> Cheers
> Maurice
>
>
>_______________________________________________
>BioPython mailing list  -  BioPython@biopython.org
>http://biopython.org/mailman/listinfo/biopython
>  
>


-- 
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9949
http://ffas.ljcrf.edu/~iddo

From eko at eijkman.go.id  Fri Dec  9 05:26:04 2005
From: eko at eijkman.go.id (Ismail Ekoprayitno Rozi)
Date: Fri Dec  9 05:44:38 2005
Subject: [BioPython] Problem to open PDBid 2mbw
Message-ID: <20051209172604.g5iabrowqoo84w4c@home.eijkman.go.id>


Hi,
I'm not so good in python and I'd like to use Bio.PDB (fromp biopython 1.41) in
my scripts.
When trying to open PDBid 2mbw, the error bellow is coming out (other PDBid
seems to be opened normally).
Any idea how to solve it?

Thanks for your help,
I. E. Rozi

-------------

Python 2.3.5 (#2, Aug 30 2005, 15:50:26)
[GCC 4.0.2 20050821 (prerelease) (Debian 4.0.1-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.PDB import PDBParser
>>> p = PDBParser(PERMISSIVE=1)
>>> structure = p.get_structure("2mbw","./pdb2mbw.ent")
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.3/site-packages/Bio/PDB/PDBParser.py", line 66, in
get_structure
    self._parse(file.readlines())
  File "/usr/lib/python2.3/site-packages/Bio/PDB/PDBParser.py", line 87, in
_parse
    self.trailer=self._parse_coordinates(coords_trailer)
  File "/usr/lib/python2.3/site-packages/Bio/PDB/PDBParser.py", line 179, in
_parse_coordinates
    structure_builder.init_residue(resname, hetero_flag, resseq, icode)
  File "/usr/lib/python2.3/site-packages/Bio/PDB/StructureBuilder.py", line 155,
in init_residue
    self.chain.add(residue)
  File "/usr/lib/python2.3/site-packages/Bio/PDB/Entity.py", line 80, in add
    raise PDBConstructionException, "%s defined twice" % entity.get_full_id()
  File "/usr/lib/python2.3/site-packages/Bio/PDB/Entity.py", line 132, in
get_full_id
    parent=self.get_parent()
  File "/usr/lib/python2.3/site-packages/Bio/PDB/Entity.py", line 102, in
get_parent
    raise PDBException, 'No parent'
PDBException: No parent



----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

From thamelry at binf.ku.dk  Fri Dec  9 05:59:39 2005
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Fri Dec  9 06:19:08 2005
Subject: [BioPython] Problem to open PDBid 2mbw
In-Reply-To: <20051209172604.g5iabrowqoo84w4c@home.eijkman.go.id>
References: <20051209172604.g5iabrowqoo84w4c@home.eijkman.go.id>
Message-ID: <33231.87.72.27.226.1134125979.squirrel@www.binf.ku.dk>


>
> Hi,
> I'm not so good in python and I'd like to use Bio.PDB (fromp biopython
> 1.41) in
> my scripts.
> When trying to open PDBid 2mbw, the error bellow is coming out (other
> PDBid
> seems to be opened normally).
> Any idea how to solve it?

Hi,

Water 230 is defined twice (the second water should be Water 239, BTW),
so it's a buggy PDB file. But if PERMISSIVE=1 this should have normally
been ignored, so it's also a bug in Bio.PDB - I'll fix it in CVS.

Cheers,

-Thomas


From douglas.kojetin at gmail.com  Fri Dec  9 10:25:02 2005
From: douglas.kojetin at gmail.com (Douglas Kojetin)
Date: Fri Dec  9 11:18:46 2005
Subject: [BioPython] using a variable as input for restriction enzyme
Message-ID: <7D01DE19-C38B-48AB-87DB-A2EBC139E726@gmail.com>

Hi All-

How do I use a variable to specify the restriction enzyme?

Example --  instead of using the following call:

   Restriction.EcoR1.elucidate()

instead (somehow) use a variable to specify the restriction enzyme:

   rsite='EcoR1'
   Restriction.rsite.elucidate()

Thanks,
Doug

From fkauff at duke.edu  Fri Dec  9 12:14:03 2005
From: fkauff at duke.edu (Frank Kauff)
Date: Fri Dec  9 13:16:21 2005
Subject: [BioPython] using a variable as input for restriction enzyme
In-Reply-To: <7D01DE19-C38B-48AB-87DB-A2EBC139E726@gmail.com>
References: <7D01DE19-C38B-48AB-87DB-A2EBC139E726@gmail.com>
Message-ID: <1134148444.4731.13.camel@osiris.biology.duke.edu>

On Fri, 2005-12-09 at 10:25 -0500, Douglas Kojetin wrote:
> Hi All-
> 
> How do I use a variable to specify the restriction enzyme?
> 
> Example --  instead of using the following call:
> 
>    Restriction.EcoR1.elucidate()
> 
> instead (somehow) use a variable to specify the restriction enzyme:
> 
>    rsite='EcoR1'
>    Restriction.rsite.elucidate()
> 

Not sure, but would

Restriction.__getattribute__(rsite).elucidate()

work?

Frank


> Thanks,
> Doug
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
-- 

From jstroud at mbi.ucla.edu  Fri Dec  9 14:57:05 2005
From: jstroud at mbi.ucla.edu (James Stroud)
Date: Fri Dec  9 15:32:38 2005
Subject: [BioPython] using a variable as input for restriction enzyme
In-Reply-To: <7D01DE19-C38B-48AB-87DB-A2EBC139E726@gmail.com>
References: <7D01DE19-C38B-48AB-87DB-A2EBC139E726@gmail.com>
Message-ID: <200512091157.05155.jstroud@mbi.ucla.edu>

Best would probably be

getattr(Restriction, 'EcoRI').elucidate()


On Friday 09 December 2005 07:25, Douglas Kojetin wrote:
> Hi All-
>
> How do I use a variable to specify the restriction enzyme?
>
> Example --  instead of using the following call:
>
>    Restriction.EcoR1.elucidate()
>
> instead (somehow) use a variable to specify the restriction enzyme:
>
>    rsite='EcoR1'
>    Restriction.rsite.elucidate()
>
> Thanks,
> Doug
>
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython

-- 
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095

http://www.jamesstroud.com/
From km at mrna.tn.nic.in  Tue Dec 13 22:39:03 2005
From: km at mrna.tn.nic.in (km)
Date: Mon Dec 12 02:47:37 2005
Subject: [BioPython] Bio.SCOP
Message-ID: <20051214033903.GA2373@mrna.tn.nic.in>

hi all,
Is there any short intro for usage of Bio.SCOP module? i need to index a astral db and use it to emit sequences with sid 

didnt find anything in biopython cookbook.
unfortunately biopython is poorly documented; basic intro of this module appreciated.

regards,
KM

From frederic.sohm at iaf.cnrs-gif.fr  Mon Dec 12 07:13:38 2005
From: frederic.sohm at iaf.cnrs-gif.fr (Frederic Sohm)
Date: Mon Dec 12 07:38:17 2005
Subject: [BioPython] using a variable as input for restriction enzyme
Message-ID: <200512121313.38669.frederic.sohm@iaf.cnrs-gif.fr>

Hi,

While the two precedent methods will work, I find simpler to use any of the 
following :
?this one especially intended for this kind of problems :

>>> from Bio.Restriction import AllEnzymes
>>> rsite = 'EcoRI'
>>> AllEnzymes.get(rsite).elucidate()
'G^AATT_C'
>>> 
If you use only commercial enzymes you can use :
>>> from Bio.Restriction import CommOnly
>>> rsite = 'EcoRI'
>>> CommOnly.get(rsite).elucidate()
G^AATT_C'
>>> 

or
You can also evaluate the string :
>>> from Bio import Restriction
>>> rsite = 'EcoRI'
>>> eval('Restriction.'+rsite).elucidate() 
'G^AATT_C'
Another way less talkative but which will put a lot of names in your 
namespace :
>>> from Bio.Restriction import *
>>> rsite = 'EcoRI'
>>> eval(rsite).elucidate()
'G^AATT_C'
>>> 


Hope this help.

Best regards

Fred
-- 
Fr?d?ric Sohm
Equipe INRA U1126 "Morphogen?se du syst?me nerveux des Chord?s"
UPR 2197 DEPSN, CNRS
Institut de Neurosciences A. Fessard
1 Avenue de la Terrasse
91 198 GIF-SUR-YVETTE
FRANCE
Phone: +33 (0) 1 69 82 34 12
Fax:+33 (0) 1 69 82 34 47


From alfl0002 at stud.uni-sb.de  Mon Dec 12 11:21:24 2005
From: alfl0002 at stud.uni-sb.de (Aline Flockerzi)
Date: Mon Dec 12 12:13:43 2005
Subject: [BioPython] ClustalW parameter
Message-ID: <20051212172124.shgs9v6t73fo0gs4@webmail.stud.uni-saarland.de>

Hello!

Does anybody know how to change the parameter is_no_end_pen in ClustalW?

Thanks
Aline

From kirbywhite at sbcglobal.net  Tue Dec 13 01:27:21 2005
From: kirbywhite at sbcglobal.net (kirby white)
Date: Tue Dec 13 01:31:20 2005
Subject: [BioPython] (no subject)
Message-ID: <20051213062721.94494.qmail@web81203.mail.mud.yahoo.com>


From kirbywhite at sbcglobal.net  Tue Dec 13 01:38:09 2005
From: kirbywhite at sbcglobal.net (kirby white)
Date: Tue Dec 13 01:42:12 2005
Subject: [BioPython] LSSITES NEWS - Lolita PICTURE & MOVIES at 45 Lolita	Sites
Message-ID: <20051213063809.34365.qmail@web81201.mail.mud.yahoo.com>


From kirbywhite at sbcglobal.net  Tue Dec 13 02:05:46 2005
From: kirbywhite at sbcglobal.net (kirby white)
Date: Tue Dec 13 02:09:45 2005
Subject: [BioPython] LSSITES NEWS - Lolita PICTURE & MOVIES at 45 Lolita	Sites
Message-ID: <20051213070546.62822.qmail@web81205.mail.mud.yahoo.com>


From as_nascimento at yahoo.com.br  Tue Dec 13 06:29:56 2005
From: as_nascimento at yahoo.com.br (Alessandro S. Nascimento)
Date: Tue Dec 13 06:34:06 2005
Subject: [BioPython] A Blast filter
Message-ID: <20051213112957.58550.qmail@web31008.mail.mud.yahoo.com>

 Hi all,
 
 I wonder if one has developed any filter for blast searching against a local database (like nr) before performing a multiple sequence alignment of large number of sequences...
 
 Any tips are pretty appreciable!  
 
 Thanks in advance!
 
 Alessandro
 

		
---------------------------------
 Yahoo! doce lar. Fa?a do Yahoo! sua homepage.
From eirik.sonneland at student.umb.no  Tue Dec 13 07:07:21 2005
From: eirik.sonneland at student.umb.no (Eirik =?iso-8859-1?Q?S=F8nneland?=)
Date: Tue Dec 13 07:36:58 2005
Subject: [BioPython] A Blast filter
In-Reply-To: <20051213112957.58550.qmail@web31008.mail.mud.yahoo.com>
References: <20051213112957.58550.qmail@web31008.mail.mud.yahoo.com>
Message-ID: <3036.128.39.177.29.1134475641.squirrel@webmail.umb.no>

Hi,

I'm working on a high throughput SNP detection pipeline, are blasting ~150
000 trace sequences against contig/refseq database and a trace archive
database downloaded from NCBI.

To find SNPs We repeat mask 150 000 traces AND contig database BEFORE
Blast. This way we focus the search in the NON repeated area of the
sequence. When selecting Blast hits (HSPs) I use e-value(>=e-17), Blast
score(>=1050) and identity (>=97%). This is very stringent but since I
know my trace sequences are about 1000bp I ensure to select hits which
have a minimum of 500bp matching/aligned(Blast score) and in this
alignment "area" of the sequences there are no less then 97% identity. You
need to tune this parametres to meet your needs.

The code for this is what is explained in the cookbook for sorting
blast.records. I can send you a extract from my script if interested.

Eirik S?nneland


>  Hi all,
>
>  I wonder if one has developed any filter for blast searching against a
> local database (like nr) before performing a multiple sequence alignment
> of large number of sequences...
>
>  Any tips are pretty appreciable!
>
>  Thanks in advance!
>
>  Alessandro
>
>
>
> ---------------------------------
>  Yahoo! doce lar. Fa?a do Yahoo! sua homepage.
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>


From biopython at maubp.freeserve.co.uk  Thu Dec 15 08:33:37 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu Dec 15 09:00:18 2005
Subject: [BioPython] Bio.Geo for NCBI's GEO microarray SOFT files
Message-ID: <43A170B1.5070007@maubp.freeserve.co.uk>

Does anyone on the discussion list use GEO files?

Peter

-------- Original Message --------
Subject: [Biopython-dev] Bio.Geo for NCBI's GEO microarry SOFT files
Date: Sat, 10 Dec 2005 18:39:13 +0000
From: Peter <biopython-dev@maubp.freeserve.co.uk>
To: biopython-dev@biopython.org

I've just been looking at the Bio.Geo module by Katharine Lindner,
contributed back in 2002 which should parse the NCBI's Gene Expression
Omnibus (GEO) microarray data files.

http://www.ncbi.nlm.nih.gov/geo/

Is anyone using Bio.Geo at the moment?

The NCBI seem to call these SOFT files, (*.soft) and the format is
documented here:

http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html#SOFTformat

Apparently in 2005, they began a switch to a revised file format, new
format files here:

ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/

Old format files here:

ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_old/
ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_old_gz/

As far as I can tell, neither the "old" or "new" versions work in
Bio.Geo, so there may have been another format change between 2002 and 2005.

In addition the 2005 change introduces new lines, before and after the
actual data:

!dataset_table_begin
!dataset_table_end

These are definitely not supported in the current Martel grammar for GEO
files.

Peter

_______________________________________________
Biopython-dev mailing list
Biopython-dev@biopython.org
http://biopython.org/mailman/listinfo/biopython-dev



From sbassi at gmail.com  Sun Dec 18 14:32:30 2005
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sun Dec 18 14:29:40 2005
Subject: [BioPython] Biopython function in a Google module
In-Reply-To: <mailman.26630.1134882125.700.biopython@biopython.org>
References: <mailman.26630.1134882125.700.biopython@biopython.org>
Message-ID: <b43bf2080512181132k35bb83e8x76b057a1d8be9071@mail.gmail.com>

I've made a Google module, that is a little page that can be inserted
into the Google personalized homepage (www.google.com/ig). This module
is very simple, it is more a proof of concept than a useful module.
If you want to test it, just log into your gmail account and then go
to www.google.com/ig. After that, you will see your personilazed
homepage. In the upperleft corner there is a "Add content" link. Click
on it, and a frame will be displayed, you will see a "Create a
section" form, then you type:
http://www.bioinformatica.info/modulomt2.xml
Press OK on the prompt about an external module (since it is not a
Google module) and the module will be placed in your Google
personalized homepage.
Now I waiting for feedback and ideas for another biopython based module.



--
<a href="http://www.spreadfirefox.com/?q=affiliates&id=24672&t=1">La
web sin popups ni spyware: Usa Firefox en lugar de Internet
Explorer</a>

From biopython at maubp.freeserve.co.uk  Sun Dec 18 15:40:15 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun Dec 18 15:37:36 2005
Subject: [BioPython] Biopython function in a Google module
In-Reply-To: <b43bf2080512181132k35bb83e8x76b057a1d8be9071@mail.gmail.com>
References: <mailman.26630.1134882125.700.biopython@biopython.org>
	<b43bf2080512181132k35bb83e8x76b057a1d8be9071@mail.gmail.com>
Message-ID: <43A5C92F.7000305@maubp.freeserve.co.uk>

Sebastian Bassi wrote:
> I've made a Google module, that is a little page that can be inserted
> into the Google personalized homepage (www.google.com/ig). This module
> is very simple, it is more a proof of concept than a useful module.

You haven't said what it does - but by looking at your XML file it turns 
out to be an Oligo Melting Point Calculator.

http://www.bioinformatica.info/modulomt2.xml

By the way, you have a typo in the XML file's description (point not poing).

Screenshot:

http://www.bioinformatica.info/omscreen.jpg

Peter

From sbassi at gmail.com  Sun Dec 18 21:36:48 2005
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sun Dec 18 22:00:31 2005
Subject: [BioPython] Biopython function in a Google module
In-Reply-To: <43A5C92F.7000305@maubp.freeserve.co.uk>
References: <mailman.26630.1134882125.700.biopython@biopython.org>
	<b43bf2080512181132k35bb83e8x76b057a1d8be9071@mail.gmail.com>
	<43A5C92F.7000305@maubp.freeserve.co.uk>
Message-ID: <b43bf2080512181836x3608f61jee9384d4d56b6d90@mail.gmail.com>

On 12/18/05, Peter <biopython@maubp.freeserve.co.uk> wrote:
> Sebastian Bassi wrote:
> > I've made a Google module, that is a little page that can be inserted
> > into the Google personalized homepage (www.google.com/ig). This module
> > is very simple, it is more a proof of concept than a useful module.
> You haven't said what it does - but by looking at your XML file it turns
> out to be an Oligo Melting Point Calculator.

Yes, sorry. Anyway, you can run it on the Google webpage to see it working.

> By the way, you have a typo in the XML file's description (point not poing).

Thank you, just changed it :)


--
<a href="http://www.spreadfirefox.com/?q=affiliates&id=24672&t=1">La
web sin popups ni spyware: Usa Firefox en lugar de Internet
Explorer</a>

From borreguero at gmail.com  Tue Dec 20 18:54:23 2005
From: borreguero at gmail.com (Jose Borreguero)
Date: Wed Dec 21 04:32:28 2005
Subject: [BioPython] Anybody used Align.fastapairwise?
Message-ID: <7cced4ed0512201554p3e300c3bh@mail.gmail.com>

I'm new to biopython. I wonder if anybody used the Align.fastapairwise
module, to get me started with some example.
jose
--
Jose M. Borreguero
jmborr@gatech.edu,  www.borreguero.com
phone: 404 707 8980
GCATT, biology department,
Georgia Tech,
250 14St NW,
Atlanta GA 30318

From volcs0 at gmail.com  Wed Dec 21 10:31:47 2005
From: volcs0 at gmail.com (Sam Volchenboum)
Date: Wed Dec 21 10:36:06 2005
Subject: [BioPython] Help with NaiveBayes
Message-ID: <8e8165be0512210731s1df9b513n354b54cef9cf76ae@mail.gmail.com>

I'm trying to get the NaiveBayes function up and running.

I just can't find any examples out there to learn from (which is how I
usually figure these things out).

I have a set of proteins - say 100 - that are on/off in
health/disease. I have 10 samples each of health and disease. This is
mass spec data.

So, I have a matrix where the rows are proteins (1-100) and the
columns are health/disease (10 each, 20 total), and the cell contents
are 1's and 0's (present/absent).

I want to create a NaiveBayes classifier based on this training data
and see if it predicts health/disease based on a new set of data (a
new set of results for the 100 proteins).

For the training_set, I've tried this format:

[[1, 0, 1, 1, 0, 1], [0, 0, 1, 1, 1], [0, 0, 0, 0, 0]]

which would be an example of three states and five proteins (on or off).

And results like this: ['Healthy', 'Disease', 'Disease']

But I get an error on NaiveBayes.train(training_set, results) - the
two lists need to be the same length (I thought they were... length =
3)...

Any help, advice, push, shove... etc., is greatly appreciated.

Thanks.

sam

From jchang at smi.stanford.edu  Wed Dec 21 14:24:46 2005
From: jchang at smi.stanford.edu (jchang@smi.stanford.edu)
Date: Wed Dec 21 16:13:35 2005
Subject: [BioPython] Help with NaiveBayes
In-Reply-To: <20051221170618.GA385@oliphaunt.duhs.duke.edu>
References: <8e8165be0512210731s1df9b513n354b54cef9cf76ae@mail.gmail.com>
	<20051221170618.GA385@oliphaunt.duhs.duke.edu>
Message-ID: <20051221192444.GE385@oliphaunt.duhs.duke.edu>

On Wed, Dec 21, 2005 at 10:31:47AM -0500, Sam Volchenboum wrote:
> I'm trying to get the NaiveBayes function up and running.
> 
> For the training_set, I've tried this format:
> 
> [[1, 0, 1, 1, 0, 1], [0, 0, 1, 1, 1], [0, 0, 0, 0, 0]]
> 
> which would be an example of three states and five proteins (on or off).

The first one contains data for 6 proteins.  If you make them all
lists of length 5, the training completes.

>>> from Bio import NaiveBayes
>>> training_set = [[1, 0, 1, 1, 0, 1], [0, 0, 1, 1, 1], [0, 0, 0, 0, 0]] 
>>> results = ['Healthy', 'Disease', 'Disease'] 
>>> nb = NaiveBayes.train(training_set, results)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/Users/jchang/lib/jchang/python/Bio/NaiveBayes.py", line 146, in train
    raise ValueError, "observations have different dimensionality"
ValueError: observations have different dimensionality
>>> training_set = [[1, 0, 1, 1, 0], [0, 0, 1, 1, 1], [0, 0, 0, 0, 0]]
>>> nb = NaiveBayes.train(training_set, results)
>>> NaiveBayes.classify(nb, [1, 0, 1, 1, 0])
'Healthy'
>>> NaiveBayes.classify(nb, [0, 0, 0, 1, 1])
'Disease'
>>> 

Jeff
From winter at biotec.tu-dresden.de  Thu Dec 22 06:17:35 2005
From: winter at biotec.tu-dresden.de (Christof Winter)
Date: Thu Dec 22 07:14:38 2005
Subject: [BioPython] Parse bit score with NCBIXML module from BLAST output
Message-ID: <43AA8B4F.9020203@biotec.tu-dresden.de>

Hi all,

I just tried to parse a BLAST XML output. To my surprise, the parser 
always returns None for the bit scores (hsp.bits), whereas raw scores 
(hsp.score) are fine. Is this a known issue? Or a problem with my 
installation? This is my code:

from Bio.Blast import NCBIXML

parser = NCBIXML.BlastParser()
record = parser.parse(open("blastout.xml"))

for alignment in record.alignments:
     for hsp in alignment.hsps:
         print hsp.score
         print hsp.bits
         print

The relevant part from blastout.xml looks like this:

<Hit>
   <Hit_num>1</Hit_num>
   <Hit_id>gi|56554556|pdb|1XI5|I</Hit_id>
   <Hit_def>Chain I, Clathrin D6 Coat</Hit_def>
   <Hit_accession>1XI5-I</Hit_accession>
   <Hit_len>1630</Hit_len>
   <Hit_hsps>
     <Hsp>
       <Hsp_num>1</Hsp_num>
       <Hsp_bit-score>3254.54</Hsp_bit-score>
       <Hsp_score>8437</Hsp_score>
       <Hsp_evalue>0</Hsp_evalue>
        ...
     </Hsp>
   </Hit_hsps>
</Hit>

The corresponding output of my script is:
8437.0
None

I checked the 1.41 version of Bio.Blast.NCBIXML.BlastParser() and could 
not find any evidence for parsing of the <Hsp_bit-score> tag. Any solution?

Thanks,
Christof


From e.picardi at unical.it  Wed Dec 21 10:45:38 2005
From: e.picardi at unical.it (Ernesto)
Date: Thu Dec 22 07:27:57 2005
Subject: [BioPython] simple class to generate random trees
References: <7cced4ed0512201554p3e300c3bh@mail.gmail.com>
Message-ID: <002201c60645$9b889f10$572561a0@mirko84cf0g99i>

Hi all,
I wrote a simple class to generate random phylogenetic trees clock (Kuhner
and Felsenstein 1994) and no clock-like (Guindon and Gascuel 2002). I
attached a copy.
I don't know if it could be useful for BioPython users.

Using RandonTree:

>>> from RandomTree import RandomTree
>>> tree = RandomTree()
>>> tree.nobr
0
>>> tree.ntips=4
>>> tree.constant_tree()
'((T3:0.01516,T4:0.01516):0.01332,(T1:0.02643,T2:0.02643):0.00205);'
>>> tree.variable_tree()
'(((T4:0.00050,T3:0.00954):0.00009,T2:0.01591):0.00595,T1:0.00531);'
>>>tree.nobr=1
>>> tree.constant_tree()
'((T2,(T1,T4)),T3);'
>>> tree.variable_tree()
'((T1,(T3,T2)),T4);'

The attributes of tree are:
ntips: number of tips for tree --> default is 10
nobr: 1 for trees without branch lengths --> default is 0
pm: probability of change per unit time --> default is 0.03
shape: gamma shape for variable trees --> default is 0.5
mean: mean of gamma distribution for variable trees --> default is 1

Regards,
Ernesto Picardi

PS: there is also an on-line version at:
http://biologia.unical.it/py_script/tree.html




Ernesto Picardi, PhD
Dept. of Cell Biology
University of Calabria
87036, Arcavacata di Rende (CS)
Italy
Phone: +39 0984 492937
Fax: +39 0984 492911
E-mail: e.picardi@unical.it



-------------- next part --------------
"""
RandomTree is a simple class to generate random rooted trees.
Clock-like trees are generated according to the methodology 
of Kuhner and Felsenstein (1994) Mol. Biol. Evol. 11: 459-468,
whereas no clock-like trees are created following Guindon and
Gascuel (2002) Mol. Biol. Evol. 19: 534-543.
Once a clock-like tree is generted, each branch length is 
multiplied by a gamma dinstributed factor. If the mean of this
distribution is equal to 1 and the shape fixed to 0.5, then the
departure from molecular clock is strong. The opposite situation
is when gamma shape is fixed to 2.0.

When the RandomTree class is invoked a simple object is created.
It contains:
ntips: number of tips for tree --> default is 10
nobr: 1 for trees without branch lengths --> default is 0
pm: probability of change per unit time --> default is 0.03
shape: gamma shape for variable trees --> default is 0.5
mean: mean of gamma distribution for variable trees --> default is 1

USING this class:
>>> from RandomTree import RandomTree
>>> tree = RandomTree()
>>> tree.nobr
0
>>> tree.ntips=4
>>> tree.constant_tree()
'((T3:0.01516,T4:0.01516):0.01332,(T1:0.02643,T2:0.02643):0.00205);'
>>> tree.variable_tree()
'(((T4:0.00050,T3:0.00954):0.00009,T2:0.01591):0.00595,T1:0.00531);'
>>>tree.nobr=1
>>> tree.constant_tree()
'((T2,(T1,T4)),T3);'
>>> tree.variable_tree()
'((T1,(T3,T2)),T4);'

Copyright (c) 2004-2005, Ernesto Picardi.
This class comes with ABSOLUTELY NO WARRANTY.
"""

import math,string,fpformat,random,re,sys  # import of standard modules

class RandomTree:

      def __init__(self,alltips=10,nobr=0,pm=0.03,shape=0.5,mean=1):
          self.alltips=alltips   # number of tips
          self.nobr=nobr     # use branch lengths
          self.pm=pm         # probability of change per unit time
          self.shape=shape   # gamma shape parameter
          self.mean=mean     # mean of gamma dinstribution

      def constant_tree(self):  # function to generate a clock-like tree
          if self.alltips <=2:
              sys.exit('At least three tips. Bye.')
          tips=[]
	  for i in range(1, self.alltips+1):
              tips.append("T"+str(i))
          Lb=[]
	  for i in range(len(tips)):
              Lb.append(0)
          n=1
	  dictionary={}
	  while len(tips)!=1:
                R=random.random()
                tyme=(-(math.log(R))/len(tips))*self.pm
	        fixtyme=fpformat.fix(tyme,5)
		brlens=float(fixtyme)
		for i in range(len(tips)):
			Lb[i]=Lb[i]+brlens
		nodeName = '@node%04i@' % n
		s1=random.choice(tips)
		i1=str(Lb[tips.index(s1)])
		del Lb[tips.index(s1)]
		tips.remove(s1)
		s2=random.choice(tips)
		i2=str(Lb[tips.index(s2)])
		del Lb[tips.index(s2)]
		tips.remove(s2)
		if self.nobr:
		   nodo="("+s1+","+s2+")"
                else:
		     nodo="("+s1+":"+i1+","+s2+":"+i2+")"
		dictionary[nodeName]=nodo
		tips.append(nodeName)
		Lb.append(0)
		n+=1
          findNodes=re.compile(r"@node.*?@", re.I) #to identify a node name
          lastNode = max(dictionary.keys())
          treestring = lastNode
          while 1:
                nodeList = findNodes.findall(treestring)
                if nodeList == []: break
                for element in nodeList:
                    treestring=treestring.replace(element, dictionary[element])
          return treestring + ';'

      def variable_tree(self):  # function to generate a variable tree
          treestring=self.constant_tree()
          findbr=re.compile(":[0-9]+.[0-9]+[\),]")
          allbr=findbr.findall(treestring)
          dicbr={}
          for i in allbr:
              br=(i.split(':'))[1]
	      brval=eval(br.strip('),'))
              beta=float(self.shape)/self.mean
	      gammafactor=random.gammavariate(self.shape,beta)
              newbr=brval*gammafactor
	      newbr1=fpformat.fix(newbr,5)
	      dicbr[i]=newbr1
          for j in dicbr:
	      if ',' in j:
	         treestring=treestring.replace(j,':'+dicbr[j]+',')
              elif ')' in j:
                   treestring=treestring.replace(i,':'+dicbr[i]+')')
          return treestring


From mdehoon at c2b2.columbia.edu  Thu Dec 22 07:38:08 2005
From: mdehoon at c2b2.columbia.edu (Michiel De Hoon)
Date: Thu Dec 22 07:43:49 2005
Subject: =?iso-8859-1?Q?RE=A0=3A_=5BBioPython=5D_Parse_bit_score_with_NCBIXML_modu?=
	=?iso-8859-1?Q?le_from_BLAST_output?=
Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AE9ECDD3@cgcmail.cgc.cpmc.columbia.edu>

> I checked the 1.41 version of Bio.Blast.NCBIXML.BlastParser() and could 
> not find any evidence for parsing of the <Hsp_bit-score> tag. Any solution?

If this is a recent addition to Blast reports, it may not have existed at the
time NCBIXML.BlastParser was written. Can you write a patch to
NCBIXML.BlastParser?

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032




From mdehoon at c2b2.columbia.edu  Fri Dec 23 12:26:29 2005
From: mdehoon at c2b2.columbia.edu (Michiel De Hoon)
Date: Fri Dec 23 12:25:38 2005
Subject: [BioPython] Parse bit score with NCBIXML module from BLAST output
Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AE9ECDD9@cgcmail.cgc.cpmc.columbia.edu>

Hi everybody,

Christof has sent me a patch to NCBIXML.py for this bug, which is in CVS now.
Thanks again, Christof!

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-------- Message d'origine--------
De: biopython-bounces@portal.open-bio.org de la part de Christof Winter
Date: jeu. 12/22/2005 6:17
?: biopython@biopython.org
Objet : [BioPython] Parse bit score with NCBIXML module from BLAST output
 
Hi all,

I just tried to parse a BLAST XML output. To my surprise, the parser 
always returns None for the bit scores (hsp.bits), whereas raw scores 
(hsp.score) are fine. Is this a known issue? Or a problem with my 
installation? This is my code:

from Bio.Blast import NCBIXML

parser = NCBIXML.BlastParser()
record = parser.parse(open("blastout.xml"))

for alignment in record.alignments:
     for hsp in alignment.hsps:
         print hsp.score
         print hsp.bits
         print

The relevant part from blastout.xml looks like this:

<Hit>
   <Hit_num>1</Hit_num>
   <Hit_id>gi|56554556|pdb|1XI5|I</Hit_id>
   <Hit_def>Chain I, Clathrin D6 Coat</Hit_def>
   <Hit_accession>1XI5-I</Hit_accession>
   <Hit_len>1630</Hit_len>
   <Hit_hsps>
     <Hsp>
       <Hsp_num>1</Hsp_num>
       <Hsp_bit-score>3254.54</Hsp_bit-score>
       <Hsp_score>8437</Hsp_score>
       <Hsp_evalue>0</Hsp_evalue>
        ...
     </Hsp>
   </Hit_hsps>
</Hit>

The corresponding output of my script is:
8437.0
None

I checked the 1.41 version of Bio.Blast.NCBIXML.BlastParser() and could 
not find any evidence for parsing of the <Hsp_bit-score> tag. Any solution?

Thanks,
Christof


_______________________________________________
BioPython mailing list  -  BioPython@biopython.org
http://biopython.org/mailman/listinfo/biopython



From srini_iyyer_bio at yahoo.com  Sat Dec 24 12:49:40 2005
From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer)
Date: Sat Dec 24 12:54:17 2005
Subject: [BioPython] Bug in GenBank module -  record.feature method ?
In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AE9ECDD9@cgcmail.cgc.cpmc.columbia.edu>
Message-ID: <20051224174941.31939.qmail@web31610.mail.mud.yahoo.com>

Hi group, 
 I have been working to parse out the GO annotations
from FEATURE section of GenBank record. 

The GO annotations are incorporated into the CDS
section of FEATURES part. 

Here is my script:

from Bio import GenBank
from sets import Set
import glob



def FeatureGOparser(myseq):
    parser = GenBank.RecordParser()
    record = parser.parse(open(myseq,'r'))
   

    ## this gives the CDS in features CDS is second in
features section ###
    feature = record.features[2]
    

    golist = feature.qualifiers[1].value """extracts
'/Note' part
    go_list =  golist.split(';') #split by ';' to get
GO secs." 
    refseq = record.version   # getting NM_
    gene_name =
(feature.qualifiers[0].value).split('"')[1]
    go_comp = []
    go_func = []
    go_proc = []
   # from here trimming of GO list obtained above#
    for i in go_list:
        line = i.strip()
        if line.startswith('go_component'):
            iline = line.split('[')[0]
            com_line =
gene_name+'\t'+refseq+'\t'+iline
            go_comp.append(com_line)

    for m in go_list:
        line = m.strip()
        if line.startswith('go_function'):
            mline = line.split('[')[0]
            func_line =
gene_name+'\t'+refseq+'\t'+mline
            go_func.append(func_line)

    for j in go_list:
        line = i.strip()
        if line.startswith('go_process'):
            jline = line.split('[')[0]
            proc_line =
gene_name+'\t'+refseq+'\t'+jline
            go_proc.append(proc_line)

    unique_go_comp = Set(go_comp)
    unique_go_func = Set(go_func)
    unique_go_proc = Set(go_proc)
    for x in unique_go_comp:
        print x

    for y in unique_go_func:
        print y

    for z in unique_go_proc:
        print z


files = glob.glob('/home/seq/genbank/refseq/*')

def main():
    for each in files:
        FeatureGOparser(each)
main()


Error:


RGS3    NM_144489.2     go_component: membrane
RGS3    NM_144489.2     go_component: cytosol
RGS3    NM_144489.2     go_component: nucleus
RGS3    NM_144489.2     go_function: protein binding
RGS3    NM_144489.2     go_function: GTPase activator
activity
RGS3    NM_144489.2     go_function: signal transducer
activity
RGS3    NM_144489.2     go_process: regulation of
G-protein coupled receptor protein signaling pathway
FREQ    NM_014286.2     go_component: Golgi stack
FREQ    NM_014286.2     go_function: calcium ion
binding
DKFZp686O24166  NM_001009913.1  go_function:
structural molecule activity
Traceback (most recent call last):
  File "genbank_go_parser_ver2.py", line 58, in ?
    main()
  File "genbank_go_parser_ver2.py", line 57, in main
    FeatureGOparser(each)
  File "genbank_go_parser_ver2.py", line 11, in
FeatureGOparser
    feature = record.features[2]
IndexError: list index out of range



# feature = record.features[2] ###
this gives the CDS part.  record.features[2]. I see
that this order is not always true. For many sequences
in FEATURES section,  'gene' is always followed by
'CDS'. However in some new RefSeq sequences,
'variation' sub-section is incorporated now.  this is
the trouble, I guess. 

So there are two things, that I need some
help/suggestions/comments.

1. Is there any more technical way to parse '/note'
sub-section in CDS section of FEATURES.  Do you think
what I am doing (record.features[2]) is more novice
and not technical/correct. Please let me know what is
the best process.

2. If there any other way to parse GO annotations for
all RefSeq sequences in GenBank format. 

thanks
srini


	
		
__________________________________ 
Yahoo! for Good - Make a difference this year. 
http://brand.yahoo.com/cybergivingweek2005/
From amorgan at mitre.org  Sat Dec 24 15:16:01 2005
From: amorgan at mitre.org (Alexander Morgan)
Date: Sat Dec 24 15:40:10 2005
Subject: [BioPython] Bug in GenBank module -  record.feature method ?
In-Reply-To: <20051224174941.31939.qmail@web31610.mail.mud.yahoo.com>
Message-ID: <BFD2EC81.7A1F%amorgan@mitre.org>

If you're not tied to the GenBank format, you might have greater ease
getting the GO codes associated with EntrezGene identifiers.

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

The gene2go file contains the GO code assignments, and the gene2accession
the mappings to other accession numbers; there is also a gene2refseq file.

They are all in an easy to parse tab delimited format, and you can zip
through them pretty fast and load what you need into a hash, a shelf file or
a DB.


On 12/24/05 9:49 AM, "Srinivas Iyyer" <srini_iyyer_bio@yahoo.com> wrote:
> 
> 2. If there any other way to parse GO annotations for
> all RefSeq sequences in GenBank format.
> 

From srini_iyyer_bio at yahoo.com  Sat Dec 24 17:13:21 2005
From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer)
Date: Sat Dec 24 17:17:03 2005
Subject: [BioPython] Bug in GenBank module -  record.feature method ?
In-Reply-To: <BFD2EC81.7A1F%amorgan@mitre.org>
Message-ID: <20051224221321.4948.qmail@web31605.mail.mud.yahoo.com>

Aaaaaaaaagrrrrrrrrrhhhhh ..... why was i floundering
when i worked on this gene2go in the past.  wasted a
lot of time despite knowing this fact....

anyways, thank you very much. 



--- Alexander Morgan <amorgan@mitre.org> wrote:

> If you're not tied to the GenBank format, you might
> have greater ease
> getting the GO codes associated with EntrezGene
> identifiers.
> 
> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> 
> The gene2go file contains the GO code assignments,
> and the gene2accession
> the mappings to other accession numbers; there is
> also a gene2refseq file.
> 
> They are all in an easy to parse tab delimited
> format, and you can zip
> through them pretty fast and load what you need into
> a hash, a shelf file or
> a DB.
> 
> 
> On 12/24/05 9:49 AM, "Srinivas Iyyer"
> <srini_iyyer_bio@yahoo.com> wrote:
> > 
> > 2. If there any other way to parse GO annotations
> for
> > all RefSeq sequences in GenBank format.
> > 
> 
> 



		
__________________________________________ 
Yahoo! DSL ? Something to write home about. 
Just $16.99/mo. or less. 
dsl.yahoo.com 

From srini_iyyer_bio at yahoo.com  Sun Dec 25 00:47:31 2005
From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer)
Date: Sun Dec 25 00:51:43 2005
Subject: [BioPython] Bug in GenBank module -  record.feature method ?
In-Reply-To: <20051224221321.4948.qmail@web31605.mail.mud.yahoo.com>
Message-ID: <20051225054731.37082.qmail@web31606.mail.mud.yahoo.com>

One problem (which might be somewhat troubling) with
gene2go
is that all the categories are written not mentioning
the category. 

It would have been good if gene2go looked like this:

9606  2345 ISS go_process: glucose metabolism  1348503
9606  2345 ISS go_function: NADP transporter 
9606  2345 ISS go_component: cytoplasm

The reason I tried to parse on my ways is to get each
GO annotation according to category. So that in
future, my enrichment analysis on GO categories could
be more meaningful. 

However, I successfully parsed GenBank records for GO
categories. 
my output looks like this now:

CNOT6   NM_015455.3     go_component: nucleus
CNOT6   NM_015455.3     go_function: hydrolase
activity
CNOT6   NM_015455.3     go_function: RNA binding
CNOT6   NM_015455.3     go_function: magnesium ion
binding
CNOT6   NM_015455.3     go_function: exonuclease
activity
CNOT6   NM_015455.3     go_process: regulation of
transcription, DNA-dependent


I can now play more easily when the GO annotations are
in this format. 

Thanks again for reminding me about gene2go




	
		
__________________________________ 
Yahoo! for Good - Make a difference this year. 
http://brand.yahoo.com/cybergivingweek2005/
From biopython at maubp.freeserve.co.uk  Mon Dec 26 12:05:20 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon Dec 26 12:26:59 2005
Subject: [BioPython] Bug in GenBank module -  record.feature method ?
In-Reply-To: <20051224174941.31939.qmail@web31610.mail.mud.yahoo.com>
References: <20051224174941.31939.qmail@web31610.mail.mud.yahoo.com>
Message-ID: <43B022D0.5040001@maubp.freeserve.co.uk>

Srinivas Iyyer wrote:
> Hi group, I have been working to parse out the GO annotations from
> FEATURE section of GenBank record.
...
> feature = record.features[2]
> golist = feature.qualifiers[1].value """extracts '/Note' part
 > go_list =  golist.split(';') #split by ';' to get GO secs."
...
> # feature = record.features[2] ### this gives the CDS part.
> record.features[2]. I see that this order is not always true. For
> many sequences in FEATURES section,  'gene' is always followed by 
> 'CDS'. However in some new RefSeq sequences, 'variation' sub-section
> is incorporated now.  this is the trouble, I guess.
...
> 1. Is there any more technical way to parse '/note' sub-section in
> CDS section of FEATURES.  Do you think what I am doing
> (record.features[2]) is more novice and not technical/correct. Please
> let me know what is the best process.

You are doing this:

feature = record.features[2]

It depends on the record you want being the third one in the file (zero
based counting: 0, 1, 2).  You might be better off doing something like:

for feature in record.features :
     if feature.type=="CDS" :
         #Do stuff...	

Also, once you have found the feature(s) you are interested in, the
qualifiers property is a python dictionary.  You should be able to
access the /note entry from the GenBank feature record by:

notes = feature.qualifiers['note']

This will be a list - for some things (like db_xref) there can be 
several different entries for a single feature.  For others, like the 
translation, there should be only one.  I'm note sure what happens with 
notes.

You could try something like:

go_list = []
for note in feature.qualifiers['note'] :
	go_list.extend(note.split(';'))

Peter

From biopyte at yahoo.de  Fri Dec 30 14:57:10 2005
From: biopyte at yahoo.de (Hans Meier)
Date: Fri Dec 30 15:00:34 2005
Subject: [BioPython] extract non-coding sequence data from .gbk with
	absolute coordinates
Message-ID: <20051230195710.17729.qmail@web26313.mail.ukl.yahoo.com>

 Dear friends,
 
 whole genome GeneBank files include the genomic 
 nucleotide sequence as the last record named 'Origin'.
 
 Is it possible with the Bio tools to extract sequence data
 from origin by giving absolute coordinates?
 That means, is there a Bio way to also read *non-coding*
 sequence data from a .gbk file?
 
 
 Best Regards, Harald
 
 
 

		
---------------------------------
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From biopyte at yahoo.de  Fri Dec 30 15:47:56 2005
From: biopyte at yahoo.de (Hans Meier)
Date: Fri Dec 30 15:51:21 2005
Subject: [BioPython] parsing error with GenBank.RecordParser
Message-ID: <20051230204756.25343.qmail@web26311.mail.ukl.yahoo.com>

 Hi,
 
 parsing of NC_000913.gbk does not work.
 
 
 Greets, Harald
 
 
 ***********************************************
 >>> from Bio import GenBank
 >>> parser = GenBank.RecordParser()
 >>> record = parser.parse(open('NC_000913.gbk'))
 
 Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File "/usr/lib/python2.3/site-packages/Bio/GenBank/__init__.py", line 240,  
   in parse self._scanner.feed(handle, self._consumer)
   File "/usr/lib/python2.3/site-packages/Bio/GenBank/__init__.py",line1259,
   in feed  self._parser.parseFile(handle)
   File "/usr/lib/python2.3/site-packages/Martel/Parser.py", line 328,
   in parse File self.parseString(fileobj.read())
   File "/usr/lib/python2.3/site-packages/Martel/Parser.py", line 356, 
   in parseString self._err_handler.fatalError(result)
   File "/usr/lib/python2.3/site-packages/_xmlplus/sax/handler.py", line 38,
   in fatalError raise exception
   
  Martel.Parser.ParserPositionException: error parsing at or beyond  
  character 856717
 *************************************************
 
 Beyond character 856717 comes the following:
 
/note="2'-(5"-phosphoribosyl)-3'-dephospho-CoA
transferase; holo-citrate lyase synthase; CitG forms the
prosthetic group precursor
2'-(5"-triphosphoribosyl)-3'-dephospho-CoA which is then
transferred to apo-ACP by CitX to produce holo-ACP and
pyrophosphate;
go_process: protein modification [goid 0006464]"
 
 
 
 

		
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From biopyte at yahoo.de  Fri Dec 30 21:54:37 2005
From: biopyte at yahoo.de (Hans Meier)
Date: Fri Dec 30 21:58:06 2005
Subject: [BioPython] Large GenBank files: impossible to handle?
Message-ID: <20051231025437.5979.qmail@web26304.mail.ukl.yahoo.com>

 Dear friends,
 
 I tried to handle a .gbk file of 4,7MB in size
 with a "700MHz, Pentium III, 256 MB RAM"-box.
 
 Parsing with "RecordParser" and indexing with "index_file"
 crushed the machine in both cases, I had to reboot
 (what happens not so often with Debian).
 My final goal is to access the .gbk file somehow like a database.
 The alternative would be to use .fna,.faa and .fnn files 
 and write my own methods. Or stuff all the data in a SQL-database.
 But I still hope that Biopython could help.
 
 Before I spend more time on this, I'd like to ask you:
 
 With the Biopython tools, is it possible to handle
 .gbk files of about 5MB in a reasonable time with 
 a low- to middle-class desktop computer? If so, how?
 
 
 All the best and a Happy New Year, Harald
 
 
 
 
 
 

		
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From sbassi at gmail.com  Sat Dec 31 10:09:26 2005
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sat Dec 31 10:14:08 2005
Subject: [BioPython] Large GenBank files: impossible to handle?
In-Reply-To: <20051231025437.5979.qmail@web26304.mail.ukl.yahoo.com>
References: <20051231025437.5979.qmail@web26304.mail.ukl.yahoo.com>
Message-ID: <b43bf2080512310709s6f89b39dn7ababdfc855df7bb@mail.gmail.com>

On 12/30/05, Hans Meier <biopyte@yahoo.de> wrote:
>  I tried to handle a .gbk file of 4,7MB in size
>  with a "700MHz, Pentium III, 256 MB RAM"-box.
...
>  With the Biopython tools, is it possible to handle
>  .gbk files of about 5MB in a reasonable time with
>  a low- to middle-class desktop computer? If so, how?

Your computer is not underpowered and the file is not so large, so it
should not hangup. Could you provide code for us to check it? (and the
datafile, you should upload it to a ftp/web server if the data is
public).


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