From aurelie.bornot at free.fr  Fri Apr  1 07:44:39 2005
From: aurelie.bornot at free.fr (=?iso-8859-1?Q?Aur=E9lie_Bornot?=)
Date: Fri Apr  1 07:39:00 2005
Subject: [BioPython] Blast and PsiBlast
Message-ID: <007501c536b8$91de1420$0b413851@YSENGARD>

Hello !

I am new in programming with python and Biopython !!
First : Thanks guies for all the work that is already done !

I must deal a lot of types of alignments, and I am in trouble for some questions ... : (
- I don't understand why qblast( ) can't "call" the program called blastx.. ?
- I am searching for how to do psiBLAST or PhiBlast on line : is it possible ?
- Is it possible to use the BlastErrorParser () (NCBIStandalone) to parse a file which come from some qblast() online ?
- I am also searching if there is a module to deal with Smith&Waterman and Needleman&Wunch ? and if not : how can I a do ?

a lot of questions......
Could someone try to answer to any of these questions ??? or give me some clues and advice

Thanks a lot
Aur?lie


From aurelie.bornot at free.fr  Fri Apr  1 08:04:15 2005
From: aurelie.bornot at free.fr (=?iso-8859-1?Q?Aur=E9lie_Bornot?=)
Date: Fri Apr  1 07:58:58 2005
Subject: [BioPython] Bioregistry...doesn't work with me
Message-ID: <008401c536bb$4ead9470$0b413851@YSENGARD>

Hello,

Sorry for "spaming"

I am trying to retrieve sequences with the script of the CookBook and it doesn't work...
I don't understand why....
Can someone tell me what I did wrong ?

>>> from Bio import db
>>> print db
db, exporting 'embl', 'embl-dbfetch-cgi', 'embl-ebi-cgi', 'embl-fast', 'embl-xem
bl-cgi', 'embl-xml', 'fasta', 'fasta-sequence-eutils', 'genbank-nucleotide', 'ge
nbank-protein', 'interpro', 'interpro-ebi-cgi', 'medline', 'medline-eutils', 'nu
cleotide-genbank-eutils', 'pdb', 'pdb-ebi-cgi', 'pdb-rcsb-cgi', 'prodoc', 'prodo
c-expasy-cgi', 'prosite', 'prosite-expasy-cgi', 'protein-genbank-eutils', 'swiss
prot', 'swissprot-expasy-cgi', 'swissprot-usmirror-cgi'
>>> db.keys()
['embl-dbfetch-cgi', 'embl-xml', 'fasta', 'prodoc-expasy-cgi', 'interpro', 'pdb-
rcsb-cgi', 'swissprot-expasy-cgi', 'swissprot', 'prosite', 'swissprot-usmirror-c
gi', 'fasta-sequence-eutils', 'interpro-ebi-cgi', 'embl', 'nucleotide-genbank-eu
tils', 'protein-genbank-eutils', 'prodoc', 'prosite-expasy-cgi', 'embl-fast', 'm
edline', 'genbank-nucleotide', 'pdb-ebi-cgi', 'medline-eutils', 'genbank-protein
', 'embl-ebi-cgi', 'embl-xembl-cgi', 'pdb']
>>> sp = db["swissprot"]
>>> sp
<Bio.config.DBRegistry.DBGroup instance at 0x00ACEB48>
>>> record_handle = sp['O23729']
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 150, in __
getitem__
    data = self._run_serial(key)
  File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 217, in _r
un_serial
    raise KeyError, "I could not get any results."
KeyError: 'I could not get any results.'


I have verified : the entry O23729 is still correct....
I must work with Windows XP, may the problem comes from this...?

Thanks !
Aur?lie




From jtk at cmp.uea.ac.uk  Fri Apr  1 09:24:14 2005
From: jtk at cmp.uea.ac.uk (Jan T. Kim)
Date: Fri Apr  1 08:23:03 2005
Subject: [BioPython] Bioregistry...doesn't work with me
In-Reply-To: <008401c536bb$4ead9470$0b413851@YSENGARD>
References: <008401c536bb$4ead9470$0b413851@YSENGARD>
Message-ID: <20050401142414.GG15157@jtkpc.cmp.uea.ac.uk>

On Fri, Apr 01, 2005 at 03:04:15PM +0200, Aur?lie Bornot wrote:
> 
> I am trying to retrieve sequences with the script of the CookBook and it doesn't work...
> I don't understand why....
> Can someone tell me what I did wrong ?

[deleted output of print commands]

> >>> from Bio import db
> >>> print db
> >>> db.keys()
> >>> sp = db["swissprot"]
> >>> sp
> <Bio.config.DBRegistry.DBGroup instance at 0x00ACEB48>
> >>> record_handle = sp['O23729']
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 150, in __
> getitem__
>     data = self._run_serial(key)
>   File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 217, in _r
> un_serial
>     raise KeyError, "I could not get any results."
> KeyError: 'I could not get any results.'
> 
> 
> I have verified : the entry O23729 is still correct....

Your example works for me:
>>> record_handle = sp['O23729']
>>> record_handle
<StringIO.StringIO instance at 0xf66b7c2c>
>>> print record_handle.readline()
ID   CHS3_BROFI     STANDARD;      PRT;   394 AA.

>>> print record_handle.readline()
AC   O23729;

>>> print record_handle.readline()
DT   15-JUL-1999 (Rel. 38, Created)

> I must work with Windows XP, may the problem comes from this...?

That's always a possiblility (I've tried on Linux), but it's more likely
a network problem, Biopython may have been unable to get the record
because e.g.

    * you are behind some firewall that doesn't allow the kind of http
      used by Biopython for retrieving the record

    * the network connectivity between your site and www.expasy.ch
      may have been transiently down

Best regards, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: jtk@cmp.uea.ac.uk                               |
 |    *NEW*    WWW:   http://www.cmp.uea.ac.uk/people/jtk             |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*
From LKatz at smith.edu  Fri Apr  1 13:22:38 2005
From: LKatz at smith.edu (Laura A. Katz)
Date: Fri Apr  1 13:18:48 2005
Subject: [BioPython] Exclusion limits
Message-ID: <a06210206be7341ea3267@[131.229.112.15]>

How can I alter my GB search scripts to exclude the following:

__ exclude ESTs __ exclude STSs __ exclude GSS __ exclude TPA 
__ exclude working draft __ exclude patents __ exclude all of the above 


Note: these exclusion sets appear under 'limits' on the NCBI web browser.


From cymon at duke.edu  Fri Apr  1 14:37:10 2005
From: cymon at duke.edu (Cymon Cox)
Date: Fri Apr  1 14:31:18 2005
Subject: [BioPython] Exclusion limits
In-Reply-To: <a06210206be7341ea3267@[131.229.112.15]>
References: <a06210206be7341ea3267@[131.229.112.15]>
Message-ID: <1112384229.29244.63.camel@isis.biology.duke.edu>

Hi Laura,

On Fri, 2005-04-01 at 13:22, Laura A. Katz wrote:
> How can I alter my GB search scripts to exclude the following:
> 
> __ exclude ESTs __ exclude STSs __ exclude GSS __ exclude TPA 
> __ exclude working draft __ exclude patents __ exclude all of the above 
> 

According to this page:
http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/InfoHubs/Exercises/infohubs_qa_ests_exclude.html

you should be able to add the qualifiers to the end of your search
string:

NOT gbdiv_est[prop] NOT gbdiv_sts[prop] NOT gbdiv_gss[prop] NOT
gbdiv_tpa[prop] NOT gbdiv_pat[prop] etc

I'm guessing at the latter and I dont know what the qualifier for
working draft might be...

Cymon

Note I'm replying to the Biopython list here for reference...


> 
> Note: these exclusion sets appear under 'limits' on the NCBI web browser.
> 
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
____________________________________________________________________

Cymon J. Cox
Research Associate
Department of Biology
Duke University
BOX 90338
Durham NC 27708

Phone : (919) 660-7370
Fax : (919) 660-7293
HomePage : http://www.duke.edu/~cymon
_____________________________________________________________________
Fedora Core release 2 (Tettnang) isis.biology.duke.edu 14:35:15 up 12
days, 1:09, 11 users, load average: 0.12, 0.09, 0.05

From mdehoon at ims.u-tokyo.ac.jp  Sun Apr  3 05:22:46 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Sun Apr  3 05:17:58 2005
Subject: [BioPython] Blast and PsiBlast
In-Reply-To: <007501c536b8$91de1420$0b413851@YSENGARD>
References: <007501c536b8$91de1420$0b413851@YSENGARD>
Message-ID: <424FB5E6.6010203@ims.u-tokyo.ac.jp>

Aur?lie Bornot wrote:

 > - I don't understand why qblast( ) can't "call" the program called blastx.. ?


As far as I know, there is no fundamental reason why qblast cannot call blastx. 
Probably it has simply not yet been implemented. If you could write a patch to 
Bio/Blast/NCBIWWW.py so that qblast can run blastx, that would be great. If you 
are familiar with blastx, maybe such a patch would not be difficult. You 
probably would only need to change the parameters in the qblast function (but 
then again, I don't use blast much, so I am no expert on this matter). We'd be 
happy to include such a patch with Biopython.

--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
From saccenti at cerm.unifi.it  Tue Apr  5 10:45:41 2005
From: saccenti at cerm.unifi.it (Edoardo Saccenti)
Date: Tue Apr  5 10:41:54 2005
Subject: [BioPython] parsing NMR PDB
In-Reply-To: <a06210206be7341ea3267@[131.229.112.15]>
References: <a06210206be7341ea3267@[131.229.112.15]>
Message-ID: <200504051645.41921.saccenti@cerm.unifi.it>

I'm parsing an NMR PDB file 
using the command

parser = PDBparser(PERMISSIVE=1)  #or = 0
structure = parser.get_structure(str_id, pdb_name)

I get the warning:
nonstandard resolution  NOT APPLICABLE.

parser works fine but I can't avoid this warning.

Any idea?

Thanks a lot
Edoardo

-- 
"Raffiniert ist der Herr Gott,
 aber boshaft ist Er nicht."

---
Dr. Edoardo Saccenti
CERM Nuclear Magnetic Resonance Research Center
Scientific Pole - University of Florence
Via Luigi Sacconi n? 6
50019 Sesto Fiorentino (FI)
tel: +39 055 4574193
fax: +39 055 4574253
saccenti@cerm.unifi.it
www.cerm.unifi.it

From thamelry at binf.ku.dk  Tue Apr  5 10:49:12 2005
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Tue Apr  5 22:06:31 2005
Subject: [BioPython] parsing NMR PDB
In-Reply-To: <200504051645.41921.saccenti@cerm.unifi.it>
References: <a06210206be7341ea3267@[131.229.112.15]>
	<200504051645.41921.saccenti@cerm.unifi.it>
Message-ID: <200504051649.12125.thamelry@binf.ku.dk>

On Tuesday 05 April 2005 16:45, Edoardo Saccenti wrote:
> I'm parsing an NMR PDB file
> using the command
>
> parser = PDBparser(PERMISSIVE=1)  #or = 0
> structure = parser.get_structure(str_id, pdb_name)
>
> I get the warning:
> nonstandard resolution  NOT APPLICABLE.
>
> parser works fine but I can't avoid this warning.
>
> Any idea?

Everything is fine: NMR structures do not have a resolution.
I think you are using an old version of Biopython, right? The current
version does not generate this warning anymore.

Best regards,

-Thomas

From rafael at nbn.ac.za  Wed Apr  6 02:27:55 2005
From: rafael at nbn.ac.za (Rafael C. Jimenez)
Date: Wed Apr  6 02:22:25 2005
Subject: [BioPython] mysql trouble
In-Reply-To: <Prayer.1.0.10.0503311130300.6437@webmail1.york.ac.uk>
References: <Prayer.1.0.10.0503311130300.6437@webmail1.york.ac.uk>
Message-ID: <d4a87e1f49dd9bdc1f4aa6f13156be1d@nbn.ac.za>

Try to create a cursor of  "conn" and then use the method execute to 
process the query.

See one example from the MySQLdb help:

#!/usr/bin/python
# import MySQL module
import MySQLdb
# connect
db = MySQLdb.connect(host="localhost", user="joe",
passwd="secret",
db="db56a")
# create a cursor
cursor = db.cursor()
# execute SQL statement
cursor.execute("""INSERT INTO animals (name, species) VALUES
("Harry",
"Hamster")""")

Good luck with your project!
Cheers,
Rafael.

On 31/03/2005, at 12:30, pap501@york.ac.uk wrote:

> Hi
>
> I am a masters student at the University of York working on a project 
> to create a database of DNA sequences.
>
> I am trying to grab information from text files using a python script 
> to insert data into a MySQL table. The problem is that although I can 
> query MySQL through Python I cannot write into MySQL through Python. I 
> am using the Windows platform with Python version 2.4 with Biopython 
> installed and MySQL Server 4.1.
>
> I have attached my python script to this email.
> The script takes each text file in turn (although only one is listed 
> in the script at the mo) and inserts the library code, Genbank code 
> (primary key), TiGR code (if there is one, null otherwise) and the DNA 
> sequence (string of characters). Each file is a library of ~2000 DNA 
> sequences. The python script runs but does not write the information 
> into my MySQL table. When I query the table in MySQL it says that the 
> table is empty.
>
> Can anyone advise me what to do? Is it soemthing to do with the setup 
> of MySQL and/or Python or a problem with the Python script?
>
> Any advice would be greatly appreciated.
>
> Many thanks
>
> Phil<library.py>_______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython

From rafael at nbn.ac.za  Fri Apr  8 04:53:21 2005
From: rafael at nbn.ac.za (Rafael C. Jimenez)
Date: Fri Apr  8 04:45:53 2005
Subject: [BioPython] biopython-epydoc
Message-ID: <3ad44acdcc95b240b88904bae39fcabf@nbn.ac.za>

I am trying to get html help pages of biopython through epydoc. Epydoc 
generate the html files but there is not information inside about the 
modules, classes, and/or functions. Any idea of how to do this?

My input/output:
----------------------------------------------------------------------
nbn213:/System/Library/Frameworks/Python.framework/Versions/2.3/bin rc$ 
ls
epydoc          epydocgui       idle            pydoc           python  
         python2.3

nbn213:/System/Library/Frameworks/Python.framework/Versions/2.3/bin rc$ 
./epydoc -o /Users/rc/Desktop/epydoc/biopython  --css blue  
--private-css green -v -n biopython -u http://biopython.org 
--inheritance listed Bio

Importing 1 modules.
   [1/1] Importing Bio
Building API documentation for 1 modules.
   [1/1] Building docs for Bio
Writing HTML docs (10 files) to '/Users/rc/Desktop/epydoc/biopython'.
   [ 1/10] Writing epydoc.css
   [ 2/10] Writing Bio-module.html
   [ 3/10] Writing indices.html
   [ 4/10] Writing trees.html
   [ 5/10] Writing help.html
   [ 6/10] Writing frames.html
   [ 7/10] Writing toc.html
   [ 8/10] Writing toc-everything.html
   [ 9/10] Writing toc-Bio-module.html
   [10/10] Writing index.html

From Frederic.Sohm at iaf.cnrs-gif.fr  Fri Apr  8 05:46:48 2005
From: Frederic.Sohm at iaf.cnrs-gif.fr (Frederic.Sohm@iaf.cnrs-gif.fr)
Date: Fri Apr  8 05:40:56 2005
Subject: [BioPython] biopython-epydoc
Message-ID: <1112953608.4256530863d31@mail.iaf.cnrs-gif.fr>

Hi,

Sorry, I have no idea about what the problem is, but I have an advice if you do 
use epydoc, because I have had the problem before. 

To avoid getting a lot of useless output and a very long documentation you 
should comment out the following lines in Bio.Restriction.Restriction.py 
which are at the bottom end of the file.

This code create the class for the restriction enzymes (and there is about 600 
of them). Epydoc will create the documentation for each enzyme. It is always 
more or less the same. The processing is very long and the doc quite useless.

If you comment these lines before running epydoc you will still get the 
documentation once (for the super class) 

Here are the line to comment out.
Don't forget to uncomment them after :-)

Sorry for not being to helping you with your problem, I have had a look and it 
doesn't ring a bell.

Fred

"""
CommOnly    = RestrictionBatch()    # commercial enzymes
NonComm     = RestrictionBatch()    # not available commercially
for TYPE, (bases, enzymes) in typedict.iteritems() :
    #
    #   The keys are the pseudo-types TYPE (stored as type1, type2...)
    #   The names are not important and are only present to differentiate
    #   the keys in the dict. All the pseudo-types are in fact 
RestrictionType.
    #   These names will not be used after and the pseudo-types are not
    #   kept in the locals() dictionary. It is therefore impossible to
    #   import them.
    #   Now, if you have look at the dictionary, you will see that not all the
    #   types are present as those without corresponding enzymes have been
    #   removed by Dictionary_Builder().
    #
    #   The values are tuples which contain
    #   as first element a tuple of bases (as string) and
    #   as second element the names of the enzymes.
    #
    #   First eval the bases.
    #
    bases = tuple([eval(x) for x in bases])
    #
    #   now create the particular value of RestrictionType for the classes
    #   in enzymes.
    #
    T = type.__new__(RestrictionType, 'RestrictionType', bases, {})
    for k in enzymes :
        #
        #   Now, we go through all the enzymes and assign them their type.
        #   enzymedict[k] contains the values of the attributes for this
        #   particular class (self.site, self.ovhg,....).
        #
        newenz = T(k, bases, enzymedict[k])
        #
        #   we add the enzymes to the corresponding batch.
        #
        #   No need to verify the enzyme is a RestrictionType -> add_nocheck
        #
        if newenz.is_comm() : CommOnly.add_nocheck(newenz)
        else : NonComm.add_nocheck(newenz)
#
#   AllEnzymes is a RestrictionBatch with all the enzymes from Rebase.
#
AllEnzymes = CommOnly | NonComm
#
#   Now, place the enzymes in locals so they can be imported.
#
names = [str(x) for x in AllEnzymes]
locals().update(dict(map(None, names, AllEnzymes)))
__all__=['FormattedSeq', 'Analysis', 
'RestrictionBatch','AllEnzymes','CommOnly','NonComm']+names
del k, x, enzymes, TYPE, bases, names
""


Le vendredi 8 Avril 2005 10:53, Rafael C. Jimenez a ?crit :
> I am trying to get html help pages of biopython through epydoc. Epydoc
> generate the html files but there is not information inside about the
> modules, classes, and/or functions. Any idea of how to do this?
>
> My input/output:
> ----------------------------------------------------------------------
> nbn213:/System/Library/Frameworks/Python.framework/Versions/2.3/bin rc$
> ls
> epydoc          epydocgui       idle            pydoc           python
>          python2.3
>
> nbn213:/System/Library/Frameworks/Python.framework/Versions/2.3/bin rc$
> ./epydoc -o /Users/rc/Desktop/epydoc/biopython  --css blue
> --private-css green -v -n biopython -u http://biopython.org
> --inheritance listed Bio
>
> Importing 1 modules.
>    [1/1] Importing Bio
> Building API documentation for 1 modules.
>    [1/1] Building docs for Bio
> Writing HTML docs (10 files) to '/Users/rc/Desktop/epydoc/biopython'.
>    [ 1/10] Writing epydoc.css
>    [ 2/10] Writing Bio-module.html
>    [ 3/10] Writing indices.html
>    [ 4/10] Writing trees.html
>    [ 5/10] Writing help.html
>    [ 6/10] Writing frames.html
>    [ 7/10] Writing toc.html
>    [ 8/10] Writing toc-everything.html
>    [ 9/10] Writing toc-Bio-module.html
>    [10/10] Writing index.html
>
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython

-- 
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 GeNuts at emw.demon.nl  Fri Apr  8 07:23:54 2005
From: GeNuts at emw.demon.nl (E.M.Wielhouwer)
Date: Fri Apr  8 07:44:56 2005
Subject: [BioPython] Installation of Biopython 1.40b on Windows XP system
 (newbee on (bio)python and programming)
Message-ID: <6.0.0.22.2.20050408132326.01b7d618@pop3.demon.nl>

Dear All,

As beginner in programming I picked up O'Reilly's "Learning Python" because 
there was a package called BioPython with nice tools for free of use of 
which I'm interested in as Biomedical Researcher. Bought both books 
(learning and programming python, however, following each of examples per 
chapter of "learning python" I stumbled upon a problem that I can't 
overcome which make me desperate due to the lack of knowledge on this 
subject. (below also questions on the installation of biopython on my 
windows XP machine)

As read at page 270 I tried to follow your example on importing scripts 
outside the python installation directory but I failed. I hope you might 
want to help me out here I'm really stuck aon this subject. Below I 
describe what I've done but first some settings of python.

----
Python version: PythonWin 2.4.1 (#65, Mar 30 2005, 09:33:37) [MSC v.1310 32 
bit (Intel)] on win32. Portions Copyright 1994-2004 Mark
                       Hammond (mhammond@skippinet.com.au) - see 
'Help/About PythonWin' for further copyright information.

Operating system: Windows-XP SP1

Program locates at:             C:\\Prgrmmr\\Python24
Specific MyScript 
path  C:\Prgrmmr\Python24\MyPythonpaths.pth           (this includes two 
lines of code: # .pth file for My own Scripts
                                                                                                                         and: 
C:\Prgrmmr\MyCode\ )
Location of my scripts: C:\\Prgrmmr\\MyCode
----

Here is my output from Python (pythonwin - IDE mode).

----
 >>> import sys
 >>> sys.path
['', 'C:\\WINDOWS\\System32\\python24.zip', 'C:\\Documents and 
Settings\\Gandalf', 'C:\\Prgrmmr\\Python24\\DLLs', 
'C:\\Prgrmmr\\Python24\\lib', 'C:\\Prgrmmr\\Python24\\lib\\plat-win', 
'C:\\Prgrmmr\\Python24\\lib\\lib-tk', 
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\pythonwin', 
'C:\\Prgrmmr\\Python24', 'C:\\Prgrmmr\\MyCode', 
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\reportlab', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\Numeric', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\PIL', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32\\lib']
---- continued below----

['', 'C:\\WINDOWS\\System32\\python24.zip',
'C:\\Documents and Settings\\Gandalf',
'C:\\Prgrmmr\\Python24\\DLLs',
'C:\\Prgrmmr\\Python24\\lib',
'C:\\Prgrmmr\\Python24\\lib\\plat-win',
'C:\\Prgrmmr\\Python24\\lib\\lib-tk',
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\pythonwin',
'C:\\Prgrmmr\\Python24',
'C:\\Prgrmmr\\MyCode',
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\reportlab',
'C:\\Prgrmmr\\Python24\\lib\\site-packages',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\Numeric',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\PIL',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32\\lib']

----continued-----
 >>> import Prgrmmr.MyCode.mod
Traceback (most recent call last):
   File "<interactive input>", line 1, in ?
ImportError: No module named Prgrmmr.MyCode.mod
 >>>
----

Similar result is obtained even when the __init__.py file is included in 
the C:\\Prgrmmr and C:\\Prgrmmr\\MyCode directory.

The __init__.py file includes the following text:       #File: 
Python\__init__.py
                                                         print 'Python init'
                                                         x=1

I hope you can help me out on this (most likely I forgot something 
mentioned in the book (which I assume)),


A few other things which seems to be difficult for me on Brad's biopython 
installation manual.

First, it's not clear to me if I should have additional libraries aside the 
ones described in Brad's Manual?

Second, (manual 3.3.2 Reportlab install) How about rl_accel 0.52, PyRXP 
1.05, etc. , etc. has that also to be installed?
www.biopython.org/docs/install/Installation.html#htoc18

Third (manual 3.4) should I install MySQL from www.mySQL.com prior to the 
install of MySQLdb or not at all? 
www.biopython.org/docs/install/Installation.html#htoc20

Third, (manual 3.4) because I've got a windows XP OS I need to compiler the 
psycog library (or do I call this differently) for that, where do I get a 
(VC++ 6) compiler from (might be a stupid question)?
www.biopython.org/docs/biosql/python_biosql_basic.html#htoc6

Finally, (manual 4.4)  where goes the documentation, tests, example code 
that exists in the biopython source file biopython-1.40b.zip. Does it have 
to be compiled and how do I do that if 4.5 does not apply? I question this 
due to the reading of section 5, paragraph 3, line 2 "Tests directory 
inside the distribution). 
www.biopython.org/docs/install/Installation.html#htoc31

I'm stuck on this and every bit help is welcome and well appreciated,


Eric
From letondal at pasteur.fr  Fri Apr  8 09:54:32 2005
From: letondal at pasteur.fr (Catherine Letondal)
Date: Fri Apr  8 09:43:53 2005
Subject: [BioPython] CFP NETTAB 2005: Network Tools and Applications in
	Biology / Workflows management
Message-ID: <fc5114af344c5088104681033c13add7@pasteur.fr>

Hi,

  {Please pass the word!}

NETTAB 2005: Network Tools and Applications in Biology
Workflows management: new abilities for the biological information 
overflow
	5-7 October, 2005, Second University of Naples
	Naples, Italy

Web page : http://www.nettab.org/2005
Call for Papers: http://www.nettab.org/2005/call.html

--
Catherine Letondal -- Institut Pasteur
www.pasteur.fr/~letondal

From aurelie.bornot at free.fr  Wed Apr 13 12:04:34 2005
From: aurelie.bornot at free.fr (aurelie.bornot@free.fr)
Date: Wed Apr 13 12:00:35 2005
Subject: [BioPython] mysql trouble
Message-ID: <1113408274.425d4312982ff@imp5-q.free.fr>

Hi,

I had a similar problem and I tried Rafael 's script on windows :
it didn't work either.... for me....  :'(
But I tried to add :
db.commit()
after
cursor.execute("""---""")
and it worked !!!

hope this help !
cheers,
Aurelie



Rafael C. Jimenez rafael at nbn.ac.za wrote :

>Try to create a cursor of  "conn" and then use the method execute to
>process the query.

>See one example from the MySQLdb help:

>#!/usr/bin/python
># import MySQL module
>import MySQLdb
># connect
>db = MySQLdb.connect(host="localhost", user="joe",
>passwd="secret",
>db="db56a")
># create a cursor
>cursor = db.cursor()
># execute SQL statement
>cursor.execute("""INSERT INTO animals (name, species) VALUES
>("Harry",
>"Hamster")""")

>Good luck with your project!
>Cheers,
>Rafael.

On 31/03/2005, at 12:30, pap501 at york.ac.uk wrote:

> Hi
>
> I am a masters student at the University of York working on a project
> to create a database of DNA sequences.
>
> I am trying to grab information from text files using a python script
> to insert data into a MySQL table. The problem is that although I can
> query MySQL through Python I cannot write into MySQL through Python. I
> am using the Windows platform with Python version 2.4 with Biopython
> installed and MySQL Server 4.1.
>
> I have attached my python script to this email.
> The script takes each text file in turn (although only one is listed
> in the script at the mo) and inserts the library code, Genbank code
> (primary key), TiGR code (if there is one, null otherwise) and the DNA
> sequence (string of characters). Each file is a library of ~2000 DNA
> sequences. The python script runs but does not write the information
> into my MySQL table. When I query the table in MySQL it says that the
> table is empty.
>
> Can anyone advise me what to do? Is it soemthing to do with the setup
> of MySQL and/or Python or a problem with the Python script?
>
> Any advice would be greatly appreciated.
>
> Many thanks
>
> Phil<library.py>_______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython


From aurelie.bornot at free.fr  Wed Apr 13 12:18:17 2005
From: aurelie.bornot at free.fr (aurelie.bornot@free.fr)
Date: Wed Apr 13 12:13:07 2005
Subject: [BioPython] Bioregistry on windows....
Message-ID: <1113409097.425d464973ac9@imp5-q.free.fr>


Hi !

I have tried hard since my first mail ("Bioregistry...doesn't work with me")to
deal with Bioregistry on windows....
And ... I am lost...


Jan T. Kim suggest it was a network problem (thanks for your clue Jan !) but if
it is I can't find it (I am a news programmer...)

can't it be a problem with fork()????
 when we do :
>>> from Bio import db
>>> print db
>>> db.keys()
>>> sp = db["swissprot"]

the db creation uses fork() (I saw that trying to follow the labyrinth (for me)
of the creation of db, but I lost myself and I don't remember where exatly...
sorry !

Can someone help ???
Thanks
Aurelie


From aurelie.bornot at free.fr  Wed Apr 13 12:24:40 2005
From: aurelie.bornot at free.fr (aurelie.bornot@free.fr)
Date: Wed Apr 13 12:18:38 2005
Subject: [BioPython] BioSQL and BioSeqDatabase
Message-ID: <1113409480.425d47c80305f@imp5-q.free.fr>

Hello,

Once again : sorry for spaming !!

Does anyone know how  I can get the structure of the BioSeqDatabase of the
BioSQL module and how to create one....???
I would like to insert the table(s) of a BioSeqDatabase in my own database....
Is it possible ???

Thanks !
Aurelie

From faheem at email.unc.edu  Wed Apr 13 14:04:59 2005
From: faheem at email.unc.edu (Faheem Mitha)
Date: Wed Apr 13 13:58:28 2005
Subject: [BioPython] parsing fasta file to list of sequences
Message-ID: <Pine.LNX.4.62.0504131404340.7045@Chrestomanci>


Hi,

I was needing to parse a fasta file into a list of sequences in the following 
fashion.

[['acg'], ['tac'],...]

where each entry is a different sequence. Is this easily possible with the 
current parsing tools? If so, would somone be kind enough to sketch an 
approach? Thanks in advance.

                                                                    Faheem.
From fkauff at duke.edu  Wed Apr 13 14:22:26 2005
From: fkauff at duke.edu (Frank Kauff)
Date: Wed Apr 13 14:18:33 2005
Subject: [BioPython] parsing fasta file to list of sequences
In-Reply-To: <Pine.LNX.4.62.0504131404340.7045@Chrestomanci>
References: <Pine.LNX.4.62.0504131404340.7045@Chrestomanci>
Message-ID: <1113416546.22662.1.camel@osiris.biology.duke.edu>

Hi Faheem,

On Wed, 2005-04-13 at 14:04 -0400, Faheem Mitha wrote:
> Hi,
> 
> I was needing to parse a fasta file into a list of sequences in the following 
> fashion.
> 
> [['acg'], ['tac'],...]
> 
> where each entry is a different sequence. Is this easily possible with the 
> current parsing tools? If so, would somone be kind enough to sketch an 
> approach? Thanks in advance.
> 

[fkauff@osiris align]$ cat fasta
>one
AAAAA
>two
CCCCCC
>three
GGGGGGGG

>>> from Bio import SeqUtils
>>> fasta=SeqUtils.quick_FASTA_reader('fasta')
>>> names,seqs=zip(*fasta)
>>> names
('one', 'two', 'three')
>>> seqs
('AAAAA', 'CCCCCC', 'GGGGGGGG')

or to get exactly what you wanted

>>> seqs2=[[s[1]] for s in fasta]
>>> seqs2
[['AAAAA'], ['CCCCCC'], ['GGGGGGGG']]

Frank


>                                                                     Faheem.
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
Fax 919-660-7293
Web http://www.lutzonilab.net/member/frankkauff.shtml




From faheem at email.unc.edu  Wed Apr 13 14:30:11 2005
From: faheem at email.unc.edu (Faheem Mitha)
Date: Wed Apr 13 14:24:29 2005
Subject: [BioPython] parsing fasta file to list of sequences
In-Reply-To: <1113416546.22662.1.camel@osiris.biology.duke.edu>
References: <Pine.LNX.4.62.0504131404340.7045@Chrestomanci>
	<1113416546.22662.1.camel@osiris.biology.duke.edu>
Message-ID: <Pine.LNX.4.62.0504131429120.7045@Chrestomanci>



On Wed, 13 Apr 2005, Frank Kauff wrote:

> [fkauff@osiris align]$ cat fasta
>> one
> AAAAA
>> two
> CCCCCC
>> three
> GGGGGGGG
>
>>>> from Bio import SeqUtils
>>>> fasta=SeqUtils.quick_FASTA_reader('fasta')
>>>> names,seqs=zip(*fasta)
>>>> names
> ('one', 'two', 'three')
>>>> seqs
> ('AAAAA', 'CCCCCC', 'GGGGGGGG')
>
> or to get exactly what you wanted
>
>>>> seqs2=[[s[1]] for s in fasta]
>>>> seqs2
> [['AAAAA'], ['CCCCCC'], ['GGGGGGGG']]

Thanks Frank. That's very helpful.                   Faheem.
From karbak at gmail.com  Thu Apr 14 01:59:01 2005
From: karbak at gmail.com (K. Arun)
Date: Thu Apr 14 01:52:35 2005
Subject: [BioPython] Bio.PDB : model count in NMR structures
Message-ID: <162452a105041322594f3237ab@mail.gmail.com>

Hello,

In the course of extracting sequence information for  a sub-set of PDB
files and writing out specific parts using the Bio.PDB classes, I ran
across an anomaly.  When parsing NMR structures, if I query the number
of models present in the structure thus :

str = p.get_structure('8tfv', '8tfv.pdb')
mdls = Selection.unfold_entities(str, 'M')

print len(mdls)

, the number of models printed always exceeds the number present in
the file by 1. A mdls[-1].get_list() yields an empty chain list. Is
this a known issue, or even, a feature ?

-arun

From thamelry at binf.ku.dk  Thu Apr 14 04:45:13 2005
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Thu Apr 14 05:49:18 2005
Subject: [BioPython] Bio.PDB : model count in NMR structures
In-Reply-To: <162452a105041322594f3237ab@mail.gmail.com>
References: <162452a105041322594f3237ab@mail.gmail.com>
Message-ID: <200504141045.14080.thamelry@binf.ku.dk>

Hi Arun,

> In the course of extracting sequence information for  a sub-set of PDB
> files and writing out specific parts using the Bio.PDB classes, I ran
> across an anomaly.  When parsing NMR structures, if I query the number
> of models present in the structure thus :
>
> str = p.get_structure('8tfv', '8tfv.pdb')
> mdls = Selection.unfold_entities(str, 'M')
>
> print len(mdls)
>
> , the number of models printed always exceeds the number present in
> the file by 1. A mdls[-1].get_list() yields an empty chain list. Is
> this a known issue, or even, a feature ?

Thanks for reporting this bug. I've fixed it in CVS.

BTW, len(str) will give you the number of models.

Best regards,

-Thomas

-- 
Thomas Hamelryck, Postdoctoral researcher
Bioinformatics center
University of Copenhagen      
Universitetsparken 15 Bygning 10                 
2100 Copenhagen, Denmark
---
http://www.binf.ku.dk/users/thamelry/

From idoerg at burnham.org  Thu Apr 14 20:53:47 2005
From: idoerg at burnham.org (Iddo Friedberg)
Date: Thu Apr 14 20:47:21 2005
Subject: [BioPython] Speakers for BOSC needed
Message-ID: <425F109B.8040507@burnham.org>

Hi all,

It's that time of year again, and BOSC 2005 will be happening on June 
23-24. The more Biopython representatives, the merrier. I will be 
around, but I will be dealing with my own SIG meeting, so I will not be 
able to give a talk. Is there someone who can give the BioPython 
"plenary"? should be a 30-40 minute talk. Also, there are slots for 
shorter talks, so if you contributed and interesting module, or had an 
interesting experience with biopython you would like to share, please 
submit a talk.

For those of you who do not know what BOSC is, it's the Bioinformatics 
Open Source Conference, which is held as a satellite meeting of ISMB. I 
highly recommend this event, it is a real eye opener with respect to the 
world of open source, and computational biology. More about it here:

http://open-bio.org/bosc/

Cheers,

Iddo

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
http://ffas.ljcrf.edu/~iddo
==========================
The First Automated Protein Function Prediction SIG
Detroit, MI June 24, 2005
http://ffas.burnham.org/AFP

From dalke at dalkescientific.com  Fri Apr 15 06:21:39 2005
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Fri Apr 15 06:20:41 2005
Subject: [BioPython] Speakers for BOSC needed
In-Reply-To: <425F109B.8040507@burnham.org>
References: <425F109B.8040507@burnham.org>
Message-ID: <6e67f5757757976119255f804d72bb3a@dalkescientific.com>

To follow up on Iddo's email, if you can't make it to BOSC
this year because you happen to be in, say, Europe you
should consider Europython.  It's 3 days after BOSC and
overlaps with ISMB.  It will be in lovely Gothenburg, Sweden
again this year.  Jag vill vara d?r nu.

    www.europython.org

Both BOSC and EuroPython have call-for-talks out so even
if you don't want to give the main Biopython talk you
might want to give one about your current work.

					Andrew
					dalke@dalkescientific.com


From wligtenberg at gmail.com  Fri Apr 15 07:36:36 2005
From: wligtenberg at gmail.com (Willem Ligtenberg)
Date: Fri Apr 15 07:32:21 2005
Subject: [BioPython] Martel: IterParser.IterHeaderFooter
Message-ID: <cbb068b3050415043630611d6d@mail.gmail.com>

I'm creating a parser and have specified this:
self.ip = IterParser.IterHeaderFooter(
			self.header, RecordReader.CountLines, (1,),
			self.record, RecordReader.CountLines, (1,),
			None, None, None, "format")

Then I can parse the records with:
for data in self.ip.iterateFile(open(fileName, "r")):

and do things with data.
But I also need the information from the header, because it specifies
with what kind of information I'm working. How can I access that data?

Thanks in advance,

Willem Ligtenberg

From marc.saric at gmx.de  Fri Apr 15 09:44:44 2005
From: marc.saric at gmx.de (Marc Saric)
Date: Fri Apr 15 09:38:23 2005
Subject: [BioPython] Martel.Parser.ParserPositionException:
Message-ID: <425FC54C.7050006@gmx.de>

Hi all,

I tried to index the the following Genbank file with this simple script
(as described in the cookbook) but it failed with the following traceback.

The file can be found in:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=BA000018

including all features (SNP, CDD, MGC, HPRD, STS)

I tried with Biopython 1.3, Biopython 1.4b and the Biopython-CVS as of
2005-04-15.

The program

===snip===
#!/usr/bin/env python
from Bio import GenBank

dict_file = "ba000018_s_aureus_n315_genome.gb"
index_file = "ba000018_s_aureus_n315_genome.idx"

GenBank.index_file(dict_file, index_file)
===snap===

The Traceback:

===snip===
Traceback (most recent call last):
   File "/home/saric/data/devel/workspace/scripts/hitman/index_gb.py",
line 37, in ?
     GenBank.index_file(dict_file, index_file) # FIXME: This breaks with
the N315 S.aureus-genome
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Bio/GenBank/__init__.py", 

line 1283, in index_file
     SimpleSeqRecord.create_flatdb([filename], indexname, indexer)
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Bio/Mindy/SimpleSeqRecord.py", 

line 152, in create_flatdb
     creator.load(filename, builder = builder, fileid_info = {})
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Bio/Mindy/BaseDB.py", 

line 52, in load
     for record in iterator.iterate(source, cont_handler = builder):
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Martel/IterParser.py", 

line 71, in iterateFile
     raise Parser.ParserPositionException(self.start_position)
Martel.Parser.ParserPositionException: error parsing at or beyond
character 5887615

===snap===

I use a x86-machine running SuSE-Linux 9.1 (kernel 2.6.5-7.147-default,
gcc version 3.3.3).

If I use a version of the file, which does not have the
feature-annotations, it gives the following traceback:

===snip===
Traceback (most recent call last):
   File "/home/saric/data/devel/workspace/scripts/hitman/index_gb.py",
line 37, in ?
     GenBank.index_file(dict_file, index_file) # FIXME: This breaks with
the N315 S.aureus-genome
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Bio/GenBank/__init__.py", 

line 1283, in index_file
     SimpleSeqRecord.create_flatdb([filename], indexname, indexer)
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Bio/Mindy/SimpleSeqRecord.py", 

line 152, in create_flatdb
     creator.load(filename, builder = builder, fileid_info = {})
   File
"/home/saric/transfer/source/biopython/biopython_cvs_20050415/biopython/build/lib.linux-i686-2.3/Bio/Mindy/BaseDB.py", 

line 36, in load
     raise TypeError("Cannot identify file as a %s format" %
TypeError: Cannot identify file as a unknown format
	
===snap===

which -to me- sounds a bit strange, as it looks like a normal Genbank-file.

If someone has a clue...

Thanks in advance.

-- 
Bye,
Marc Saric  http://www.marcsaric.de
From mls5w at virginia.edu  Fri Apr 15 13:39:03 2005
From: mls5w at virginia.edu (Michael Sierk)
Date: Fri Apr 15 13:28:07 2005
Subject: [BioPython] Alternate Conformations in PDB
Message-ID: <c17fc5ea6c96fa5014ae361d5e831cf7@virginia.edu>

How does the PDB module deal with alternate conformations?  It appears  
to me that it is completely ignoring them, at least in the polypeptide  
builder.

Thanks,
Mike Sierk


Here's the snippet of code:

>         print "id: ", id
>         pdb_file = '/rd0/users/mls5w/cathdoms/' + id + '.pdb'
>         p = PDBParser()
>         s = p.get_structure('1', pdb_file)  # The structure
>         ppb=CaPPBuilder()
>         for pp in ppb.build_peptides(s):
>             print pp.get_sequence()
>

Here's the output:

> id:  11baA0
> Seq('KESAAAKFERQHMDS', <class Bio.Alphabet.ProteinAlphabet at  
> 0x62f300>)
> Seq('SNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRIT  
> ...', <class Bio.Alphabet.ProteinAlphabet at 0x62f300>)

And here's the relevant section of the PDB file:

> ATOM     89  N   HIS A  12       7.245  -5.906  13.618  1.00 13.83      
>       N
> ATOM     90  CA  HIS A  12       7.227  -6.425  14.964  1.00 13.71      
>       C
> ATOM     91  C   HIS A  12       7.373  -5.379  16.042  1.00 14.43      
>       C
> ATOM     92  O   HIS A  12       7.253  -5.726  17.224  1.00 14.41      
>       O
> ATOM     93  CB  HIS A  12       8.405  -7.418  15.156  1.00 11.77      
>       C
> ATOM     94  CG  HIS A  12       8.257  -8.620  14.267  1.00  9.61      
>       C
> ATOM     95  ND1 HIS A  12       7.438  -9.677  14.614  1.00  8.63      
>       N
> ATOM     96  CD2 HIS A  12       8.761  -8.909  13.054  1.00  9.08      
>       C
> ATOM     97  CE1 HIS A  12       7.469 -10.573  13.653  1.00  8.45      
>       C
> ATOM     98  NE2 HIS A  12       8.244 -10.136  12.692  1.00  9.30      
>       N
> ATOM     99  N   MET A  13       7.676  -4.145  15.632  1.00 15.20      
>       N
> ATOM    100  CA  MET A  13       7.908  -3.151  16.679  1.00 16.58      
>       C
> ATOM    101  C   MET A  13       6.710  -2.207  16.806  1.00 18.05      
>       C
> ATOM    102  O   MET A  13       6.222  -1.682  15.802  1.00 18.98      
>       O
> ATOM    103  CB  MET A  13       9.150  -2.336  16.326  1.00 16.39      
>       C
> ATOM    104  CG  MET A  13      10.462  -3.110  16.502  1.00 14.43      
>       C
> ATOM    105  SD  MET A  13      10.738  -3.774  18.125  1.00 14.79      
>       S
> ATOM    106  CE  MET A  13      10.504  -2.444  19.253  1.00 13.41      
>       C
> ATOM    107  N   ASP A  14       6.232  -2.054  18.027  1.00 18.73      
>       N
> ATOM    108  CA  ASP A  14       5.248  -1.020  18.349  1.00 20.36      
>       C
> ATOM    109  C   ASP A  14       5.471  -0.573  19.800  1.00 21.48      
>       C
> ATOM    110  O   ASP A  14       4.799  -0.915  20.761  1.00 19.90      
>       O
> ATOM    111  CB  ASP A  14       3.850  -1.536  18.122  1.00 20.82      
>       C
> ATOM    112  CG  ASP A  14       2.763  -0.518  18.409  1.00 20.73      
>       C
> ATOM    113  OD1 ASP A  14       3.013   0.679  18.204  1.00 21.16      
>       O
> ATOM    114  OD2 ASP A  14       1.676  -0.922  18.878  1.00 20.89      
>       O
> ATOM    115  N   SER A  15       6.531   0.266  19.929  1.00 22.96      
>       N
> ATOM    116  CA  SER A  15       7.021   0.672  21.236  1.00 25.33      
>       C
> ATOM    117  C   SER A  15       6.142   1.732  21.895  1.00 25.92      
>       C
> ATOM    118  O   SER A  15       5.631   2.643  21.240  1.00 26.33      
>       O
> ATOM    119  CB  SER A  15       8.431   1.278  21.165  1.00 25.96      
>       C
> ATOM    120  OG  SER A  15       9.224   0.674  20.169  1.00 28.77      
>       O
> ATOM    121  N  AGLY A  16       5.838   1.525  23.178  0.50 26.35      
>       N
> ATOM    122  N  BGLY A  16       6.124   1.705  23.225  0.50 25.97      
>       N
> ATOM    123  CA AGLY A  16       4.936   2.410  23.894  0.50 27.02      
>       C
> ATOM    124  CA BGLY A  16       5.414   2.708  24.008  0.50 26.33      
>       C
> ATOM    125  C  AGLY A  16       4.234   1.754  25.072  0.50 27.16      
>       C
> ATOM    126  C  BGLY A  16       3.966   2.816  23.527  0.50 26.37      
>       C
> ATOM    127  O  AGLY A  16       4.212   0.540  25.212  0.50 27.16      
>       O
> ATOM    128  O  BGLY A  16       3.341   3.874  23.573  0.50 26.73      
>       O
> ATOM    129  N  AASN A  17       3.636   2.582  25.913  0.50 27.76      
>       N
> ATOM    130  N  BASN A  17       3.485   1.689  23.016  0.50 26.24      
>       N
> ATOM    131  CA AASN A  17       2.987   2.195  27.145  0.50 28.39      
>       C
> ATOM    132  CA BASN A  17       2.127   1.580  22.548  0.50 25.85      
>       C
> ATOM    133  C  AASN A  17       1.661   1.467  26.992  0.50 28.38      
>       C
> ATOM    134  C  BASN A  17       1.516   0.294  23.105  0.50 25.52      
>       C
> ATOM    135  O  AASN A  17       1.453   0.474  27.719  0.50 28.66      
>       O
> ATOM    136  O  BASN A  17       2.210  -0.697  23.262  0.50 25.46      
>       O
> ATOM    137  CB AASN A  17       2.763   3.460  27.988  0.50 29.72      
>       C
> ATOM    138  CB BASN A  17       1.985   1.538  21.029  0.50 26.31      
>       C
> ATOM    139  CG AASN A  17       2.781   3.204  29.473  0.50 30.83      
>       C
> ATOM    140  CG BASN A  17       0.521   1.841  20.683  0.50 26.41      
>       C
> ATOM    145  N  ASER A  18       0.750   1.899  26.127  0.50 28.07      
>       N
> ATOM    146  N  BSER A  18       0.240   0.382  23.399  0.50 25.45      
>       N
> ATOM    147  CA ASER A  18      -0.539   1.242  25.929  0.50 27.72      
>       C
> ATOM    148  CA BSER A  18      -0.525  -0.705  23.998  0.50 25.06      
>       C
> ATOM    149  C  ASER A  18      -1.045   1.350  24.492  0.50 27.14      
>       C
> ATOM    150  C  BSER A  18      -1.777  -1.015  23.183  0.50 24.72      
>       C
> ATOM    151  O  ASER A  18      -1.950   2.120  24.156  0.50 26.94      
>       O
> ATOM    152  O  BSER A  18      -2.368  -0.143  22.535  0.50 24.51      
>       O
> ATOM    153  CB ASER A  18      -1.621   1.834  26.845  0.50 28.33      
>       C
> ATOM    154  CB BSER A  18      -0.997  -0.266  25.397  0.50 24.82      
>       C
> ATOM    155  OG ASER A  18      -1.392   1.513  28.209  0.50 29.30      
>       O
> ATOM    156  OG BSER A  18      -2.132  -1.021  25.794  0.50 25.79      
>       O
> ATOM    157  N  APRO A  19      -0.468   0.545  23.598  0.50 26.85      
>       N
> ATOM    158  N  BPRO A  19      -2.203  -2.267  23.241  0.50 24.66      
>       N
> ATOM    159  CA APRO A  19      -0.783   0.550  22.177  0.50 26.33      
>       C
> ATOM    160  CA BPRO A  19      -3.401  -2.682  22.525  0.50 24.80      
>       C
> ATOM    161  C  APRO A  19      -2.171   0.081  21.778  0.50 25.90      
>       C
> ATOM    162  C  BPRO A  19      -4.683  -2.125  23.129  0.50 25.11      
>       C
> ATOM    163  O  APRO A  19      -2.629   0.411  20.667  0.50 25.39      
>       O
> ATOM    164  O  BPRO A  19      -5.696  -2.031  22.426  0.50 25.01      
>       O
> ATOM    165  CB APRO A  19       0.313  -0.344  21.569  0.50 26.13      
>       C
> ATOM    166  CB BPRO A  19      -3.325  -4.213  22.567  0.50 24.85      
>       C
> ATOM    167  CG APRO A  19       0.703  -1.221  22.715  0.50 26.33      
>       C
> ATOM    168  CG BPRO A  19      -1.877  -4.499  22.849  0.50 24.41      
>       C
> ATOM    169  CD APRO A  19       0.728  -0.284  23.894  0.50 26.61      
>       C
> ATOM    170  CD BPRO A  19      -1.454  -3.407  23.797  0.50 24.40      
>       C
> ATOM    171  N  ASER A  20      -2.876  -0.674  22.618  0.50 25.65      
>       N
> ATOM    172  N  BSER A  20      -4.653  -1.682  24.379  0.50 25.23      
>       N
> ATOM    173  CA ASER A  20      -4.230  -1.118  22.259  0.50 25.89      
>       C
> ATOM    174  CA BSER A  20      -5.848  -1.272  25.101  0.50 25.72      
>       C
> ATOM    175  C  ASER A  20      -5.291  -0.139  22.750  0.50 25.73      
>       C
> ATOM    176  C  BSER A  20      -6.254   0.166  24.944  0.50 26.25      
>       C
> ATOM    177  O  ASER A  20      -6.480  -0.463  22.793  0.50 26.21      
>       O
> ATOM    178  O  BSER A  20      -7.348   0.525  25.439  0.50 27.13      
>       O
> ATOM    179  CB ASER A  20      -4.540  -2.530  22.712  0.50 25.71      
>       C
> ATOM    180  CB BSER A  20      -5.570  -1.510  26.607  0.50 24.71      
>       C
> ATOM    181  OG ASER A  20      -4.728  -2.715  24.098  0.50 25.54      
>       O
> ATOM    182  OG BSER A  20      -4.669  -0.508  27.054  0.50 24.26      
>       O
> ATOM    183  N  ASER A  21      -4.886   1.088  23.074  0.50 25.75      
>       N
> ATOM    184  N  BSER A  21      -5.466   1.026  24.306  0.50 26.72      
>       N
> ATOM    185  CA ASER A  21      -5.768   2.144  23.524  0.50 25.75      
>       C
> ATOM    186  CA BSER A  21      -5.907   2.416  24.149  0.50 27.32      
>       C
> ATOM    187  C  ASER A  21      -6.611   2.788  22.422  0.50 26.28      
>       C
> ATOM    188  C  BSER A  21      -6.794   2.644  22.931  0.50 27.72      
>       C
> ATOM    189  O  ASER A  21      -6.206   3.117  21.302  0.50 26.12      
>       O
> ATOM    190  O  BSER A  21      -6.464   2.331  21.778  0.50 28.30      
>       O
> ATOM    191  CB ASER A  21      -4.993   3.250  24.251  0.50 24.73      
>       C
> ATOM    192  CB BSER A  21      -4.704   3.354  24.068  0.50 26.81      
>       C
> ATOM    193  OG ASER A  21      -5.885   4.221  24.785  0.50 24.45      
>       O
> ATOM    194  OG BSER A  21      -5.089   4.561  23.427  0.50 27.93      
>       O
> ATOM    195  N  ASER A  22      -7.889   2.965  22.778  0.50 26.48      
>       N
> ATOM    196  N  BSER A  22      -7.965   3.250  23.169  0.50 27.84      
>       N
> ATOM    197  CA ASER A  22      -8.920   3.579  21.976  0.50 26.69      
>       C
> ATOM    198  CA BSER A  22      -8.918   3.570  22.113  0.50 27.56      
>       C
> ATOM    199  C  ASER A  22      -8.428   4.801  21.209  0.50 26.80      
>       C
> ATOM    200  C  BSER A  22      -8.537   4.831  21.343  0.50 27.43      
>       C
> ATOM    201  O  ASER A  22      -8.764   4.977  20.033  0.50 26.70      
>       O
> ATOM    202  O  BSER A  22      -9.053   5.066  20.240  0.50 27.39      
>       O
> ATOM    203  CB ASER A  22     -10.060   4.097  22.893  0.50 26.60      
>       C
> ATOM    204  CB BSER A  22     -10.326   3.759  22.688  0.50 27.51      
>       C
> ATOM    205  OG ASER A  22      -9.541   4.989  23.880  0.50 26.51      
>       O
> ATOM    206  OG BSER A  22     -10.313   4.024  24.085  0.50 26.99      
>       O
> ATOM    207  N   SER A  23      -7.640   5.631  21.902  1.00 27.00      
>       N
> ATOM    208  CA  SER A  23      -7.169   6.864  21.294  1.00 26.84      
>       C
> ATOM    209  C   SER A  23      -6.336   6.629  20.054  1.00 26.48      
>       C
> ATOM    210  O   SER A  23      -6.133   7.548  19.242  1.00 26.87      
>       O
> ATOM    211  CB  SER A  23      -6.294   7.609  22.306  1.00 28.70      
>       C
> ATOM    212  OG  SER A  23      -6.859   7.488  23.616  1.00 32.19      
>       O
> ATOM    213  N   ASN A  24      -5.845   5.405  19.860  1.00 25.76      
>       N
> ATOM    214  CA  ASN A  24      -5.059   5.083  18.679  1.00 25.09      
>       C
> ATOM    215  C   ASN A  24      -5.839   4.660  17.454  1.00 23.88      
>       C
> ATOM    216  O   ASN A  24      -5.270   4.417  16.381  1.00 23.10      
>       O
> ATOM    217  CB  ASN A  24      -4.125   3.903  19.074  1.00 28.98      
>       C
> ATOM    218  CG  ASN A  24      -2.816   4.508  19.592  1.00 31.51      
>       C
> ATOM    219  OD1 ASN A  24      -2.010   4.982  18.768  1.00 33.38      
>       O
> ATOM    220  ND2 ASN A  24      -2.623   4.518  20.908  1.00 32.55      
>       N
> ATOM    221  N   TYR A  25      -7.172   4.572  17.571  1.00 21.77      
>       N
> ATOM    222  CA  TYR A  25      -8.002   4.106  16.460  1.00 19.42      
>       C
> ATOM    223  C   TYR A  25      -7.721   4.816  15.163  1.00 18.30      
>       C
> ATOM    224  O   TYR A  25      -7.485   4.187  14.119  1.00 18.39      
>       O
> ATOM    225  CB  TYR A  25      -9.493   4.208  16.852  1.00 17.65      
>       C
> ATOM    226  CG  TYR A  25     -10.419   3.819  15.695  1.00 16.80      
>       C
> ATOM    227  CD1 TYR A  25     -10.770   2.507  15.449  1.00 15.58      
>       C
> ATOM    228  CD2 TYR A  25     -10.926   4.825  14.879  1.00 15.90      
>       C
> ATOM    229  CE1 TYR A  25     -11.574   2.188  14.353  1.00 16.54      
>       C
> ATOM    230  CE2 TYR A  25     -11.738   4.520  13.803  1.00 16.61      
>       C
> ATOM    231  CZ  TYR A  25     -12.059   3.198  13.561  1.00 15.96      
>       C
> ATOM    232  OH  TYR A  25     -12.862   2.927  12.478  1.00 17.88      
>       O
> ATOM    233  N   CYS A  26      -7.720   6.149  15.146  1.00 17.44      
>       N
> ATOM    234  CA  CYS A  26      -7.559   6.858  13.875  1.00 16.90      
>       C
> ATOM    235  C   CYS A  26      -6.186   6.627  13.271  1.00 17.07      
>       C
> ATOM    236  O   CYS A  26      -5.981   6.456  12.073  1.00 16.96      
>       O
> ATOM    237  CB  CYS A  26      -7.769   8.356  14.136  1.00 16.94      
>       C
> ATOM    238  SG  CYS A  26      -9.578   8.741  14.286  1.00 15.18      
>       S


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
+++++++
Michael Sierk, Postdoctoral Fellow             email:  
mls5w<AT>virginia<dot>edu
Biochemistry & Molecular Genetics Dept.    Phone (W): (434) 924-2821
University of Virginia                           (H): (434) 970-2268
------------------------------------------------------------------------ 
------
"There is something fascinating about science. One gets such wholesome
returns of conjecture out of such a trifling investment of fact."
-- Mark Twain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
+++++++



++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
+++++++
Michael Sierk, Postdoctoral Fellow             email:  
mls5w<AT>virginia<dot>edu
Biochemistry & Molecular Genetics Dept.    Phone (W): (434) 924-2821
University of Virginia                           (H): (434) 970-2268
------------------------------------------------------------------------ 
------
"There is something fascinating about science. One gets such wholesome
returns of conjecture out of such a trifling investment of fact."
-- Mark Twain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
+++++++

From letondal at pasteur.fr  Sat Apr 16 11:13:47 2005
From: letondal at pasteur.fr (Catherine Letondal)
Date: Sat Apr 16 11:03:33 2005
Subject: [BioPython] suggestions for Bio.PDB
Message-ID: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>

Hi,

Would it be possible for the get_structure() method in PDBParser to 
accept a filehandle, instead of just accepting just a filename?
That would be very nice to enable different origins for data (an url, a 
string + StringIO, a pipe, ...).

Another suggestion: it could be useful to keep a record of the read 
structure, just in case the user would like to benefit from biopython  
PDB modules, but also do some custom analysis.

My suggestions could be impleted like this:

     def get_structure(self, id, filename=None, filehandle=None):
         """Return the structure.

         Arguments:
         o id - string, the id that will be used for the structure
         o filename - name of the PDB file
         o filehandle - a filehandle on a PDB structure
         """
         self.header=None
         self.trailer=None
         # Make a StructureBuilder instance (pass id of structure as 
parameter)
         self.structure_builder.init_structure(id)
         if filename is None:
             file=open(filename)
         elif filehandle is not None:
             file = filehandle
         else:
             return None
         pdb_lines = file.readlines()
         self.pdb_text = "".join(pdb_lines)
         self._parse(pdb_lines)
         if filehandle is None:
             file.close()
         self.structure_builder.set_header(self.header)
         # Return the Structure instance
         return self.structure_builder.get_structure()


Thanks for providing this biopython PDB modules!


--
Catherine Letondal -- Institut Pasteur
www.pasteur.fr/~letondal

From biopython at maubp.freeserve.co.uk  Sat Apr 16 14:44:01 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat Apr 16 14:31:02 2005
Subject: [BioPython] Martel.Parser.ParserPositionException:
In-Reply-To: <425FC54C.7050006@gmx.de>
References: <425FC54C.7050006@gmx.de>
Message-ID: <42615CF1.7030306@maubp.freeserve.co.uk>

Marc Saric wrote:
> Hi all,
> 
> I tried to index the the following Genbank file with this simple script
> (as described in the cookbook) but it failed with the following traceback.
> 
> The file can be found in:
> 
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=BA000018
> 
> including all features (SNP, CDD, MGC, HPRD, STS)
> 
> I tried with Biopython 1.3, Biopython 1.4b and the Biopython-CVS as of
> 2005-04-15.
> 
> The program
> 
> ===snip===
> #!/usr/bin/env python
> from Bio import GenBank
> 
> dict_file = "ba000018_s_aureus_n315_genome.gb"
> index_file = "ba000018_s_aureus_n315_genome.idx"
> 
> GenBank.index_file(dict_file, index_file)

I have just tried this on Windows 2000 with Python 2.3, and suspect 
the problem may be due to an extra blank line at the very end of the 
file.

I went to the link you gave above, ticked the boxes for SNP, CDD, 
MGC, HPRD, STS and then clicked on the "Send" to file button.  This 
gave me a file that was about 5.6 MB in size, which I called 
ba000018_s_aureus_n315_genome.gb following your example.

Initially I got a very similar error to yours - in my case the exact 
position was 5887555, corresponding to the end of the file. I would 
assume the numerical difference is due to Windows versus Unix new 
line characters.

If I then edited the GenBank file to remove the final blank new 
line, the sample program seemed to work.

This should be a quick an easy thing for you to try, and if it does 
fix the error, I think we will have identified a minor bug...

Peter
From thamelry at binf.ku.dk  Sun Apr 17 09:03:15 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Sun Apr 17 09:37:37 2005
Subject: [BioPython] Alternate Conformations in PDB
In-Reply-To: <c17fc5ea6c96fa5014ae361d5e831cf7@virginia.edu>
References: <c17fc5ea6c96fa5014ae361d5e831cf7@virginia.edu>
Message-ID: <32815.83.92.3.59.1113742995.squirrel@www.binf.ku.dk>

> How does the PDB module deal with alternate conformations?  It appears
> to me that it is completely ignoring them, at least in the polypeptide
> builder.

Bio.PDB's representation of alternate conformation is actually quite
sophisticated IMO (it can even deal with point mutations, ie. for
example a Ser and a Pro residue in the same position).

OTOH CaPPBuilder indeed breaks the chain if it finds a disordered
CA atom, which is a bit questionable, especially since
PPBuilder does take disorder into account. So I'll submit a more
sophisticated version of CaPPBuilder to CVS today.

Best regards,

-Thomas

From thamelry at binf.ku.dk  Sun Apr 17 09:39:54 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Sun Apr 17 09:37:40 2005
Subject: [BioPython] suggestions for Bio.PDB
In-Reply-To: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
References: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
Message-ID: <32950.83.92.3.59.1113745194.squirrel@www.binf.ku.dk>

Hi,

> Would it be possible for the get_structure() method in PDBParser to
> accept a filehandle

You're not the first to suggest this - it's already in
the CVS version, also for generating PDB output with PDBIO.

> Another suggestion: it could be useful to keep a record of the read
> structure, just in case the user would like to benefit from biopython
> PDB modules, but also do some custom analysis.

I don't think this would be very useful, it's easy enough to just read in
the file separately.

BTW, I'm soon going to start to implement a parser for the new
PDB XML format. Any suggestions, comments, etc. regarding this
are welcome.

Cheers,

-Thomas

From dalke at dalkescientific.com  Sun Apr 17 12:59:54 2005
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Sun Apr 17 12:53:15 2005
Subject: [BioPython] suggestions for Bio.PDB
In-Reply-To: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
References: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
Message-ID: <55a2235c25137c06ff5da0b79071ee81@dalkescientific.com>

Catherine Letondal wrote:
> Would it be possible for the get_structure() method in PDBParser to 
> accept a filehandle, instead of just accepting just a filename?

>     def get_structure(self, id, filename=None, filehandle=None):
>         """Return the structure.

I've also seen this sort of API done like this

    def get_structure(self, id, infile):
       if isinstance(infile, basestring):
         infile = open(infile)

so that there is only one parameter instead of two.

					Andrew
					dalke@dalkescientific.com

From thamelry at binf.ku.dk  Sun Apr 17 13:05:43 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Sun Apr 17 13:09:27 2005
Subject: [BioPython] suggestions for Bio.PDB
In-Reply-To: <55a2235c25137c06ff5da0b79071ee81@dalkescientific.com>
References: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
	<55a2235c25137c06ff5da0b79071ee81@dalkescientific.com>
Message-ID: <33426.83.92.3.59.1113757543.squirrel@www.binf.ku.dk>

> Catherine Letondal wrote:
>> Would it be possible for the get_structure() method in PDBParser to
>> accept a filehandle, instead of just accepting just a filename?
>
>>     def get_structure(self, id, filename=None, filehandle=None):
>>         """Return the structure.
>
> I've also seen this sort of API done like this
>
>     def get_structure(self, id, infile):
>        if isinstance(infile, basestring):
>          infile = open(infile)
>
> so that there is only one parameter instead of two.

I used:

def get_structure(self, id, file):
    ...
    if type(file)==types.StringType:
            file=open(file)

So there's indeed only one parameter.
If 'file' is not a string it's assumed to have the
interface of a file handle.

-Thomas

From dalke at dalkescientific.com  Sun Apr 17 13:50:30 2005
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Sun Apr 17 13:43:59 2005
Subject: [BioPython] suggestions for Bio.PDB
In-Reply-To: <33426.83.92.3.59.1113757543.squirrel@www.binf.ku.dk>
References: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
	<55a2235c25137c06ff5da0b79071ee81@dalkescientific.com>
	<33426.83.92.3.59.1113757543.squirrel@www.binf.ku.dk>
Message-ID: <08a231012f0bd5886de1dc2b93f2835e@dalkescientific.com>

Hi Thomas,

> I used:
>
> def get_structure(self, id, file):
>     ...
>     if type(file)==types.StringType:
>             file=open(file)

You should use
   isinstance(file, basestring)

for two reasons.  As of a few Python releases ago, Python
allows unicode filenames but your check doesn't because

 >>> import types
 >>> type("") == types.StringType
True
 >>> type(u"") == types.StringType
False
 >>>

Also, some people do derive from string.  The most relevant
example is the 'path' module at
   http://www.jorendorff.com/articles/python/path/

which points out in the "Warts" section

      A function that checks the type of its parameters
      with code like if type(s) is type(''): ..., will
      fail to recognize a path object as a string. This
      may be considered a bug in the function, though.
      The test should be written
         if isinstance(s, (str, unicode)),
      or in Python 2.3,
         if isinstance(s, basestring),
      both of which allow for string subclasses.


					Andrew
					dalke@dalkescientific.com

From thamelry at binf.ku.dk  Sun Apr 17 14:03:23 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Sun Apr 17 14:04:33 2005
Subject: [BioPython] suggestions for Bio.PDB
In-Reply-To: <08a231012f0bd5886de1dc2b93f2835e@dalkescientific.com>
References: <a5032f81273d6fe27019eea821b551ab@pasteur.fr>
	<55a2235c25137c06ff5da0b79071ee81@dalkescientific.com>
	<33426.83.92.3.59.1113757543.squirrel@www.binf.ku.dk>
	<08a231012f0bd5886de1dc2b93f2835e@dalkescientific.com>
Message-ID: <33589.83.92.3.59.1113761003.squirrel@www.binf.ku.dk>


Andrew wrote:

> You should use
>    isinstance(file, basestring)
>
> for two reasons.  As of a few Python releases ago, Python
> allows unicode filenames but your check doesn't because
>
>  >>> import types
>  >>> type("") == types.StringType
> True
>  >>> type(u"") == types.StringType
> False

Thanks for pointing this out.
I've updated it in CVS.

Cheers,

-Thomas

From thamelry at binf.ku.dk  Sun Apr 17 14:10:56 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Sun Apr 17 14:04:35 2005
Subject: [BioPython] Alternate Conformations in PDB
In-Reply-To: <c17fc5ea6c96fa5014ae361d5e831cf7@virginia.edu>
References: <c17fc5ea6c96fa5014ae361d5e831cf7@virginia.edu>
Message-ID: <33606.83.92.3.59.1113761456.squirrel@www.binf.ku.dk>

> How does the PDB module deal with alternate conformations?  It appears
> to me that it is completely ignoring them, at least in the polypeptide
> builder.

I've updated CaPPBuilder in CVS and it works on your example
now. PPBuilder works in Biopython 1.4b for what you want, I'd
like to point out (since you have a full atom model).

Thanks for reporting the problem,

-Thomas

From eirik.sonneland at student.umb.no  Mon Apr 18 04:30:56 2005
From: eirik.sonneland at student.umb.no (=?ISO-8859-1?Q?Eirik_S=F8nneland?=)
Date: Mon Apr 18 04:27:12 2005
Subject: [BioPython] Name of database for NCBIWWW.qblast
Message-ID: <42637040.5030702@student.umb.no>

Dear all,

I'm writing my Master on SNP mining in BOS TAURUS (using Biopython) as a 
part of the BOVINE genome sequencing project. My question  is:

Q: from NCBI Trace Archives i get my FASTA and .scf 
files(chromatograms). I want to (MEGA)BLAST these FASTA files against 
the BOVINE CONTIGS using Biopython code:

 b_results = NCBIWWW.qblast('blastn', '???????', f_record).read().

When reading the NCBI infosite  I can find some databases but not the 
BOVINE CONTIGS on http://www.ncbi.nlm.nih.gov/BLAST/docs/netblast.html  
. What is the name of this database to put into my code?

An answer to this would really help allot! Please....:-)

Thank you !

Regards,
Eirik S?nneland
www.south-pole.net
From eirik.sonneland at student.umb.no  Mon Apr 18 04:30:56 2005
From: eirik.sonneland at student.umb.no (=?ISO-8859-1?Q?Eirik_S=F8nneland?=)
Date: Mon Apr 18 04:27:34 2005
Subject: [BioPython] Name of database for NCBIWWW.qblast
Message-ID: <42637040.5030702@student.umb.no>

Dear all,

I'm writing my Master on SNP mining in BOS TAURUS (using Biopython) as a 
part of the BOVINE genome sequencing project. My question  is:

Q: from NCBI Trace Archives i get my FASTA and .scf 
files(chromatograms). I want to (MEGA)BLAST these FASTA files against 
the BOVINE CONTIGS using Biopython code:

 b_results = NCBIWWW.qblast('blastn', '???????', f_record).read().

When reading the NCBI infosite  I can find some databases but not the 
BOVINE CONTIGS on http://www.ncbi.nlm.nih.gov/BLAST/docs/netblast.html  
. What is the name of this database to put into my code?

An answer to this would really help allot! Please....:-)

Thank you !

Regards,
Eirik S?nneland
www.south-pole.net
From idoerg at burnham.org  Tue Apr 19 13:29:16 2005
From: idoerg at burnham.org (Iddo Friedberg)
Date: Tue Apr 19 13:22:44 2005
Subject: [BioPython] BOSC 2005
Message-ID: <42653FEC.2010907@burnham.org>



{Please pass the word!}

SECOND CALL FOR SPEAKERS
 
The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 13th International Conference
on Intelligent Systems for Molecular Biology.
 
see http://www.iscb.org/ismb2005 for more information.
 
Because of the power of many Open Source bioinformatics packages in
use by the Research Community today, it is not too presumptuous to say 
that the work of the Open Source Bioinformatics Community represents 
the cutting edge of Bioinformatics in general. This has been repeatedly 
demonstrated by the quality of presentations at previous BOSC conferences.
This year, at BOSC 2005, we want to continue this tradition of excellence, 
while presenting this message to a wider part of the Research Community.  
Please, pass this message on to anyone you know that is interested in
Bioinformatics software. 
 
 
BOSC PROGRAM & CONTACT INFO

* Web: http://www.open-bio.org/bosc2005/
* Online Registration: https://www.cteusa.com/iscb4/
* Email: bosc@open-bio.org

FEES


* Corporate : $195 ($245 after May 16th)
* Academic : $170 ($220 after May 16th)
* Student : $145 ($195 after May 16th) 

SPEAKERS & ABSTRACTS WANTED

The program committee is currently seeking abstracts for talks at BOSC 
2005. BOSC is a great opportunity for you to tell the community about 
your use, development, or philosophy of open source software development 
in bioinformatics. The committee will select several submitted abstracts 
for 25-minute talks and others for shorter "lightning" talks. Accepted 
abstracts will be published on the BOSC web site.

If you are interested in speaking at BOSC 2005, 
please send us before April 26, 2005:

* an abstract (no more than a few paragraphs)
* a URL for the project page, if applicable
* information about the open source license used for your software or 
  your release plans.
 
Abstracts will be accepted for submission until April 26, 2005.
Abstracts chosen for presentation will be announced May 12, 2005 
(before the ISMB Early Registration Deadline).
 
LIGHTNING-TALK SPEAKERS WANTED!

The program committee is currently seeking speakers for the lightning 
talks at BOSC 2005. Lightning talks are quick - only five minutes 
long - and a great opportunity for you to give people a quick 
summary of your open source project, code, idea, or vision of the future.
 
If you are interested in giving a lightning talk at BOSC 2005, 
please send us:
 
* a brief title and summary (one or two lines)
* a URL for the project page, if applicable
* information about the open source license used for your software or 
  your release plans.
 
We will accept entries on-line until BOSC starts, but
space for demos and lightning talks is limited.<br/
   
SOFTWARE DEMONSTRATIONS WANTED!
If you are involved in the development of Open Source Bioinformatics Software, 
you are invited to provide a short demonstration to attendees of BOSC 2005.
 
If you are interested in giving a software demonstration at BOSC 2005,
please send us:
 
* a brief title and summary (one or two lines)
* a URL for the project page, if applicable
* Internet connectivity requirements (e.g. website Application served on the 
  world wide web, or web based client application).
 
  We will accept entries on-line until the BOSC starts, but
  space for demos and lightning talks is limited. 
 
 ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for
  projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy.
  See the following websites for further details:
  href="http://www.opensource.org/licenses/
  href="http://www.opensource.org/docs/definition.php
 
 
 SESSION CHAIRS WANTED
 If you would like to be involved BOSC 2005, we invite you to chair a session.  This will 
 not require much of your time.  You will be given a schedule of presenters during your session. 
 You simply introduce each speaker, and manage the time of their presentation (25 minutes for full 
 presentations, 5-10 minutes for lightning talks/demos, depending on the number of entries).
 
 If you are interested in chairing a session, please send us your name and affiliation (if applicable).
 
-- 
cheers,

Bosc Organizing Committee


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


From edeveaud at pasteur.fr  Thu Apr 21 05:11:19 2005
From: edeveaud at pasteur.fr (edeveaud@pasteur.fr)
Date: Thu Apr 21 05:12:14 2005
Subject: [BioPython] NCBIStandalone Parser problem
Message-ID: <20050421091119.GA12744@hebus.sis.pasteur.fr>

	Hi,
	
I just wanted to mention a problem with the NCBIStandalone Parser 

when I try to parse a blast nucleic report file with No hits found 
using the following code (reduced to the minimum)


saint-moret:~ > cat blast_pb.py
#! /local/cours/bin/python
from Bio.Blast import NCBIStandalone
import sys

blast_bin='/local/cours/bin/blastall'
blast_prog = 'blastn'
blastDB='/local/cours/bank/test_db'
query = sys.argv[1]

# blast exec
OUT, ERR = NCBIStandalone.blastall(blast_bin, blast_prog, blastDB, query)

# parser instanciation
parser=NCBIStandalone.BlastParser()

# parsing
record = parser.parse(OUT)



execution fails with the following traceback
saint-moret:~ > ./blast_pb.py query2
Traceback (most recent call last):
  File "./blast_pb.py", line 17, in ?
    record = parser.parse(OUT)
  File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
line 567, in parse
    self._scanner.feed(handle, self._consumer)
  File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
line 95, in feed
    self._scan_header(uhandle, consumer)
  File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
line 129, in _scan_header
    read_and_call_while(uhandle, consumer.noevent, blank=1)
  File "/local/cours/lib/python2.3/site-packages/Bio/ParserSupport.py", line
314, in read_and_call_while
    line = safe_readline(uhandle)
  File "/local/cours/lib/python2.3/site-packages/Bio/ParserSupport.py", line
411, in safe_readline
    raise SyntaxError, "Unexpected end of stream."
SyntaxError: Unexpected end of stream.

blast manualy run give me the following results



saint-moret:~ > blastall -p blastn -d /local/bank/hpylori/blast2/hp26695_genome
-i query2
BLASTN 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= no_hits
         (120 letters)

Database: Hpylori 
           1 sequences; 1,667,867 total letters

Searching[NULL_Caption] WARNING:  [000.000]  no_hits: SetUpBlastSearch failed.
[NULL_Caption] ERROR:  [000.000]  no_hits: BLASTSetUpSearch: Unable to
calculate Karlin-Altschul params, check query sequence
[NULL_Caption] ERROR:  [000.000]  no_hits: BLASTSetUpSearch: Unable to
calculate Karlin-Altschul params, check query sequence
done

 ***** No hits found ******

  Database: Hpylori
    Posted date:  May 3, 2004  3:55 AM
  Number of letters in database: 1,667,867
  Number of sequences in database:  1
  
Lambda     K      H
   -1.00    -1.00    -1.00 




the parser works perfectly with blastn reports with hits.
we discover the problem, trying to work on a blast report of multiple sequences
versus one bank using the NCBIStandalone.iterator.

some details
running Python 2.3.4, Biopython 1.30 and blastall 2.2.10 Release on MacOSX 

	thank's for any information 

	Eric

From aurelie.bornot at free.fr  Mon Apr 25 05:42:29 2005
From: aurelie.bornot at free.fr (aurelie.bornot@free.fr)
Date: Mon Apr 25 05:35:59 2005
Subject: [BioPython] Big GenBank files 
Message-ID: <1114422149.426cbb8506bc7@imp4-q.free.fr>

Hi !

I am trying to make a program that do automatically blasts of a base of
sequences against the genbank sequences. And I would like to retrieve (also
automatically) the most interesting GenBank files..... to keep informations
about them in my database.

But I've got a problem (again..sorry ! :'( ) :

I've 2*512 Mega of RAM but it seems that my computer can't deal with 'big'
GenBank files like 'BA000028.3'(7 M) or 'AP008212' (37 M)

for example :
fichier = open('AP008212.fasta',"w")
record_parser = GenBank.RecordParser()
ncbi_dict = GenBank.NCBIDictionary ('nucleotide','genbank',parser=record_parser)
gb_record = ncbi_dict['AP008212']
fichier.close()

...never ends...
I suppose it is because the files are to big for the algo of the transformation
in registry....
For 'AP008212' (37 M) :
ncbi_dict = GenBank.NCBIDictionary ('nucleotide','fasta')
doesn't works either...


I tried to understand how all this works to try to retrieve the header of the
connexion (maybe there is a possibility of give up the download of these big
files...) but I am not very used to python and to all that concern
connexions...
I have been on this problem for 3 days... and I am lost...
I don't known what to do...
Could someone help me ?!

Thanks !
Aurelie



From biopython at maubp.freeserve.co.uk  Mon Apr 25 07:16:35 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon Apr 25 07:15:37 2005
Subject: [BioPython] Big GenBank files
In-Reply-To: <1114422149.426cbb8506bc7@imp4-q.free.fr>
References: <1114422149.426cbb8506bc7@imp4-q.free.fr>
Message-ID: <426CD193.5030801@maubp.freeserve.co.uk>

aurelie.bornot@free.fr wrote:
> Hi !
> 
> I am trying to make a program that do automatically blasts of a base of
> sequences against the genbank sequences. And I would like to retrieve (also
> automatically) the most interesting GenBank files..... to keep informations
> about them in my database.
> 
> But I've got a problem (again..sorry ! :'( ) :
> 
> I've 2*512 Mega of RAM but it seems that my computer can't deal with 'big'
> GenBank files like 'BA000028.3'(7 M) or 'AP008212' (37 M)

Have a look at bug 1747 which should help with reading large GenBank 
files (however I'm not sure if it will affect GenBank.NCBIDictionary)

http://bugzilla.open-bio.org/show_bug.cgi?id=1747

The test code used was based on Section 3.4.2 of the Tutorial, Parsing 
GenBank records:

http://www.biopython.org/docs/tutorial/Tutorial.html#htoc35

See also the discussion last month:-

http://www.biopython.org/pipermail/biopython/2005-March/002568.html

Peter

-- 
PhD Student
MOAC Doctoral Training Centre
University of Warwick, UK
From julie.bernauer at ibbmc.u-psud.fr  Mon Apr 25 07:47:50 2005
From: julie.bernauer at ibbmc.u-psud.fr (Julie Bernauer)
Date: Mon Apr 25 07:45:48 2005
Subject: [BioPython] Psi blast
Message-ID: <1114429670.9366.8.camel@fifi.ibbmc.u-psud.fr>

Hello !

I hope this question hasn't been answered yet. Please excuse me in case
it has.

I'd like to get the result of phi-blast after 5 runs (html page):

Here is a piece of my code :

while 1:
                cur_record=s_iterator.next()
                if cur_record is None:
                        break

                f_record=Fasta.Record()
                f_record.title=cur_record.accessions[0]
                f_record.sequence=cur_record.sequence
                print f_record.title

                b_results=NCBIWWW.qblast('blastp','swissprot',f_record)
                save_file=open('resultats/blast/'+id+'.html','w')
                blast_results=b_results.read()
                save_file.write(blast_results)
                save_file.close()

I's like to have sthg like :
b_results=NCBIWWW.qblast('blastp','swissprot',f_record,run_psiblast=5)

Would you please help me ?

Thanks in advance

-- 
Julie BERNAUER
Equipe de G?nomique Structurale          http://www.genomics.eu.org
IBBMC - UMR 8619 - U.P.S. B?t.430          Tel. : +33 1 69 15 31 57
91405 Orsay - FRANCE                       Fax. : +33 1 69 85 37 15

From mdehoon at ims.u-tokyo.ac.jp  Tue Apr 26 04:25:59 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Tue Apr 26 04:17:04 2005
Subject: [BioPython] NCBIStandalone Parser problem
In-Reply-To: <20050421091119.GA12744@hebus.sis.pasteur.fr>
References: <20050421091119.GA12744@hebus.sis.pasteur.fr>
Message-ID: <426DFB17.5010409@ims.u-tokyo.ac.jp>

Could you try this again with Biopython version 1.40b and see if the problem 
still occurs there? If so, could you send me the query that you are using so I 
can replicate this error?

--Michiel.

edeveaud@pasteur.fr wrote:

> 	Hi,
> 	
> I just wanted to mention a problem with the NCBIStandalone Parser 
> 
> when I try to parse a blast nucleic report file with No hits found 
> using the following code (reduced to the minimum)
> 
> 
> saint-moret:~ > cat blast_pb.py
> #! /local/cours/bin/python
> from Bio.Blast import NCBIStandalone
> import sys
> 
> blast_bin='/local/cours/bin/blastall'
> blast_prog = 'blastn'
> blastDB='/local/cours/bank/test_db'
> query = sys.argv[1]
> 
> # blast exec
> OUT, ERR = NCBIStandalone.blastall(blast_bin, blast_prog, blastDB, query)
> 
> # parser instanciation
> parser=NCBIStandalone.BlastParser()
> 
> # parsing
> record = parser.parse(OUT)
> 
> 
> 
> execution fails with the following traceback
> saint-moret:~ > ./blast_pb.py query2
> Traceback (most recent call last):
>   File "./blast_pb.py", line 17, in ?
>     record = parser.parse(OUT)
>   File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
> line 567, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
> line 95, in feed
>     self._scan_header(uhandle, consumer)
>   File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
> line 129, in _scan_header
>     read_and_call_while(uhandle, consumer.noevent, blank=1)
>   File "/local/cours/lib/python2.3/site-packages/Bio/ParserSupport.py", line
> 314, in read_and_call_while
>     line = safe_readline(uhandle)
>   File "/local/cours/lib/python2.3/site-packages/Bio/ParserSupport.py", line
> 411, in safe_readline
>     raise SyntaxError, "Unexpected end of stream."
> SyntaxError: Unexpected end of stream.
> 
> blast manualy run give me the following results
> 
> 
> 
> saint-moret:~ > blastall -p blastn -d /local/bank/hpylori/blast2/hp26695_genome
> -i query2
> BLASTN 2.2.10 [Oct-19-2004]
> 
> 
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= no_hits
>          (120 letters)
> 
> Database: Hpylori 
>            1 sequences; 1,667,867 total letters
> 
> Searching[NULL_Caption] WARNING:  [000.000]  no_hits: SetUpBlastSearch failed.
> [NULL_Caption] ERROR:  [000.000]  no_hits: BLASTSetUpSearch: Unable to
> calculate Karlin-Altschul params, check query sequence
> [NULL_Caption] ERROR:  [000.000]  no_hits: BLASTSetUpSearch: Unable to
> calculate Karlin-Altschul params, check query sequence
> done
> 
>  ***** No hits found ******
> 
>   Database: Hpylori
>     Posted date:  May 3, 2004  3:55 AM
>   Number of letters in database: 1,667,867
>   Number of sequences in database:  1
>   
> Lambda     K      H
>    -1.00    -1.00    -1.00 
> 
> 
> 
> 
> the parser works perfectly with blastn reports with hits.
> we discover the problem, trying to work on a blast report of multiple sequences
> versus one bank using the NCBIStandalone.iterator.
> 
> some details
> running Python 2.3.4, Biopython 1.30 and blastall 2.2.10 Release on MacOSX 
> 
> 	thank's for any information 
> 
> 	Eric
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
> 

-- 
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
From gvwilson at cs.utoronto.ca  Tue Apr 26 13:34:35 2005
From: gvwilson at cs.utoronto.ca (Greg Wilson)
Date: Tue Apr 26 15:40:20 2005
Subject: [BioPython] ann: Data Crunching
Message-ID: <d4ltp1$37n$7@sea.gmane.org>

Readers of this newsgroup might be interested in a new book on data 
crunching, which is available from Amazon:

http://www.amazon.com/exec/obidos/ASIN/0974514071

or directly from the Pragmatic Programmers:

http://www.pragmaticprogrammer.com/titles/gwd/index.html

The book covers basic text processing, regular expressions, XML 
manipulation, binary data handling, and the 10% of relational databases 
that every programmer should know.  Most of the examples are in Python 
(though Unix command line tools, XSL, and SQL are in there as well). 
The book is aimed at beginner and intermediate programmers; I hope that 
people with a background in science and engineering will find it 
particularly useful.

Thanks,
Greg Wilson (its grinning author)

From pap501 at york.ac.uk  Tue Apr 26 17:04:27 2005
From: pap501 at york.ac.uk (pap501@york.ac.uk)
Date: Tue Apr 26 16:57:38 2005
Subject: [BioPython] ann: Data Crunching
In-Reply-To: <d4ltp1$37n$7@sea.gmane.org>
References: <d4ltp1$37n$7@sea.gmane.org>
Message-ID: <Prayer.1.0.10.0504262204270.11118@webmail1.york.ac.uk>

No thanks

there was an email circulated before about books not to buy and yours is 
one of them

On Apr 26 2005, Greg Wilson wrote:

> Readers of this newsgroup might be interested in a new book on data 
> crunching, which is available from Amazon:
> 
> http://www.amazon.com/exec/obidos/ASIN/0974514071
> 
> or directly from the Pragmatic Programmers:
> 
> http://www.pragmaticprogrammer.com/titles/gwd/index.html
> 
> The book covers basic text processing, regular expressions, XML 
> manipulation, binary data handling, and the 10% of relational databases 
> that every programmer should know.  Most of the examples are in Python 
> (though Unix command line tools, XSL, and SQL are in there as well). 
> The book is aimed at beginner and intermediate programmers; I hope that 
> people with a background in science and engineering will find it 
> particularly useful.
> 
> Thanks,
> Greg Wilson (its grinning author)
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
From gvwilson at cs.utoronto.ca  Tue Apr 26 17:20:30 2005
From: gvwilson at cs.utoronto.ca (Greg Wilson)
Date: Tue Apr 26 17:17:42 2005
Subject: [BioPython] ann: Data Crunching
In-Reply-To: <Prayer.1.0.10.0504262204270.11118@webmail1.york.ac.uk>
References: <d4ltp1$37n$7@sea.gmane.org>
	<Prayer.1.0.10.0504262204270.11118@webmail1.york.ac.uk>
Message-ID: <d4mb0j$gr$1@sea.gmane.org>

 > Phil [pap501@york.ac.uk] wrote:
> No thanks
> 
> there was an email circulated before about books not to buy and yours is 
> one of them

Wow, that was quick --- it's only been on the market two weeks.  I'd be 
grateful if you could point me at the "don't buy" message; I'd obviously 
be interested in finding out what I got wrong.

Thanks,
Greg

>> Readers of this newsgroup might be interested in a new book on data 
>> crunching, which is available from Amazon:
>>
>> http://www.amazon.com/exec/obidos/ASIN/0974514071
>>
>> or directly from the Pragmatic Programmers:
>>
>> http://www.pragmaticprogrammer.com/titles/gwd/index.html

From pap501 at york.ac.uk  Tue Apr 26 17:47:08 2005
From: pap501 at york.ac.uk (pap501@york.ac.uk)
Date: Tue Apr 26 17:40:30 2005
Subject: Fwd: Re: [BioPython] ann: Data Crunching
Message-ID: <Prayer.1.0.10.0504262247080.12530@webmail1.york.ac.uk>

Dear all

Sorry for the previous email.

A friend of mine thought it would be funny to send an email while I was 
away from my computer.

I have apologised to Greg and hopefully he accepts my apologies



---------- Forwarded message ----------
From: pap501@york.ac.uk
To: Greg Wilson <gvwilson@cs.utoronto.ca>
Subject: Re: [BioPython] ann: Data Crunching
Date: 26 Apr 2005 22:42:40 +0100

Dear Greg

Sorry my friend thought it would be funny to send an email while I wasnt at 
my computer! I am doing my MRes bioinformatics at York university, England 
and would be interested in a book like yours. Do you have a link to more 
details about your book?

I am rather embarassed that you forwarded the email to biopython as some of 
my lecturers are in the email list!

Best wishes 

Phil

On Apr 26 2005, Greg Wilson wrote:

>  > Phil [pap501@york.ac.uk] wrote:
> > No thanks
> > 
> > there was an email circulated before about books not to buy and yours 
> > is one of them
> 
> Wow, that was quick --- it's only been on the market two weeks.  I'd be 
> grateful if you could point me at the "don't buy" message; I'd obviously 
> be interested in finding out what I got wrong.
> 
> Thanks,
> Greg
> 
> >> Readers of this newsgroup might be interested in a new book on data 
> >> crunching, which is available from Amazon:
> >>
> >> http://www.amazon.com/exec/obidos/ASIN/0974514071
> >>
> >> or directly from the Pragmatic Programmers:
> >>
> >> http://www.pragmaticprogrammer.com/titles/gwd/index.html
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 

From gvwilson at cs.utoronto.ca  Tue Apr 26 18:31:39 2005
From: gvwilson at cs.utoronto.ca (Greg Wilson)
Date: Tue Apr 26 18:27:34 2005
Subject: Fwd: Re: [BioPython] ann: Data Crunching
In-Reply-To: <Prayer.1.0.10.0504262247080.12530@webmail1.york.ac.uk>
References: <Prayer.1.0.10.0504262247080.12530@webmail1.york.ac.uk>
Message-ID: <d4mf5v$dvl$1@sea.gmane.org>

> Dear all
> Sorry for the previous email.
> A friend of mine thought it would be funny to send an email while I was 
> away from my computer.

Don't ya hate it when that happens? ;-)  Sorry for replying here before
checking with Phil --- hope his friend gets sent to bed without supper.

Thanks,
Greg

From fkauff at duke.edu  Wed Apr 27 10:14:12 2005
From: fkauff at duke.edu (Frank Kauff)
Date: Wed Apr 27 10:09:34 2005
Subject: [BioPython] drawing trees
Message-ID: <1114611252.4523.12.camel@osiris.biology.duke.edu>

Hi all,

it's a little bit off topic, but anyway: I need to print phylogenetic
trees. drawtree.py from Rick Ree does a very nice job generating pdf or
eps files, but the trees are always printed on only one page. If the
trees are large, squeezing them into in page makes the output
unreadlible. Does anybody know a easy way to manipulate a eps or pdf
file or to tell my printer somehow to print a file streched over
multiple pages?

Thanks,
Frank

From karthik at rishi.serc.iisc.ernet.in  Thu Apr 28 06:34:08 2005
From: karthik at rishi.serc.iisc.ernet.in (Karthik Raman)
Date: Thu Apr 28 05:55:45 2005
Subject: [BioPython] Help with Biopython BLAST
Message-ID: <Pine.LNX.4.58.0504281602540.26146@tycho.serc.iisc.ernet.in>

Hi

How do I access query_letters from Blast Headers?

I've been trying to access it as b_record (from the standard example in 
the cookbook):

b_record.header.query_letters

What is the mistake I am doing?

Regards

Karthik

********************************************************

    KARTHIK RAMAN
    Graduate Research Student
    Supercomputer Education and Research Centre
    Indian Institute of Science
    Bangalore - 560 012

    Phone: +91-80-22932469 (Ext 24)
	   +91-80-23601409 (Ext 24)			
           +91-98862-22404 (Mobile)
	
    E-mail  :  karthik AT rishi.serc.iisc.ernet.in
    Webpage :  http://rishi.serc.iisc.ernet.in/~karthik/
    Blog    :  karthikraman.blogspot.com

*******************************************************

From mdehoon at ims.u-tokyo.ac.jp  Thu Apr 28 08:05:23 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Thu Apr 28 07:53:21 2005
Subject: [BioPython] Help with Biopython BLAST
In-Reply-To: <Pine.LNX.4.58.0504281602540.26146@tycho.serc.iisc.ernet.in>
References: <Pine.LNX.4.58.0504281602540.26146@tycho.serc.iisc.ernet.in>
Message-ID: <4270D183.90403@ims.u-tokyo.ac.jp>

You can check b_record.__dict__.keys() to find out the members of b_record.

It appears that you should use b_record.query_letters instead of 
b_record.header.query_letters.

--Michiel.

Karthik Raman wrote:

> Hi
> 
> How do I access query_letters from Blast Headers?
> 
> I've been trying to access it as b_record (from the standard example in 
> the cookbook):
> 
> b_record.header.query_letters
> 
> What is the mistake I am doing?
> 
> Regards
> 
> Karthik
> 
> ********************************************************
> 
>     KARTHIK RAMAN
>     Graduate Research Student
>     Supercomputer Education and Research Centre
>     Indian Institute of Science
>     Bangalore - 560 012
> 
>     Phone: +91-80-22932469 (Ext 24)
> 	   +91-80-23601409 (Ext 24)			
>            +91-98862-22404 (Mobile)
> 	
>     E-mail  :  karthik AT rishi.serc.iisc.ernet.in
>     Webpage :  http://rishi.serc.iisc.ernet.in/~karthik/
>     Blog    :  karthikraman.blogspot.com
> 
> *******************************************************
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
> 

-- 
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
From MAG at Stowers-Institute.org  Fri Apr 29 10:40:07 2005
From: MAG at Stowers-Institute.org (Goel, Manisha)
Date: Fri Apr 29 10:35:08 2005
Subject: [BioPython] Reading in many multiple seq alignmnet for substitution
	matrices
Message-ID: <200504291433.j3TEXAfY006631@portal.open-bio.org>

Hi,

I have been trying to use the SubsMat module to make substitution
matrices for my data.
All seems to be fine except that I need help with the following two
issues -
1) My data is in the form of many multiple sequence alignments .. Can I
read all these MSAs in sequentially and generate a common replace_info
at the end.
2) What other format can be read in for MSA except Clustalw.

-Thanks for all the help.


-Manisha Goel

Post-doc Associate
1000E 50th St.
Kansas city MO-64110