From eirik.sonneland at student.umb.no  Tue Mar  1 03:43:47 2005
From: eirik.sonneland at student.umb.no (=?ISO-8859-1?Q?Eirik_S=F8nneland?=)
Date: Tue Mar  1 03:38:58 2005
Subject: [BioPython] Human genome
Message-ID: <42242B43.4000100@student.umb.no>

Hi!

Need to Blast my sequence file against the human genome. Have tried to 
search http://www.ncbi.nlm.nih.gov/BLAST/docs/netblast.html for finding 
this database to put into the following code (as second argument):

NCBIWWW.qblast('blastn', '???', f_record),

Have anybody knowledge  of the name of this parameter ??

Would be highly appreciated!

cheers,
Eirik
From eirik.sonneland at student.umb.no  Tue Mar  1 04:34:38 2005
From: eirik.sonneland at student.umb.no (=?ISO-8859-1?Q?Eirik_S=F8nneland?=)
Date: Tue Mar  1 04:30:34 2005
Subject: [BioPython] Human genome
In-Reply-To: <42242EE4.4080101@mpiib-berlin.mpg.de>
References: <42242B43.4000100@student.umb.no>
	<42242EE4.4080101@mpiib-berlin.mpg.de>
Message-ID: <4224372E.1040102@student.umb.no>

Hi & thanks for replying!

Yes, I'm aware of the cookbook and the links to NCBI, but it doesn't 
seem to be any database which is only for human, as there is for 
forexample "Drosophila genom".
Interesting aspect that you've changed to standalone blast and that it 
isn't faster...hmmm,


regards
Eirik

DroMartina wrote:

> Hallo Eirik,
>
> have a look at the cookbook:
> http://www.biopython.org/docs/tutorial/Tutorial004.html#toc10
>
> I just tried to do the same, but each query took 1-2min. So I switched 
> to standalone Blast, but its not faster yet.
>
> Martina
>
> Eirik S?nneland wrote:
>
>> Hi!
>>
>> Need to Blast my sequence file against the human genome. Have tried 
>> to search http://www.ncbi.nlm.nih.gov/BLAST/docs/netblast.html for 
>> finding this database to put into the following code (as second 
>> argument):
>>
>> NCBIWWW.qblast('blastn', '???', f_record),
>>
>> Have anybody knowledge  of the name of this parameter ??
>>
>> Would be highly appreciated!
>>
>> cheers,
>> Eirik
>> _______________________________________________
>> BioPython mailing list  -  BioPython@biopython.org
>> http://biopython.org/mailman/listinfo/biopython
>

From idoerg at burnham.org  Tue Mar  1 20:47:28 2005
From: idoerg at burnham.org (Iddo Friedberg)
Date: Tue Mar  1 20:42:22 2005
Subject: [BioPython] PDB import thingy?
Message-ID: <42251B30.2030306@burnham.org>

Hi,

I tried this PDB import (it's part of som really old code I have), and 
got the following:

Python 2.3.3 (#2, Feb 17 2004, 11:45:40)
[GCC 3.3.2 (Mandrake Linux 10.0 3.3.2-6mdk)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> from PDBUtil import PDBUtil
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/idoerg/soft/PDBUtil/PDBUtil.py", line 7, in ?
    from Bio.PDB.PDBParser import PDBParser
  File 
"/home/idoerg/biopy_cvs/biopython/build/lib.linux-i686-2.3/Bio/PDB/__init__.py", 
line 13, in ?
    from MMCIFParser import MMCIFParser
  File 
"/home/idoerg/biopy_cvs/biopython/build/lib.linux-i686-2.3/Bio/PDB/MMCIFParser.py", 
line 6, in ?
    from MMCIF2Dict import MMCIF2Dict
  File 
"/home/idoerg/biopy_cvs/biopython/build/lib.linux-i686-2.3/Bio/PDB/MMCIF2Dict.py", 
line 2, in ?
    import Bio.PDB.mmCIF.MMCIFlex
ImportError: No module named MMCIFlex


Curiously enough, the second import works.

 >>> from PDBUtil import PDBUtil
 >>>



Huh?

./I

-- 
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 fkauff at duke.edu  Wed Mar  2 09:04:09 2005
From: fkauff at duke.edu (Frank Kauff)
Date: Wed Mar  2 08:59:00 2005
Subject: [BioPython] Human genome
In-Reply-To: <4224372E.1040102@student.umb.no>
References: <42242B43.4000100@student.umb.no>
	<42242EE4.4080101@mpiib-berlin.mpg.de>
	<4224372E.1040102@student.umb.no>
Message-ID: <1109772250.5116.5.camel@osiris.biology.duke.edu>

On Tue, 2005-03-01 at 10:34 +0100, Eirik S?nneland wrote:
> Hi & thanks for replying!
> 
> Yes, I'm aware of the cookbook and the links to NCBI, but it doesn't 
> seem to be any database which is only for human, as there is for 
> forexample "Drosophila genom".
> Interesting aspect that you've changed to standalone blast and that it 
> isn't faster...hmmm,
> 

Standalone blast needs a lot of resources on your local computer, of
which often memory is the bottleneck. Without plenty of memory, blast
can't keep the database in ram and the search takes quite a long time.
The nt database on a local machine with less than a few GB of ram can be
rather stressful for your harddisk. NCBI on the other side can be very
fast, e.g. if you're blasting during the (US) night or early morning. 

Frank

> regards
> Eirik
> 
> DroMartina wrote:
> 
> > Hallo Eirik,
> >
> > have a look at the cookbook:
> > http://www.biopython.org/docs/tutorial/Tutorial004.html#toc10
> >
> > I just tried to do the same, but each query took 1-2min. So I switched 
> > to standalone Blast, but its not faster yet.
> >
> > Martina
> >
> > Eirik S?nneland wrote:
> >
> >> Hi!
> >>
> >> Need to Blast my sequence file against the human genome. Have tried 
> >> to search http://www.ncbi.nlm.nih.gov/BLAST/docs/netblast.html for 
> >> finding this database to put into the following code (as second 
> >> argument):
> >>
> >> NCBIWWW.qblast('blastn', '???', f_record),
> >>
> >> Have anybody knowledge  of the name of this parameter ??
> >>
> >> Would be highly appreciated!
> >>
> >> cheers,
> >> Eirik
> >> _______________________________________________
> >> BioPython mailing list  -  BioPython@biopython.org
> >> http://biopython.org/mailman/listinfo/biopython
> >
> 
> _______________________________________________
> 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 thamelry at binf.ku.dk  Wed Mar  2 10:41:39 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Wed Mar  2 12:35:46 2005
Subject: [BioPython] PDB import thingy?
In-Reply-To: <42251B30.2030306@burnham.org>
References: <42251B30.2030306@burnham.org>
Message-ID: <35879.83.92.3.59.1109778099.squirrel@www.binf.ku.dk>


> ImportError: No module named MMCIFlex

See if the C/Flex module is compiled in Bio/PDB/mmCIF.
Maybe this is another of my modules that should be disabled
by default, this time because because it depends on Flex.

I should really stop using 'fancy' stuff like C++ or lex,
apparantly :-)

Cheers,

-Thomas

From scott.rifkin at yale.edu  Fri Mar  4 17:15:08 2005
From: scott.rifkin at yale.edu (Scott Rifkin)
Date: Fri Mar  4 19:53:40 2005
Subject: [BioPython] kcluster and distances
Message-ID: <Pine.LNX.4.44.0503041648310.19193-100000@argos.its.yale.edu>

The euclidean distance function in cluster.c is:

{ double result = 0.;
  double tweight = 0;
  int i;
  if (transpose==0) /* Calculate the distance between two rows */
  { for (i = 0; i < n; i++)
    { if (mask1[index1][i] && mask2[index2][i])
      { double term = data1[index1][i] - data2[index2][i];
        result = result + weight[i]*term*term;
        tweight += weight[i];
      }
    }
  }
  else
  { for (i = 0; i < n; i++)
    { if (mask1[i][index1] && mask2[i][index2])
      { double term = data1[i][index1] - data2[i][index2];
        result = result + weight[i]*term*term;
        tweight += weight[i];
      }
    }
  }
  if (!tweight) return 0; /* usually due to empty clusters */
  result /= tweight;
  result *= n;
  return result;
}

why at the end is the result multiplied by n?  and why isn't the square 
root of result given as the distance?

thanks
scott rifkin



From mdehoon at ims.u-tokyo.ac.jp  Sat Mar  5 00:05:49 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Sat Mar  5 00:01:02 2005
Subject: [BioPython] kcluster and distances
In-Reply-To: <Pine.LNX.4.44.0503041648310.19193-100000@argos.its.yale.edu>
References: <Pine.LNX.4.44.0503041648310.19193-100000@argos.its.yale.edu>
Message-ID: <42293E2D.7080409@ims.u-tokyo.ac.jp>

Scott Rifkin wrote:
> The euclidean distance function in cluster.c is:
> 
> { double result = 0.;
 > ...
>   result /= tweight;
>   result *= n;
>   return result;
> }
> 
> why at the end is the result multiplied by n?

Typically, all the weights are one. Then tweight is equal to n, and the 
result is equal to the usual definition of the Euclidean distance.

In the latest version of the C Clustering Library (which is not yet 
uploaded to the Biopython CVS), I removed the multiplication by n. The 
euclid function then returns the mean square distance, which may be 
easier to interpret.

> and why isn't the square root of result given as the distance?

Taking the square root adds another calculation step, but won't affect 
the (hierarchical) clustering result. So we may as well leave it out. If 
desired, users can take the square root of the node distances after the 
clustering calculation has finished.

Within the context of k-means clustering, not taking the square root is 
actually the right thing, as we want to minimize the sum of square 
distances.

--Michiel.
From mdehoon at ims.u-tokyo.ac.jp  Mon Mar  7 06:19:28 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Mon Mar  7 06:19:29 2005
Subject: [BioPython] Removing spam from the biopython-dev archives
Message-ID: <422C38C0.6060300@ims.u-tokyo.ac.jp>

Dear Biopythoneers,

I have good news and bad news for you. The good news is that the 
biopython-dev mailing list archives are now spam-free. See
http://www.biopython.org/pipermail/biopython-dev/
If you sent a message to biopython-dev during the past couple of days, 
it may be missing in the archives. If you find out that a message you 
sent is missing, please send it again to make sure that it is preserved 
for future generations of Biopythoneers.

The bad news is that when the biopython-dev archive was replaced on the 
biopython.org webserver, the source file for the biopython archive was 
accidentally overwritten. The biopython archive is still there, but the 
source file from which the archives are generated is not. There is a 
backup file until about March 2004, but for messages between March 2004 
and early March 2005 we no longer have the source file. If you happen to 
have a copy of these messages, please let us know.

--Michiel.
From wong at ebgm.jussieu.fr  Mon Mar  7 09:51:36 2005
From: wong at ebgm.jussieu.fr (WONG Hua)
Date: Mon Mar  7 09:46:30 2005
Subject: [BioPython] non root having problem to install biopython 1.40
Message-ID: <20050307145136.GA7691@bach.ebgm.jussieu.fr>

I am trying to install the new version of biopython 1.40

I am surprised to see that the "Numeric" tweaks I did on the setup.py doesn't seems to work :(

Here is the line:

NUMPY_EXTENSIONS = [
    Extension('Bio.Cluster.cluster',
              ['Bio/Cluster/clustermodule.c',
               'Bio/Cluster/cluster.c',
               'Bio/Cluster/ranlib.c',
               'Bio/Cluster/com.c',
               'Bio/Cluster/linpack.c'],
              include_dirs=["Bio/Cluster","users/invites/wong/module/include/python2.3/Numeric"]
              ),

And the error:

running build_ext
building 'Bio.Cluster.cluster' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -D_GNU_SOURCE -fPIC -fPIC -IBio/Cluster -Iusers/invites/wong/module/include/python2.3 -I/usr/include/python2.3 -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-2.3/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:2:33: Numeric/arrayobject.h: No such file or directory

...followed by various Bio/Cluster/clustermodule.c: errors...


Although I modified this line, it still can't find Numeric.
Worst is that in fact I don't even need or use the cluster and trees feature...
I am mostly interested in the Bio.PDB part.
Numeric is properly installed (not in root directories, but it is installed). "Import Numeric" works fine when running Python.

Is there a way I can shortcircuit this?

Else, what have I forgot to do in order to point where Numeric is?

Thanks

Wong Hua

#####################################################################
6  Notes for installing with non-administrator permissions
# That's exactly me

Building some C modules, such as Bio.Cluster require that the Numeric include files (normally installed in your_dir/include/python/Numeric) be available. If the compiler can't find these directories you'll normally get an error like:

Bio/Cluster/clustermodule.c:2: Numeric/arrayobject.h: No such file or directory
    

Followed by a long messy list of syntax errors. ##Exact

To fix this, you'll have to edit the setup.py file to let it know where the include directories are located. Look for the line in setup.py that looks like:

    include_dirs=["Bio/Cluster"]
    

and adjust it so that it includes the include directory where the numeric libraries were installed:

    include_dirs=["Bio/Cluster", "your_dir/include/python"]
    

Then you should be able to install everything happily.
# No happy endings :(


From jtk at cmp.uea.ac.uk  Mon Mar  7 12:02:45 2005
From: jtk at cmp.uea.ac.uk (Jan T. Kim)
Date: Mon Mar  7 11:00:47 2005
Subject: [BioPython] Minor GenBank Parsing Problems
Message-ID: <20050307170245.GE32158@jtkpc.cmp.uea.ac.uk>

Dear All,

I have noticed the following problems with the Bio.GenBank.FeatureParser:

    * The parser appears to depend on additional information in the
      LOCUS line, it works with

        LOCUS       U00096               4639675 bp    DNA     circular BCT 24-JUN-2004
      while the undecorated line

        LOCUS       U00096

      results in a Martel.Parser.ParserPositionException.

    * The parser also doesn't like some accession types, the line

        ACCESSION   U00096 AE000111-AE000510

      while trimming that to

        ACCESSION   U00096

      results in a file that now parses ok.

Are these known problems? I would assume that this could be fixed by
modifying some regular expressions somewhere in the parser. Should I
try to look into this?

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 thamelry at binf.ku.dk  Mon Mar  7 09:57:51 2005
From: thamelry at binf.ku.dk (thamelry@binf.ku.dk)
Date: Mon Mar  7 11:59:47 2005
Subject: [BioPython] non root having problem to install biopython 1.40
In-Reply-To: <20050307145136.GA7691@bach.ebgm.jussieu.fr>
References: <20050307145136.GA7691@bach.ebgm.jussieu.fr>
Message-ID: <33815.83.92.3.59.1110207471.squirrel@www.binf.ku.dk>

> "users/invites/wong/module/include/python2.3/Numeric"

Shouldn't there be a "/" in the beginning?

Cheers,

-Thomas

From mdehoon at ims.u-tokyo.ac.jp  Mon Mar  7 23:20:45 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Mon Mar  7 23:16:00 2005
Subject: [BioPython] non root having problem to install biopython 1.40
In-Reply-To: <20050307145136.GA7691@bach.ebgm.jussieu.fr>
References: <20050307145136.GA7691@bach.ebgm.jussieu.fr>
Message-ID: <422D281D.7020707@ims.u-tokyo.ac.jp>

WONG Hua wrote:
> NUMPY_EXTENSIONS = [
>     Extension('Bio.Cluster.cluster',
>               ['Bio/Cluster/clustermodule.c',
>                'Bio/Cluster/cluster.c',
>                'Bio/Cluster/ranlib.c',
>                'Bio/Cluster/com.c',
>                'Bio/Cluster/linpack.c'],
>               include_dirs=["Bio/Cluster","users/invites/wong/module/include/python2.3/Numeric"]
>               ),
> 
> And the error:
> 
> Bio/Cluster/clustermodule.c:2:33: Numeric/arrayobject.h: No such file or directory
> 

clustermodule.c tries to import Numeric/arrayobject.h, not 
arrayobject.h. So you should remove the Numeric in 
users/invites/wong/module/include/python2.3/Numeric, otherwise you'll 
end up with one Numeric too many.

--Michiel.
From mdehoon at ims.u-tokyo.ac.jp  Tue Mar  8 23:53:02 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Tue Mar  8 23:47:48 2005
Subject: [BioPython] Removing spam from the biopython-dev archives
In-Reply-To: <422C38C0.6060300@ims.u-tokyo.ac.jp>
References: <422C38C0.6060300@ims.u-tokyo.ac.jp>
Message-ID: <422E812E.1010903@ims.u-tokyo.ac.jp>

> The bad news is that when the biopython-dev archive was replaced on the 
> biopython.org webserver, the source file for the biopython archive was 
> accidentally overwritten. The biopython archive is still there, but the 
> source file from which the archives are generated is not. There is a 
> backup file until about March 2004, but for messages between March 2004 
> and early March 2005 we no longer have the source file. If you happen to 
> have a copy of these messages, please let us know.

Bartek Wilczynski sent me his copy of the Biopython messages since mid 
August 2004, which allowed me to recover all messages since then except 
for one message in September. From March 2004 to mid August 2004, there 
is still a gap. So if you have saved some of those messages, please let 
me know.
Note that Netscape and Mozilla don't actually delete a message from the 
source file until you compact the mail folders. So if you delete 
biopython messages but don't compact the mail folders, you probably 
still have those messages even if they don't show up in Netscape.

--Michiel
From mdehoon at ims.u-tokyo.ac.jp  Thu Mar 10 01:56:32 2005
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Thu Mar 10 01:51:21 2005
Subject: [BioPython] Removing spam from the biopython-dev archives
In-Reply-To: <422E812E.1010903@ims.u-tokyo.ac.jp>
References: <422C38C0.6060300@ims.u-tokyo.ac.jp>
	<422E812E.1010903@ims.u-tokyo.ac.jp>
Message-ID: <422FEFA0.60500@ims.u-tokyo.ac.jp>

I have created a new source file for the biopython mailing list archive 
from the contributions of various people. As far as I can tell, the 
archive is complete now. I have asked the biopython.org mailing list 
administrator to upload and install the new archive, which by the way is 
spam-free.
Thanks everybody!

--Michiel.

Michiel Jan Laurens de Hoon wrote:
>> The bad news is that when the biopython-dev archive was replaced on 
>> the biopython.org webserver, the source file for the biopython archive 
>> was accidentally overwritten. The biopython archive is still there, 
>> but the source file from which the archives are generated is not. 
>> There is a backup file until about March 2004, but for messages 
>> between March 2004 and early March 2005 we no longer have the source 
>> file. If you happen to have a copy of these messages, please let us know.
> 
> 
> Bartek Wilczynski sent me his copy of the Biopython messages since mid 
> August 2004, which allowed me to recover all messages since then except 
> for one message in September. From March 2004 to mid August 2004, there 
> is still a gap. So if you have saved some of those messages, please let 
> me know.
> Note that Netscape and Mozilla don't actually delete a message from the 
> source file until you compact the mail folders. So if you delete 
> biopython messages but don't compact the mail folders, you probably 
> still have those messages even if they don't show up in Netscape.
> 
> --Michiel
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
> 

From jtk at cmp.uea.ac.uk  Thu Mar 10 07:20:00 2005
From: jtk at cmp.uea.ac.uk (Jan T. Kim)
Date: Thu Mar 10 06:27:23 2005
Subject: [BioPython] Patch: Minor GenBank Parsing Problems
In-Reply-To: <20050307170245.GE32158@jtkpc.cmp.uea.ac.uk>
References: <20050307170245.GE32158@jtkpc.cmp.uea.ac.uk>
Message-ID: <20050310122000.GA25350@jtkpc.cmp.uea.ac.uk>

Dear Biopython Maintainers,

I've patched Bio/expressions/genbank.py to solve the parsing
problems I recently reported. The patch is marginal, so I just
attach it to this message; I hope that's ok.

The test doesn't introduce new failures into the regression tests (I
currently get a failure on Restriction, which is somewhat strange, but
at any rate, unrelated to the subject here). I haven't added any tests
myself.

On Mon, Mar 07, 2005 at 05:02:45PM +0000, Jan T. Kim wrote:

> I have noticed the following problems with the Bio.GenBank.FeatureParser:
> 
>     * The parser appears to depend on additional information in the
>       LOCUS line, it works with
> 
>         LOCUS       U00096               4639675 bp    DNA     circular BCT 24-JUN-2004
>       while the undecorated line
> 
>         LOCUS       U00096
> 
>       results in a Martel.Parser.ParserPositionException.

I solved this  by making everything following the locus value optional.
It appears that Biopython doesn't need the additional information, at
least for me, this fixes the problem without introducing any new ones.

Note: You probably won't get records with the additional info missing
from NCBI, but if you use EMBOSS to write GenBank formatted files, the
additional info is lost, and having to make that up manually just to
satisfy BioPython is a bit annoying.

>     * The parser also doesn't like some accession types, the line
> 
>         ACCESSION   U00096 AE000111-AE000510
> 
>       while trimming that to
> 
>         ACCESSION   U00096
> 
>       results in a file that now parses ok.

This was solved by allowing a "-" in accession numbers. While this fixes
the problem for now, this may not be entirely ideal as the accession
number "AE000111-AE000510" may be invalid, it seems to denote a range
of accession numbers AE000111, AE000112, ..., AE000510, but I'm not
certain about this.

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  >=-----*
-------------- next part --------------
diff -Naur biopython-1.40b/Bio/expressions/genbank.py biopython-1.40b-hacked/Bio/expressions/genbank.py
--- biopython-1.40b/Bio/expressions/genbank.py	2004-03-18 00:53:24.000000000 +0000
+++ biopython-1.40b-hacked/Bio/expressions/genbank.py	2005-03-10 11:34:37.134325592 +0000
@@ -116,20 +116,22 @@
 data_file_division = Martel.Group("data_file_division",
                                   Martel.Alt(*divisions))
 
+# JTK: made everything followgin "LOCUS XXXXXX" optional -- seqret of EMBOSS
+# doesn't supply all this base count, division, linear/circular etc. stuff
 locus_line = Martel.Group("locus_line",
                           Martel.Str("LOCUS") +
                           blank_space +
                           locus +
-                          blank_space +
-                          size +
-                          blank_space +
-                          Martel.Re("bp|aa") +
-                          blank_space +
-                          Martel.Opt(residue_type +
-                                     blank_space) +
-                          data_file_division +
-                          blank_space +
-                          date +
+                          Martel.Opt(blank_space +
+                                     size +
+                                     blank_space +
+                                     Martel.Re("bp|aa") +
+                                     blank_space +
+                                     Martel.Opt(residue_type +
+                                                blank_space) +
+                                     data_file_division +
+                                     blank_space +
+                                     date) +
                           Martel.AnyEol())
 
 # definition line
@@ -141,8 +143,11 @@
 
 # accession line
 # ACCESSION   AC007323
+# JTK: allowed also a "-" in accession, to allow for
+# ACCESSION   U00096 AE000111-AE000510
+# as found in E. coli K12 GenBank record
 accession = Martel.Group("accession",
-                         Martel.Re("[\w]+"))
+                         Martel.Re("[\w\-]+"))
 
 accession_block = Martel.Group("accession_block",
                                Martel.Str("ACCESSION") +
From idoerg at burnham.org  Thu Mar 10 12:40:44 2005
From: idoerg at burnham.org (Iddo Friedberg)
Date: Thu Mar 10 12:35:20 2005
Subject: [BioPython] Call for Papers -- Science Track at EuroPython 2005
Message-ID: <4230869C.5050100@burnham.org>

Dear former participants,

Dear list subscribers,

EuroPython 2005 will be held in Goteborg, Sweden from June 27 to July 1.

For the fourth consecutive year, EuroPython will host a Science Track
dedicated to talks about the use of Python in any kind of scientific
project. 

To quote the website : """The Science track will focus on the use of Python in 
science and industry, where tasks imply modelling complex systems (thermics, 
fluid dynamics, mechanics, aeronautics, biology, chemistry, etc.), processing 
very large data sets and achieving very CPU-intensive and long calculations. 
Speakers will present tool sets, frameworks and examples of successful 
applications based on Python and integrated with the other usual tools and 
applications used in the field.
"""

For archives of previous years, please see the website at

	http://www.europython.org/

If you would like to submit a talk proposal, please write to me directly
as another two weeks will be needed before the website gets upgraded and
updated for this year's conference. 

The deadline for submitting proposals is expected to be set to mid-april.

-- 
Nicolas Chauvat

logilab.fr - services en informatique avanc?e et gestion de connaissances  


-- 

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 krebsj at cip.ifi.lmu.de  Fri Mar 11 09:45:09 2005
From: krebsj at cip.ifi.lmu.de (Joerg Krebs)
Date: Fri Mar 11 09:40:00 2005
Subject: [BioPython] Parsing Swissprot-Files
Message-ID: <Pine.LNX.4.44.0503111542380.25940-100000@bern.cip.ifi.lmu.de>

Hi,
does anyone know how to handle Swissprot Files containing RX and RG entries
in the annotation Part?
I get error messages when I try to read some Swissprot files, looking like
this:

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

Traceback (most recent call last):
  File "SwPr2Fasta.py", line 19, in ?
    record = sp.next()
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 166,
in n
ext
    return self._parser.parse(File.StringHandle(data))
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 290,
in p
arse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 333,
in f
eed
    self._scan_record(uhandle, consumer)
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 338,
in _
scan_record
    fn(self, uhandle, consumer)
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 414,
in _
scan_reference
    self._scan_ra(uhandle, consumer)
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 436,
in _
scan_ra
    one_or_more=1)
  File "/usr/lib/python2.3/site-packages/Bio/SwissProt/SProt.py", line 360,
in _
scan_line
    read_and_call(uhandle, event_fn, start=line_type)
  File "/usr/lib/python2.3/site-packages/Bio/ParserSupport.py", line 300, in
rea
d_and_call
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'RA':
RG   The German cDNA consortium;

--------

It would be great of someone could help me with my problem.

Thanks

	Joerg


From eirik.sonneland at student.umb.no  Mon Mar 14 07:51:32 2005
From: eirik.sonneland at student.umb.no (=?ISO-8859-1?Q?Eirik_S=F8nneland?=)
Date: Mon Mar 14 07:46:02 2005
Subject: [BioPython] Re: [Biopython-dev] [Bug 1761] New: BLAST not returning
	final results
In-Reply-To: <200503141204.j2EC4ANE021948@portal.open-bio.org>
References: <200503141204.j2EC4ANE021948@portal.open-bio.org>
Message-ID: <423588D4.3080504@student.umb.no>


Kate,

I belive it should be NCBIWWW.qblast(..........

regards
Eirik

bugzilla-daemon@portal.open-bio.org wrote:

>http://bugzilla.open-bio.org/show_bug.cgi?id=1761
>
>           Summary: BLAST not returning final results
>           Product: Biopython
>           Version: Not Applicable
>          Platform: PC
>        OS/Version: Windows XP
>            Status: NEW
>          Severity: normal
>          Priority: P2
>         Component: Other
>        AssignedTo: biopython-dev@biopython.org
>        ReportedBy: genesniffer@hotmail.com
>
>
>Hi,
>I'm just trying to run BLAST at NCBI using NCBIWWW using the script below.  
>The request seems to be sent fine, but the returned page ends with "This page 
>will automatically be updated...."  ie the final results are not being 
>returned.  The module doesn't not seem to be polling for the final result.  Is 
>this a bug in the program or am I doing something wrong?  I look forward to 
>hearing from you...
>Kate
>
>from Bio.Blast import NCBIWWW
>blast_results = NCBIWWW.blast('blastp', 'nr', protein_seq, entrez_query="Homo 
>sapiens [ORGN]")
>blast_results = blast_results.readlines()
>print blast_results
>
>
>
>------- You are receiving this mail because: -------
>You are the assignee for the bug, or are watching the assignee.
>_______________________________________________
>Biopython-dev mailing list
>Biopython-dev@biopython.org
>http://biopython.org/mailman/listinfo/biopython-dev
>  
>

From Stephan.Herschel at biovertis.com  Tue Mar 15 12:23:10 2005
From: Stephan.Herschel at biovertis.com (Stephan Herschel)
Date: Tue Mar 15 12:41:43 2005
Subject: [BioPython] GenBank Parser and large files?
Message-ID: <H000008000030185.1110907389.bvmail.biovertis.intern@MHS>


   Hi,
   I'm parsing some genebank files. When parsing large files it appears
   the parser eats up all of my memory until nothing is left, i.e. it's
   not possible to parse large files (>25 MB).
   That's the way I do it:
   >>> from Bio import GenBank
   >>> fh=open(fname,'r')
   >>> feature_parser=GenBank.FeatureParser()
   >>> gb_iterator = GenBank.Iterator(fh, feature_parser)
   >>> cur_record = gb_iterator.next()
   Is there a way to circumvent this problem?
   Thanks,
   Stephan

From biopython at maubp.freeserve.co.uk  Tue Mar 15 16:27:08 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue Mar 15 16:16:01 2005
Subject: [BioPython] GenBank Parser and large files?
In-Reply-To: <H000008000030185.1110907389.bvmail.biovertis.intern@MHS>
References: <H000008000030185.1110907389.bvmail.biovertis.intern@MHS>
Message-ID: <4237532C.2080809@maubp.freeserve.co.uk>

Stephan Herschel wrote:
 > Hi,
 > I'm parsing some genebank files. When parsing large files it
 > appears the parser eats up all of my memory until nothing is
 > left, i.e. it's not possible to parse large files (>25 MB).

You are not the only one to find this...

 > That's the way I do it:
 > >>> from Bio import GenBank
 > >>> fh=open(fname,'r')
 > >>> feature_parser=GenBank.FeatureParser()
 > >>> gb_iterator = GenBank.Iterator(fh, feature_parser)
 > >>> cur_record = gb_iterator.next()

The code looks fine.

 > Is there a way to circumvent this problem?
 > Thanks,
 > Stephan

Yes - please try out my patch available on bug 1747,

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

If you don't know how to use the diff file, tell me which version of 
BioPython you are using (1.30 or 1.40b I would assume) and I can 
email you a replacement python file instead:

Bio/GenBank/__init__.py

As a short term measure, depending on which bits of the GenBank file 
you care about, you can try editing the GenBank file by hand before 
parsing to remove most of the features (leave at least one), or most 
of the sequence.

Peter
From biopython at maubp.freeserve.co.uk  Wed Mar 16 07:27:02 2005
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed Mar 16 07:25:12 2005
Subject: [BioPython] GenBank Parser and large files?
In-Reply-To: <29408998.1110965792461.JavaMail.root@bvmail>
References: <29408998.1110965792461.JavaMail.root@bvmail>
Message-ID: <42382616.6070609@maubp.freeserve.co.uk>

Stephan Herschel wrote:
> Hi Peter,
> 
> Thanks for the the fast solution! (I guessed that I could not be the
> only one having this problem ...)
>
> Apparently I applied the patch successfully - only the 'Reversed
> patch'- message was confusing - as you can see here:

Yeah - that was the first time I ever created a patch file, and in the 
absence of any instructions on the BioPython developers list, I just 
improvised:

diff my_version.py vcs_version.py > patch.txt

Would the reversed patch messages would go away if I had done this?

diff vcs_version.py my_version.py > patch.txt

> (Stripping trailing CRs from patch.)

Those are because I did this on Windows.

> can't find file to patch at input line 1
> 
> Perhaps you should have used the -p or --strip option?

The --strip option doesn't exist on my version of diff, and -p is an 
alias for --show-c-function (Show which C function each change is in) 
which doesn't seem relevant:-

diff (GNU diffutils) 2.8.7
(The cygwin version running on Windows)

> Tested the parser - works just fine!

Great.

Please let me know (or post on the bug) if you have any trouble with the 
patch - or even if it works fine for you.

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

What sort of GenBank files are you using, and where are they from?

I have mainly been using bacteria from the NCBI - watch out for bug 1758 
and bug 1762 as my patch will probably also fail on those.

Peter
-- 
PhD Student
MOAC Doctoral Training Centre
University of Warwick, UK
From jtk at cmp.uea.ac.uk  Wed Mar 16 09:26:13 2005
From: jtk at cmp.uea.ac.uk (Jan T. Kim)
Date: Wed Mar 16 08:24:30 2005
Subject: [BioPython] Patches (was: GenBank Parser and large files?)
In-Reply-To: <42382616.6070609@maubp.freeserve.co.uk>
References: <29408998.1110965792461.JavaMail.root@bvmail>
	<42382616.6070609@maubp.freeserve.co.uk>
Message-ID: <20050316142613.GA1033@jtkpc.cmp.uea.ac.uk>

On Wed, Mar 16, 2005 at 12:27:02PM +0000, Peter wrote:
> Stephan Herschel wrote:
> >Hi Peter,
> >
> >Thanks for the the fast solution! (I guessed that I could not be the
> >only one having this problem ...)
> >
> >Apparently I applied the patch successfully - only the 'Reversed
> >patch'- message was confusing - as you can see here:
> 
> Yeah - that was the first time I ever created a patch file, and in the 
> absence of any instructions on the BioPython developers list, I just 
> improvised:
> 
> diff my_version.py vcs_version.py > patch.txt
> 
> Would the reversed patch messages would go away if I had done this?
> 
> diff vcs_version.py my_version.py > patch.txt

Yes. The direction of patches is old -> new, by convention. If the patch
program can tell whether the order was reversed, and it prints the
'Reversed patch' message.

With a plain diff, as you sent it, patch can reliably tell whether the
file being patched is the "old" or the "new" version, so there should not
be any problem.

> >(Stripping trailing CRs from patch.)
> 
> Those are because I did this on Windows.

Most Windows editors can switch the extraneous CRs on or off these
days. But again, this should not cause any serious problem.

> >can't find file to patch at input line 1
> >
> >Perhaps you should have used the -p or --strip option?
> 
> The --strip option doesn't exist on my version of diff, and -p is an 
> alias for --show-c-function (Show which C function each change is in) 
> which doesn't seem relevant:-

These options pertain to patch: -pnum or --strip=num: Strip the smallest
prefix containing num leading slashes from each file name found in the
patch file.

Plain diffs tend to trigger some informational messages or requests for
interactive input (request for the file to be patched etc.) when fed into
patch, because this information is not contained in a plain diff. Unified
context diffs contain this information, as seen in the (very minor)
patch I recently submitted:

    diff -Naur biopython-1.40b/Bio/expressions/genbank.py biopython-1.40b-hacked/Bio/expressions/genbank.py
    --- biopython-1.40b/Bio/expressions/genbank.py  2004-03-18 00:53:24.000000000 +0000
    +++ biopython-1.40b-hacked/Bio/expressions/genbank.py   2005-03-10 11:34:37.134325592 +0000

> diff (GNU diffutils) 2.8.7
> (The cygwin version running on Windows)

This should accept the options -Naur (-N: treat new files as empty in other
directory, -a: treat lines as text, -u: write unified format, -r: recursive).

This allows changes that have affected multiple files to be rolled into one
patch (which wasn't the case here), but once you pick up this habit, you'll
use it by default (like I did).

> >Tested the parser - works just fine!
> 
> Great.

I'll give it a try as soon as I get around to do so too -- in fact, I
must confess that I've started using ad hoc hacks to work with eukaryotic
pseudochromosome files since an attempt to parse one with Biopython didn't
terminate in more than 24 hours...

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 karbak at gmail.com  Wed Mar 23 23:51:37 2005
From: karbak at gmail.com (K. Arun)
Date: Wed Mar 23 23:46:11 2005
Subject: [BioPython] AAIndex parser ?
Message-ID: <162452a1050323205165ab1617@mail.gmail.com>

Hello,

Back in April 2004, there were a few messages about an AAIndex [1]
parser that was to be committed to the Biopython tree. I can't seem to
find the module/file in the current release. Does anyone know if the
code is available somewhere ? Thanks,

-arun 

[1] http://www.genome.jp/aaindex/
From kal03 at hampshire.edu  Sat Mar 26 11:50:30 2005
From: kal03 at hampshire.edu (Kari Linder)
Date: Sat Mar 26 10:39:46 2005
Subject: [BioPython] Interacting with GenBank
Message-ID: <2dad2c1ed63c377bcdaad2ed5688d57e@hampshire.edu>

Here is the script I am working with :

from Bio.WWW import NCBI


search_command = 'Search'
search_database = 'Nucleotide'
return_format = 'Fasta'
search_term = 'Ciliphora'


result_handle = NCBI.query(search_command, search_database, term = 
search_term, doptcmdl = return_format)

import os

result_file_name = os.path.join(os.getcwd(), 'results.html')
result_file = open(result_file_name, 'w')
result_file.write(result_handle.read())
result_file.close()

It is basically from section  "2.5 Connecting with biological 
databases" in the biopython tutorial, and it works being that it gives 
me an html file, however when I open the file it says that the results 
cannot be displayed. Has anyone had this problem?

Thanks
Kari

From jtk at cmp.uea.ac.uk  Sat Mar 26 15:52:32 2005
From: jtk at cmp.uea.ac.uk (Jan T. Kim)
Date: Sat Mar 26 14:50:53 2005
Subject: [BioPython] Interacting with GenBank
In-Reply-To: <2dad2c1ed63c377bcdaad2ed5688d57e@hampshire.edu>
References: <2dad2c1ed63c377bcdaad2ed5688d57e@hampshire.edu>
Message-ID: <20050326205232.GB2271@jtkpc.cmp.uea.ac.uk>

On Sat, Mar 26, 2005 at 10:50:30AM -0600, Kari Linder wrote:
> Here is the script I am working with :
> 
> from Bio.WWW import NCBI
> 
> 
> search_command = 'Search'
> search_database = 'Nucleotide'
> return_format = 'Fasta'
> search_term = 'Ciliphora'
> 
> 
> result_handle = NCBI.query(search_command, search_database, term = 
> search_term, doptcmdl = return_format)
> 
> import os
> 
> result_file_name = os.path.join(os.getcwd(), 'results.html')
> result_file = open(result_file_name, 'w')
> result_file.write(result_handle.read())
> result_file.close()
> 
> It is basically from section  "2.5 Connecting with biological 
> databases" in the biopython tutorial, and it works being that it gives 
> me an html file, however when I open the file it says that the results 
> cannot be displayed. Has anyone had this problem?

Not me...

Can you be more specific about which is "it" which "says that the results
cannot be displayed"? If "it" is your operating system, then there's
little that Biopython or Genbank can do about that, if, however, "it"
is a Biopython routine, then perhaps some HTML has changed such that
the parser cannot understand it anymore or something like that. Please
provide a transcript of the error.

Best regards (and happy Easter), 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 syd.diamond at gmail.com  Wed Mar 30 17:07:34 2005
From: syd.diamond at gmail.com (Syd Diamond)
Date: Wed Mar 30 17:01:42 2005
Subject: [BioPython] native python sequence alignment
Message-ID: <a76ba315050330140768a4b704@mail.gmail.com>

Hi yall,

I need to do pairwise sequence alignment of short alphanumeric strings,
and I turned to biopython to look for this tool.  I was hoping to do it
natively and not need to repeatedly use a wrapper to ClustalW or something
like that.  In scriptcentral, I found:

http://starship.python.net/crew/gherman/potpurri/align/

60% of the time, it works every time.  However, it's not quite perfect,
and before I went diving into the heart of the alignment function, I
wanted to see if anyone knew of a better approach or alternate code.  I've
googled extensively without luck.

Many thanks,
Joel
From fkauff at duke.edu  Wed Mar 30 17:14:54 2005
From: fkauff at duke.edu (Frank Kauff)
Date: Wed Mar 30 17:09:12 2005
Subject: [BioPython] native python sequence alignment
In-Reply-To: <a76ba315050330140768a4b704@mail.gmail.com>
References: <a76ba315050330140768a4b704@mail.gmail.com>
Message-ID: <1112220894.5142.76.camel@osiris.biology.duke.edu>

Hi,

there's the pairwise2 module in biopython which is pretty
straightforward and does a nice job. Not excitingly fast, but if you
have short seqs anyway, it shouldn't matter.

Frank

On Wed, 2005-03-30 at 17:07 -0500, Syd Diamond wrote:
> Hi yall,
> 
> I need to do pairwise sequence alignment of short alphanumeric strings,
> and I turned to biopython to look for this tool.  I was hoping to do it
> natively and not need to repeatedly use a wrapper to ClustalW or something
> like that.  In scriptcentral, I found:
> 
> http://starship.python.net/crew/gherman/potpurri/align/

> 60% of the time, it works every time.  However, it's not quite perfect,
> and before I went diving into the heart of the alignment function, I
> wanted to see if anyone knew of a better approach or alternate code.  I've
> googled extensively without luck.
> 
> Many thanks,
> Joel
> _______________________________________________
> 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 pap501 at york.ac.uk  Thu Mar 31 05:21:34 2005
From: pap501 at york.ac.uk (pap501@york.ac.uk)
Date: Thu Mar 31 05:18:40 2005
Subject: [BioPython] Problem with python and mysql
Message-ID: <Prayer.1.0.10.0503311121340.6437@webmail1.york.ac.uk>

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
-------------- next part --------------
import cStringIO
import os
import MySQLdb
conn= MySQLdb.connect (host="localhost",
                       user ="root",
                      passwd ="p1geon1",
                       db="phil")
allfilenames=('F50',)

for a in allfilenames:
    print a
    input8=open ('SsGI_library_#'+a+'.txt','r')
    outfile=open('outtest.txt', 'w')

    i8=input8.read()
 #   print i8
    listofentries=i8.split('>')
    

    for li in listofentries:
        print li
        numbers=li.split('\n')[0]
        print numbers
        seq=li.split('\n')[1]
       # print numbers
        bothnumbers=numbers.split('\t')
        print bothnumbers
        gb=bothnumbers[0]

        if len(bothnumbers)==2:
             tnum= bothnumbers [1]

        else:
            tnum='NULL'

        qry="insert into sequences2 values('%s','%s','%s','%s');"% (a, gb, tnum, seq)
        print qry
        conn.query(qry)
From l.heisler at utoronto.ca  Thu Mar 31 11:00:00 2005
From: l.heisler at utoronto.ca (Larry)
Date: Thu Mar 31 10:52:11 2005
Subject: [BioPython] Problem with python and mysql
References: <Prayer.1.0.10.0503311121340.6437@webmail1.york.ac.uk>
Message-ID: <00a501c5360a$b3ee7810$1651968e@Larry>

Hi Phil,
I don't believe .query can be used with a MySQLdb connection.  I am not an
expert on this, but the way I have done this in the past is

1. set up the connection
conn= MySQLdb.connect (host="localhost",
                       user ="root",
                      passwd ="p1geon1",
                       db="phil")

2. set up a cursor
mycursor=conn.cursor()

3. create your query
qry="insert into sequences2 values('%s','%s','%s','%s');"% (a, gb, tnum,
seq)

4. execute your query
mycursor.execute(qry)


others may be able to give you more details on this, ie. using .query which
i believe works with _mysql
ie
use _mysql
conn= _mysql.connect (host="localhost", user ="root", passwd
="p1geon1",db="phil")
conn.query(qry)

Larry



----- Original Message ----- 
From: <pap501@york.ac.uk>
To: <biopython@biopython.org>
Sent: Thursday, March 31, 2005 5:21 AM
Subject: [BioPython] Problem with python and mysql


> 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


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


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From pap501 at york.ac.uk  Thu Mar 31 05:30:30 2005
From: pap501 at york.ac.uk (pap501@york.ac.uk)
Date: Tue Apr  5 22:06:18 2005
Subject: [BioPython] mysql trouble
Message-ID: <Prayer.1.0.10.0503311130300.6437@webmail1.york.ac.uk>

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
-------------- next part --------------
import cStringIO
import os
import MySQLdb
conn= MySQLdb.connect (host="localhost",
                       user ="root",
                      passwd ="p1geon1",
                       db="phil")
allfilenames=('F50',)

for a in allfilenames:
    print a
    input8=open ('SsGI_library_#'+a+'.txt','r')
    outfile=open('outtest.txt', 'w')

    i8=input8.read()
 #   print i8
    listofentries=i8.split('>')
    

    for li in listofentries:
        print li
        numbers=li.split('\n')[0]
        print numbers
        seq=li.split('\n')[1]
       # print numbers
        bothnumbers=numbers.split('\t')
        print bothnumbers
        gb=bothnumbers[0]

        if len(bothnumbers)==2:
             tnum= bothnumbers [1]

        else:
            tnum='NULL'

        qry="insert into sequences2 values('%s','%s','%s','%s');"% (a, gb, tnum, seq)
        print qry
        conn.query(qry)