[BioPython] Doubt about the MEME parser
Sameet
sameet at nccs.res.in
Mon Aug 22 00:14:25 EDT 2005
Hi,
I found the module to deal with MEME output files in the latest CVS.
However, I couldn't get it working. Any pointers will be helpful.
Regards
Sameet
-----Original Message-----
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Sent: Friday, August 19, 2005 9:11 PM
To: biopython at biopython.org
Subject: BioPython Digest, Vol 32, Issue 2
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Today's Topics:
1. Re: Changes in NCBI BLAST output format !!?? (Aur?lie Bornot)
2. Blast and multiple processors (Daniel Tomso)
3. RE: Changes in NCBI BLAST output format !!?? (Michiel De Hoon)
4. re: software skills course (Greg Wilson)
5. where to find an updated cookbook? (xuying)
6. Re: re: software skills course (Ann Loraine)
7. RE: where to find an updated cookbook? (Michiel De Hoon)
8. Vector NTI file import (Jerome PANSANEL)
9. Re: Vector NTI file import (Frederic Sohm)
10. Re: Vector NTI file import (Sebastian Bassi)
11. Re: Vector NTI file import (Jerome PANSANEL)
----------------------------------------------------------------------
Message: 1
Date: Wed, 3 Aug 2005 20:54:36 +0200
From: Aur?lie Bornot <aurelie.bornot at free.fr>
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??
To: <biopython at biopython.org>
Message-ID: <001b01c5985c$cc046360$0b413851 at YSENGARD>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=response
Thank you very much Alexander !!
I didn't dare to change the code in the Bio.Blast.NCBIWWW on my own because
I didn't have time to make tests...
So I simply automatiquely added the <p> in the Blast file... not very nice..
I know !
I will try your method instead !
Thanks !
Aurilie
--------------
Aurelie BORNOT
MNHN
Paris
----- Original Message -----
From: "Alexander A. Morgan" <amorgan at mitre.org>
To: <aurelie.bornot at free.fr>
Cc: <biopython at biopython.org>
Sent: Tuesday, August 02, 2005 10:07 PM
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??
> Hello:
> I've just run into the same problem, and I haven't seen a suggested fix
> go by, so I apologize if this is redundant information, but it seems that
> the files I've been getting from NCBI have a <p> removed from the header
> between the "RID: " line and the "<p>Query" line, and it is just a blank
> line now. If you edit Bio.Blast.NCBIWWW to not look for the "<p>", it
> seems to work okay.
>
> class _Scanner:
> ....
> def _scan_header(self, uhandle, consumer):
> ....
>
> change:
> attempt_read_and_call(uhandle, consumer.noevent, start='<p>')
> to: attempt_read_and_call(uhandle, consumer.noevent)
>
>
>
>
>
> aurelie.bornot at free.fr wrote:
>
>>Thank you very much Jessica !!!
>>
>>Unfortunately, I need a lot of thing in the BLAST reports.....
>>It will be difficult to do the same thing as you did....
>>
>>I will try to do something in the code of parser of Python.
>>But it will be difficult for me..
>>so if you or someone has advices !!!
>>
>>Thanks a lot again for your answer Jessica !
>>Aurilie
>>
>>
>>--------------
>>Aurelie BORNOT
>>MNHN
>>Paris
>>
>>
>>_______________________________________________
>>BioPython mailing list - BioPython at biopython.org
>>http://biopython.org/mailman/listinfo/biopython
>>
>
>
>
>
------------------------------
Message: 2
Date: Thu, 4 Aug 2005 16:40:17 -0400
From: "Daniel Tomso" <dtomso at athenixcorp.com>
Subject: [BioPython] Blast and multiple processors
To: <biopython at biopython.org>
Message-ID: <EA9922370F61CC4B9A2A842E2A57830F1871A4 at helios.athenixdom>
Content-Type: text/plain; charset="us-ascii"
Hello, all.
I'm working on improving my BLAST throughput, and I have some questions
about how the program handles multiple processors and multiple
processes.
Specifically, I've been experimenting with using BioPython's
NCBIStandalone to handle 3 or 4 simultaneous blast requests, since my
system has 4 processors. I spin out the requests via
NCBIStandalone.blastall(blah, blah), then grab the blast_out and
blast_err file handles in a list. Afterwards, I use blast_out.read() to
collect the reports from each of the 4 processes.
Is this wise and/or efficient? My execution times do drop off when I
do, say, 4 jobs at a time instead of 1 at a time, so it is helping. Do
the processor flags for blastall accomplish this more efficiently?
Sorry if this is not specific enough, but any insight would be
welcome!!!!
Dan T.
Daniel J. Tomso
Senior Scientist, Bioinformatics
Athenix Corporation
2202 Ellis Road
Suite B
Durham, NC 27703
919.281.0920
dtomso at athenixcorp.com
www.athenixcorp.com
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------------------------------
Message: 3
Date: Sun, 7 Aug 2005 20:08:24 -0400
From: "Michiel De Hoon" <mdehoon at c2b2.columbia.edu>
Subject: RE: [BioPython] Changes in NCBI BLAST output format !!??
To: "Alexander A. Morgan" <amorgan at mitre.org>
Cc: biopython at biopython.org
Message-ID:
<6CA15ADD82E5724F88CB53D50E61C9AE7AC297 at cgcmail.cgc.cpmc.columbia.edu>
Content-Type: text/plain; charset="iso-8859-1"
I've updated Biopython in CVS with this fix. See Bio/Blast/NCBIWWW.py
revision 1.41. Please let me know if you find any problems. Thanks for
finding this solution.
--Michiel.
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032
-----Original Message-----
From: Alexander A. Morgan [mailto:amorgan at mitre.org]
Sent: Wed 8/3/2005 2:48 PM
To: Michiel De Hoon
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??
Michiel:
I couldn't find anything wrong with it. The Blast record objects seem
to be correct and have the right alignments. However, I don't know of a
thorough way to test it. In general the parser is pretty fragile though
and will break for even the most minor changes in NCBI format, but it
would be very challenging to try to make it more robust.
Thanks,
-Alex
Michiel De Hoon wrote:
>Do you happen to know if this change can break anything else in the Blast
>parser? From running Biopython's tests for Blast, it seems that this change
>is OK. On the other hand, I don't use Blast much myself, so I don't trust
my
>own judgement in this matter.
>If making this change does not cause any new bugs, I'd be happy to include
it
>in CVS.
>
>--Michiel.
>
>
>Michiel de Hoon
>Center for Computational Biology and Bioinformatics
>Columbia University
>1150 St Nicholas Avenue
>New York, NY 10032
>
>
>
>-----Original Message-----
>From: biopython-bounces at portal.open-bio.org on behalf of Alexander A.
Morgan
>Sent: Tue 8/2/2005 4:07 PM
>To: aurelie.bornot at free.fr
>Cc: biopython at biopython.org
>Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??
>
>Hello:
> I've just run into the same problem, and I haven't seen a suggested
>fix go by, so I apologize if this is redundant information, but it seems
>that the files I've been getting from NCBI have a <p> removed from the
>header between the "RID: " line and the "<p>Query" line, and it is just
>a blank line now. If you edit Bio.Blast.NCBIWWW to not look for the
>"<p>", it seems to work okay.
>
>class _Scanner:
>....
> def _scan_header(self, uhandle, consumer):
>....
>
> change:
> attempt_read_and_call(uhandle, consumer.noevent, start='<p>')
> to:
> attempt_read_and_call(uhandle, consumer.noevent)
>
>
>
>
>
>aurelie.bornot at free.fr wrote:
>
>
>
>>Thank you very much Jessica !!!
>>
>>Unfortunately, I need a lot of thing in the BLAST reports.....
>>It will be difficult to do the same thing as you did....
>>
>>I will try to do something in the code of parser of Python.
>>But it will be difficult for me..
>>so if you or someone has advices !!!
>>
>>Thanks a lot again for your answer Jessica !
>>Aurilie
>>
>>
>>--------------
>>Aurelie BORNOT
>>MNHN
>>Paris
>>
>>
>>_______________________________________________
>>BioPython mailing list - BioPython at biopython.org
>>http://biopython.org/mailman/listinfo/biopython
>>
>>
>>
>>
>
>
>_______________________________________________
>BioPython mailing list - BioPython at biopython.org
>http://biopython.org/mailman/listinfo/biopython
>
>
>
------------------------------
Message: 4
Date: Tue, 09 Aug 2005 09:13:10 -0400
From: Greg Wilson <gvwilson at cs.utoronto.ca>
Subject: [BioPython] re: software skills course
To: biopython at biopython.org
Message-ID: <dda9ul$ovc$2 at sea.gmane.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
I'm working with support from the Python Software Foundation to develop
an open source course on basic software development skills for people
with backgrounds in science and engineering. I have a beta version of
the course notes ready for review, and would like to pull in people
in sci&eng to look it over and give me feedback. If you know anyone
who fits this bill (particularly people who might be interested in
following along with a trial run of the course this fall), I'd be
grateful for pointers.
Thanks,
Greg Wilson
------------------------------
Message: 5
Date: Wed, 10 Aug 2005 13:55:09 +0800
From: "xuying" <xuying at sibs.ac.cn>
Subject: [BioPython] where to find an updated cookbook?
To: "biopython" <biopython at biopython.org>
Message-ID: <20050810055436.9B14C10DECC at smtp.sibsnet.org>
Content-Type: text/plain; charset="gb2312"
Can anyone tell me where to find an updated biopython tutorial?
Examples in the online tutorial are full of errors. Thanks!
!!!!!!!!!!!!!!!!xuying
!!!!!!!!!!!!!!!!xuying at sibs.ac.cn
!!!!!!!!!!!!!!!!!!!!2005-08-10
------------------------------
Message: 6
Date: Wed, 10 Aug 2005 13:11:49 -0700
From: Ann Loraine <loraine at loraine.net>
Subject: Re: [BioPython] re: software skills course
To: Greg Wilson <gvwilson at cs.utoronto.ca>
Cc: biopython at biopython.org
Message-ID: <6f16141077ca7fbb9bd08da6746e2b5d at loraine.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hello,
I would appreciate the chance to see the notes. It would be helpful to
the postdocs and students I supervise who would like to learn python.
Yours,
Ann Loraine
On Aug 9, 2005, at 6:13 AM, Greg Wilson wrote:
> Hi,
>
> I'm working with support from the Python Software Foundation to develop
> an open source course on basic software development skills for people
> with backgrounds in science and engineering. I have a beta version of
> the course notes ready for review, and would like to pull in people
> in sci&eng to look it over and give me feedback. If you know anyone
> who fits this bill (particularly people who might be interested in
> following along with a trial run of the course this fall), I'd be
> grateful for pointers.
>
> Thanks,
> Greg Wilson
>
> _______________________________________________
> BioPython mailing list - BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
------------------------------
Message: 7
Date: Thu, 11 Aug 2005 13:59:35 -0400
From: "Michiel De Hoon" <mdehoon at c2b2.columbia.edu>
Subject: RE: [BioPython] where to find an updated cookbook?
To: "xuying" <xuying at sibs.ac.cn>, "biopython"
<biopython at biopython.org>
Message-ID:
<6CA15ADD82E5724F88CB53D50E61C9AE7AC2B0 at cgcmail.cgc.cpmc.columbia.edu>
Content-Type: text/plain; charset="iso-8859-1"
> Can anyone tell me where to find an updated biopython tutorial?
> Examples in the online tutorial are full of errors. Thanks!
Can you make a list of the errors that you found? Then it'll be easier for
us
to fix those errors. If you have a solution to the errors that you found,
even better!
--Michiel.
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032
------------------------------
Message: 8
Date: Fri, 19 Aug 2005 09:41:10 +0200
From: Jerome PANSANEL <j.pansanel at pansanel.net>
Subject: [BioPython] Vector NTI file import
To: biopython at biopython.org
Message-ID: <200508190941.11168.j.pansanel at pansanel.net>
Content-Type: text/plain; charset="iso-8859-1"
Hello,
I would like to write some support for Vector NTI file (derived from GenBank
format) for biopython. Is already someone working on it ?
Is someone interested for debugging ?
Thanks,
Jerome Pansanel
------------------------------
Message: 9
Date: Fri, 19 Aug 2005 11:39:09 +0200
From: Frederic Sohm <frederic.sohm at iaf.cnrs-gif.fr>
Subject: Re: [BioPython] Vector NTI file import
To: biopython at biopython.org, Jerome PANSANEL <j.pansanel at pansanel.net>
Message-ID: <200508191139.09551.frederic.sohm at iaf.cnrs-gif.fr>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I am definitely. Interested I mean. How do you plane to work on the NTI file
format? I have had a look to it and it seems particularly complex. What kind
of support do you have in mind?
Cheers
Fred
Le vendredi 19 Ao{t 2005 09:41, Jerome PANSANEL a icrit :
> Hello,
>
> I would like to write some support for Vector NTI file (derived from
> GenBank format) for biopython. Is already someone working on it ?
> Is someone interested for debugging ?
>
> Thanks,
>
> Jerome Pansanel
>
> _______________________________________________
> BioPython mailing list - BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
--
Fridiric Sohm
Equipe INRA U1126 "Morphogenhse du systhme nerveux des Chordis"
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
------------------------------
Message: 10
Date: Fri, 19 Aug 2005 09:31:55 -0300
From: Sebastian Bassi <sbassi at genesdigitales.com>
Subject: Re: [BioPython] Vector NTI file import
To: biopython at biopython.org
Message-ID: <4305D13B.3060308 at genesdigitales.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Jerome PANSANEL wrote:
> I would like to write some support for Vector NTI file (derived from
GenBank
> format) for biopython. Is already someone working on it ?
> Is someone interested for debugging ?
I do have a valid license for VNTI (not mine, but from the place I
work), I could provide files.
First obvious question: Is it documented?
I could check manual if needed :)
PS: Just changed email address, sorry if it is duplicate.
------------------------------
Message: 11
Date: Fri, 19 Aug 2005 17:43:18 +0200
From: Jerome PANSANEL <j.pansanel at pansanel.net>
Subject: Re: [BioPython] Vector NTI file import
To: biopython at biopython.org
Message-ID: <200508191743.19070.j.pansanel at pansanel.net>
Content-Type: text/plain; charset="iso-8859-1"
Le Vendredi 19 Ao{t 2005 14:31, Sebastian Bassi a icrit :
> Jerome PANSANEL wrote:
> > I would like to write some support for Vector NTI file (derived from
> > GenBank format) for biopython. Is already someone working on it ?
> > Is someone interested for debugging ?
>
> I do have a valid license for VNTI (not mine, but from the place I
> work), I could provide files.
It would be great !
> First obvious question: Is it documented?
> I could check manual if needed :)
I have not found any documentation. I only known that it's very similar to
genbank file format.
The main differences are :
The header who can only contain LOCUS and SOURCE
a lot of COMMENT
Jerome Pansanel
>
>
> PS: Just changed email address, sorry if it is duplicate.
> _______________________________________________
> BioPython mailing list - BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
------------------------------
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