From googleposition at quickemail.de Sun Aug 3 07:17:36 2003 From: googleposition at quickemail.de (googleposition@quickemail.de) Date: Sun Aug 3 07:17:54 2003 Subject: [BioPython] =?iso-8859-1?q?Analyse_f=FCr_Ihre_Webseite?= Message-ID: <200308031117.h73BHap7005930@ns1.smart-weblications.de> Guten Tag. Kurze Frage: Mit welchen Keywörtern stehen Sie heute bei Google, yahoo oder Altavista auf welcher Position? Wir analysieren es für Sie! Der erste Test ist für Sie kostenlos. Senden Sie uns Ihre 10 wichtigen Keywords zu. Ihre Analyse dauert ca. 7 Tage*. 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kombinieren 0 19.05.2003 neue BahnCard 1 19.05.2003 http://www.bahn.de/pv/angebote/neue_preise/die_bahn_04_bahncard.shtml Gewinnspiel 0 19.05.2003 Mitfahrerbörse 7 19.05.2003 http://www.bahn.de/pv/home/info/die_bahn_gewinner_mitfahrerboerse.shtml Mitfahrersuche 0 19.05.2003 From gtg269c at mail.gatech.edu Tue Aug 5 03:13:00 2003 From: gtg269c at mail.gatech.edu (Amin Momin) Date: Tue Aug 5 00:19:35 2003 Subject: [BioPython] Biopython parsers Message-ID: <001301c35b21$019c6160$a0853d80@GEORGIAYO1AA9A> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: sanitizer.log Type: text/sanitizer-log Size: 1496 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20030805/36d03cf6/sanitizer-0001.bin From thamelry at vub.ac.be Tue Aug 5 04:35:10 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Tue Aug 5 05:26:01 2003 Subject: [BioPython] Updated Logo In-Reply-To: <20030731115312.M1354@pc10.inb.mu-luebeck.de> References: <20030731115312.M1354@pc10.inb.mu-luebeck.de> Message-ID: <200308051035.10193.thamelry@vub.ac.be> Hi everybody, An updated version of the biopython logo (now white background and right-turning snakes) is available at: http://homepages.vub.ac.be/~thamelry/biopython.jpg Regards, --- Thomas Hamelryck COMO-ULTR Vrije Universiteit Brussel (VUB) Belgium http://homepages.vub.ac.be/~thamelry From jefftc at stanford.edu Wed Aug 6 00:34:30 2003 From: jefftc at stanford.edu (Jeffrey Chang) Date: Wed Aug 6 00:34:22 2003 Subject: [BioPython] Updated Logo In-Reply-To: <200308051035.10193.thamelry@vub.ac.be> Message-ID: <450C65D3-C7C7-11D7-8CEB-000A956845CE@stanford.edu> Awesome. Thanks very much! Does the logo scale well, for use either as an icon or small image suitable for a web link? If it does not look good smaller, would it be hard to generate a smaller version, but perhaps with less detail? Jeff On Tuesday, August 5, 2003, at 01:35 AM, Thomas Hamelryck wrote: > Hi everybody, > > An updated version of the biopython logo (now white background and > right-turning snakes) is available at: > > http://homepages.vub.ac.be/~thamelry/biopython.jpg > > Regards, > > --- > Thomas Hamelryck > COMO-ULTR > Vrije Universiteit Brussel (VUB) > Belgium > http://homepages.vub.ac.be/~thamelry > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From thamelry at vub.ac.be Wed Aug 6 03:30:54 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Wed Aug 6 03:28:46 2003 Subject: [BioPython] Updated Logo In-Reply-To: <450C65D3-C7C7-11D7-8CEB-000A956845CE@stanford.edu> References: <450C65D3-C7C7-11D7-8CEB-000A956845CE@stanford.edu> Message-ID: <200308060728.h767SWTN005027@kira.skynet.be> On Wednesday 06 August 2003 06:34 am, Jeffrey Chang wrote: > Awesome. Thanks very much! Does the logo scale well, for use either > as an icon or small image suitable for a web link? If it does not look > good smaller, would it be hard to generate a smaller version, but > perhaps with less detail? Smaller versions coming up soon. Greetings, -Thomas From gebauer-jung at ice.mpg.de Wed Aug 6 10:37:49 2003 From: gebauer-jung at ice.mpg.de (Steffi Gebauer-Jung) Date: Wed Aug 6 10:16:18 2003 Subject: [BioPython] Problems with Bio.Application.generic_run() In-Reply-To: <200307181358.h6IDvqqu030052@localhost.localdomain> References: <200307181358.h6IDvqqu030052@localhost.localdomain> Message-ID: <3F3112BD.8060508@ice.mpg.de> Hello, using the Bio.Application package, I got some trouble. When using generic_run() to run blast, which in this case produced a --very-- large output and several warnings, the blast process fell asleep. Running this blast as standalone, there were no problems. Looking around in the Python Reference etc. I found that there is possibly a dead lock of parent and child processes. For now I solved this problem using a recipe from the Python Cookbook as follows: ------------------------------------------------------------------------------------------- def generic_run(commandline): """Run an application with the given commandline. This expects a pre-built commandline that derives from AbstractCommandline, and returns a ApplicationResult object to get results from a program, along with handles of the standard output and standard error. This is a deadlock save version. It was derived from http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52296 Comment: Differnet Approach: Using Tempfiles, Tobias Polzin, 2002/09/03 """ outfile = tempfile.mktemp() errfile = tempfile.mktemp() errorlevel = os.system("( %s ) > %s 2> %s" % (str(commandline),outfile,errfile)) >> 8 r_out = open(outfile,"r").read() os.remove(outfile) e_out = open(errfile,"r").read() os.remove(errfile) return ApplicationResult(commandline), \ File.UndoHandle(StringIO.StringIO(r_out)), \ File.UndoHandle(StringIO.StringIO(e_out)) ------------------------------------------------------------------------------------------- Please could you have a look at this quite central method or tell me a more save one to use instead? Thanks in advance, Steffi From thamelry at vub.ac.be Thu Aug 7 13:42:55 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Thu Aug 7 13:48:28 2003 Subject: [BioPython] Updated Logo In-Reply-To: <450C65D3-C7C7-11D7-8CEB-000A956845CE@stanford.edu> References: <450C65D3-C7C7-11D7-8CEB-000A956845CE@stanford.edu> Message-ID: <200308071740.h77HeVTN011918@kira.skynet.be> Hi, Here's a smaller version of the biopython logo (300x89). The large image scales well using gimp, BTW, or so I think. Can it now be added to the biopython homepage? Regards, --- Thomas Hamelryck ULTR/COMO Institute for molecular biology/Computer Science Department Vrije Universiteit Brussel (VUB) Brussels, Belgium http://homepages.vub.ac.be/~thamelry -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython_small.jpg Type: image/jpeg Size: 8188 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20030807/d9973e32/biopython_small-0001.jpg From thamelry at vub.ac.be Thu Aug 7 13:48:03 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Thu Aug 7 13:48:29 2003 Subject: [BioPython] Biopython logo in crystal Message-ID: <200308071745.h77Hjd0g020025@sojef.skynet.be> Some time ago I mentioned that the biopython logo was burned into a crystal block. Here's a computer generated file of what it looks like. The perfect birthday gift for biopython affictionados :-) The technique itself is actually quite interesting : you can burn any 3D shape into such a crystal block. Cheers, --- Thomas Hamelryck ULTR/COMO Institute for molecular biology/Computer Science Department Vrije Universiteit Brussel (VUB) Brussels, Belgium http://homepages.vub.ac.be/~thamelry -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython_crystal.jpg Type: image/jpeg Size: 395002 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20030807/e5d362e8/biopython_crystal-0001.jpg From jchang at smi.stanford.edu Thu Aug 7 14:05:02 2003 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Thu Aug 7 14:04:42 2003 Subject: [BioPython] Biopython logo in crystal In-Reply-To: <200308071745.h77Hjd0g020025@sojef.skynet.be> Message-ID: Hey Thomas, That is one of the coolest things I have ever seen! Do you actually have one of those sitting on your desk? Jeff On Thursday, August 7, 2003, at 10:48 AM, Thomas Hamelryck wrote: > > > Some time ago I mentioned that the biopython logo was burned into a > crystal > block. Here's a computer generated file of what it looks like. The > perfect > birthday gift for biopython affictionados :-) The technique itself is > actually quite interesting : you can burn any 3D shape into such a > crystal > block. > > Cheers, > > --- > Thomas Hamelryck > ULTR/COMO > Institute for molecular biology/Computer Science Department > Vrije Universiteit Brussel (VUB) > Brussels, Belgium > http://homepages.vub.ac.be/ > ~thamelry_______________________________________ > ________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From thamelry at vub.ac.be Thu Aug 7 14:16:27 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Thu Aug 7 14:13:45 2003 Subject: [BioPython] Biopython logo in crystal Message-ID: <200308071814.h77IE3J5004576@sarek.skynet.be> > That is one of the coolest things I have ever seen! Do you actually > have one of those sitting on your desk? Yep :-) I have a real picture of it too, but the computer generated picture is actually closer to the real thing. Henrik Vestergaard has started up a company that burns these things. He can burn any 3D object (decribed eg. in a VRML or 3DMAX file) into a crystal. Cheers, -Thomas From pan at uchicago.edu Thu Aug 7 16:04:32 2003 From: pan at uchicago.edu (pan@uchicago.edu) Date: Thu Aug 7 16:04:08 2003 Subject: [BioPython] Biopython logo in crystal In-Reply-To: <200308071814.h77IE3J5004576@sarek.skynet.be> References: <200308071814.h77IE3J5004576@sarek.skynet.be> Message-ID: <1060286672.3f32b0d039ac4@webmail.uchicago.edu> man, that's cool ... Is there any way to make it colorful ? pan Quoting Thomas Hamelryck : > > > > That is one of the coolest things I have ever seen! Do you actually > > have one of those sitting on your desk? > > Yep :-) > > I have a real picture of it too, but the computer generated picture is > actually closer to the real thing. Henrik Vestergaard has started up a > company that burns these things. He can burn any 3D object (decribed > eg. in a VRML or 3DMAX file) into a crystal. > > Cheers, > > -Thomas > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From thamelry at vub.ac.be Thu Aug 7 16:21:43 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Thu Aug 7 16:19:00 2003 Subject: [BioPython] Biopython logo in crystal In-Reply-To: <1060286672.3f32b0d039ac4@webmail.uchicago.edu> References: <200308071814.h77IE3J5004576@sarek.skynet.be> <1060286672.3f32b0d039ac4@webmail.uchicago.edu> Message-ID: <200308072019.h77KJKTN023851@kira.skynet.be> > man, that's cool ... Yes :-) > Is there any way to make it colorful ? I don't think that exists yet. It should in principle be possible using some kind of material that changes color depending on the intensity of the radiation. -Thomas From mgollery at unr.edu Fri Aug 8 16:06:54 2003 From: mgollery at unr.edu (Martin Gollery) Date: Fri Aug 8 16:10:03 2003 Subject: [BioPython] fasta retrieval Message-ID: <1060373214.3f3402de63751@webmail.unr.edu> Hello, I need to extract 702 sequences from a database of about 25000 fasta sequences. Does anyone have a script for that? thanks, Marty Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 New phone number! 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From chapmanb at uga.edu Fri Aug 8 18:19:00 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Fri Aug 8 18:22:46 2003 Subject: [BioPython] Problems with Bio.Application.generic_run() In-Reply-To: <3F3112BD.8060508@ice.mpg.de> References: <200307181358.h6IDvqqu030052@localhost.localdomain> <3F3112BD.8060508@ice.mpg.de> Message-ID: <20030808221900.GF47653@evostick.agtec.uga.edu> Hi Steffi; > using the Bio.Application package, I got some trouble. > > When using generic_run() to run blast, which in this case produced a > --very-- large output and several warnings, the blast process fell asleep. > Running this blast as standalone, there were no problems. Hmmm. This is definitely a problem, and not something I know much at all about. Thanks for reporting it. > Looking around in the Python Reference etc. I found that there is > possibly a dead lock of parent and child processes. > > For now I solved this problem using a recipe from the Python Cookbook as > follows: [...] > http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52296 Thanks for looking into this. I definitely agree that we need a solution to this type of problem. However, looking at the solution, the following line looks very UNIX-specific: > errorlevel = os.system("( %s ) > %s 2> %s" % > (str(commandline),outfile,errfile)) >> 8 I know next to nothing about Windows and the DOS commandline, but I don't know if it has redirects like the UNIX ones. Am I true in thinking this? Can anyone that knows anything about Windows help me out? So yeah, I'd like to have a solution that isn't UNIX-specific if that's possible. Does the same BLAST lock up when run using 'blastall' in Bio.Blast.NCBIStandalone? It looks like Jeff and I run the programs in the same way, but one never knows. I'm not sure if this rambling reply helped much. Yes, so I'd like to fix it but am worried about your solution being UNIX-specific. Hope this made some sense! Brad From chapmanb at uga.edu Fri Aug 8 18:29:43 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Fri Aug 8 18:33:29 2003 Subject: [BioPython] fasta retrieval In-Reply-To: <1060373214.3f3402de63751@webmail.unr.edu> References: <1060373214.3f3402de63751@webmail.unr.edu> Message-ID: <20030808222943.GG47653@evostick.agtec.uga.edu> Hi Marty; > I need to extract 702 sequences from a database of about 25000 fasta sequences. > Does anyone have a script for that? It should be easy enough to write one. With Biopython, and assuming the 702 sequence titles you want are in a file each on there own line, it would look something like: from Bio import Fasta input_handle = open("your_seqs.txt") interest_titles = [] for line in input_handle.xreadlines(): interest_titles.append(line) input_handle.close() fasta_handle = open("fasta_database.fasta") parser = Fasta.RecordParser() iterator = Fasta.Iterator(fasta_handle, parser) output_handle = open("your_seqs.fasta", "w") while 1: rec = iterator.next() if not rec: break if rec.title in interest_titles: output_handle.write(str(rec) + "\n") fasta_handle.close() output_handle.close() That's off the top of my head in a mail client so no promises that it works exactly, but it should give the idea. Hopefully this helps. Brad From thamelry at vub.ac.be Mon Aug 11 04:43:39 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Mon Aug 11 05:36:42 2003 Subject: [Biopython-dev] Re: [BioPython] Updated Logo In-Reply-To: References: <200308071740.h77HeVTN011918@kira.skynet.be> <20030808212919.GC47653@evostick.agtec.uga.edu> Message-ID: <200308111043.39043.thamelry@vub.ac.be> > There's no difference between the major and minor grooves! The > horror! I knew somebody would bring that up :-) > Just kidding. I like it. It would be nice if the web site colors > matched up with the logo more or vice versa. Well, orange is the complemenary color of blue: I think the logo colors go well with the blue section titles.... -Thomas From sbassi at asalup.org Sun Aug 17 23:42:09 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Sun Aug 17 23:44:13 2003 Subject: [BioPython] Instal problem: No dir? Message-ID: <3F404B11.5030805@asalup.org> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello, I tried to install Biopython 1.1 on a Mandrake (MDK) box. The MDK version is 9.0. The Python included is 2.2.1. I installed Numpy from RPM (numpy was on the MDK CD) and eg-mxtexttools from RPM (downloaded from original site). So I thought I had all the requiered pakages to install Biopython. Then I went with python setup.py install And I got (after some garbage text): XX: Invalid Python installation: unable to open /usr/lib/python2.2/config/Makefile (No such file or directory) XX stands for: distutils.errors.DistutilsPlatforError (anyway, I think this is not relevant). The installer seems not to find a Makefile on the config directory. That is somehow expect, since there is no such "config" directory under python2.2. (and I'm sure this Python works, even the IDLE works!) I wave a working Biopython installation on Windows, and this Python2.2 doesn't have a config directory neither. What's wrong here? I also have a dumb question: May I just copy the Bio directory (under site-packages) from my Win instalation over the Linux one? -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAj9ASxEACgkQ6lc7ixf6gKqCIQCeM2NU7sutRSq86Vre3nVnXOCz pJ4An0l1HciqaZr88H8KUQGlCSi6uOSd =SlJ/ -----END PGP SIGNATURE----- From dyoo at hkn.eecs.berkeley.edu Mon Aug 18 00:05:13 2003 From: dyoo at hkn.eecs.berkeley.edu (Danny Yoo) Date: Mon Aug 18 00:04:49 2003 Subject: [BioPython] Instal problem: No dir? In-Reply-To: <3F404B11.5030805@asalup.org> Message-ID: > I tried to install Biopython 1.1 on a Mandrake (MDK) box. The MDK > version is 9.0. The Python included is 2.2.1. I installed Numpy from RPM > (numpy was on the MDK CD) and eg-mxtexttools from RPM (downloaded from > original site). So I thought I had all the requiered pakages to install > Biopython. > Then I went with > python setup.py install > And I got (after some garbage text): > XX: Invalid Python installation: unable to open > /usr/lib/python2.2/config/Makefile (No such file or directory) > > XX stands for: distutils.errors.DistutilsPlatforError (anyway, I think > this is not relevant). Hi Sebastian, Please don't ever make that kind of assumption when submitting a bug report. *grin* Seriously though: it helps us if you don't paraphrase the error message. One technique we often do to pinpoint these errors is string searching through source text to localize the problem. Doing a paraphrase defeats that debugging technique and forces us to work that much harder. We're lazy bums. *grin* Next time, can you show us the exact error message, as well as those lines of "garbage text"? Anyway, I think I know what's going on. You may want to make sure that you've installed the 'libpython2.2-devel' package. Since you're running an RPM-based system, it's very possible that you're simply missing a 'development' library. Building biopython from source requires the Python development packages. Try installing the 'libpython2.2-devel' development package, and then do the 'python setup.py install' on biopython: you should get better results. > I also have a dumb question: May I just copy the Bio directory (under > site-packages) from my Win instalation over the Linux one? Unfortunately, no: biopython consists of a few C binary extensions too, so copying the library from Windows to Linux won't work well. Good luck to you! From anunberg at oriongenomics.com Mon Aug 18 16:24:45 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Mon Aug 18 16:24:02 2003 Subject: [BioPython] need to find Martel Message-ID: <01961B63-D1BA-11D7-B9CB-000A95A001EE@oriongenomics.com> Hi, I was trying to install biopython on a redhat machine at work when i came across the following error: *** Martel *** is either not installed or out of date. This package is required for many Biopython features. Please install it before you install Biopython. You can find Martel at http://www.biopython.org/~dalke/Martel/. this link is broken, where can I find Martel? --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From jchang at jeffchang.com Mon Aug 18 16:38:20 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Mon Aug 18 16:37:38 2003 Subject: [BioPython] need to find Martel In-Reply-To: <01961B63-D1BA-11D7-B9CB-000A95A001EE@oriongenomics.com> Message-ID: Martel is distributed as part of Biopython now. If you are installing from source, there is a Martel/ directory, within which you can do the usual: > python setup.py install Jeff On Monday, August 18, 2003, at 01:24 PM, Andrew Nunberg wrote: > Hi, > I was trying to install biopython on a redhat machine at work when i > came across the following error: > *** Martel *** is either not installed or out of date. > > This package is required for many Biopython features. Please install > it before you install Biopython. > You can find Martel at http://www.biopython.org/~dalke/Martel/. > > this link is broken, where can I find Martel? > > --------------------------------------------------- > Andrew Nunberg Ph.D > Bioinfomagician > Orion Genomics > 4041 Forest Park > St Louis, MO > 314-615-6989 > anunberg@oriongenomics.com > www.oriongenomics.com > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From anunberg at oriongenomics.com Mon Aug 18 17:22:56 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Mon Aug 18 17:22:11 2003 Subject: [BioPython] need to find Martel In-Reply-To: Message-ID: <22C9295F-D1C2-11D7-B9CB-000A95A001EE@oriongenomics.com> Thanks, I was able to find and install biopython I noticed there is a new version of biopython, i have 1.10 installed on another machine is there a need to update asap? I am still learning the basics.. Andy On Monday, August 18, 2003, at 03:38 PM, Jeffrey Chang wrote: > Martel is distributed as part of Biopython now. If you are installing > from source, there is a Martel/ directory, within which you can do the > usual: > > python setup.py install > > Jeff > > > On Monday, August 18, 2003, at 01:24 PM, Andrew Nunberg wrote: > >> Hi, >> I was trying to install biopython on a redhat machine at work when i >> came across the following error: >> *** Martel *** is either not installed or out of date. >> >> This package is required for many Biopython features. Please install >> it before you install Biopython. >> You can find Martel at http://www.biopython.org/~dalke/Martel/. >> >> this link is broken, where can I find Martel? >> >> --------------------------------------------------- >> Andrew Nunberg Ph.D >> Bioinfomagician >> Orion Genomics >> 4041 Forest Park >> St Louis, MO >> 314-615-6989 >> anunberg@oriongenomics.com >> www.oriongenomics.com >> >> _______________________________________________ >> BioPython mailing list - BioPython@biopython.org >> http://biopython.org/mailman/listinfo/biopython > > --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From anunberg at oriongenomics.com Tue Aug 19 15:46:27 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Tue Aug 19 15:45:42 2003 Subject: [BioPython] Help with installing MySQLdb Message-ID: I have successfully installed MySQLdb on my mac and then tried to install it on a red hat 7.2 machine I installed all the prerequisite libraries for biopyton, but when i try import MySQLdb on the redhat machine i get: *** You don't have the (right) mxDateTime binaries installed ! is this a path problem? that is python is looking at an older binary first? --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From hytechhk at sina.com Wed Aug 20 17:51:58 2003 From: hytechhk at sina.com (HY Tech) Date: Wed Aug 20 17:51:05 2003 Subject: [BioPython] New price list for mp3 player, digital camera, cd/vcd/mp3 player and USB flash drive! 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From chapmanb at uga.edu Thu Aug 21 12:41:51 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Aug 21 12:45:04 2003 Subject: [BioPython] Help with installing MySQLdb In-Reply-To: References: Message-ID: <20030821164151.GA96431@evostick.agtec.uga.edu> Hey Andy; > I have successfully installed MySQLdb on my mac and then tried to > install it on a red hat 7.2 machine > I installed all the prerequisite libraries for biopyton, but when i try > import MySQLdb on the redhat machine i get: > *** You don't have the (right) mxDateTime binaries installed ! I don't exactly know what the problem is since I don't use red hat and all that, but I guess I'd just listen to the error message and look at what version of mxDateTime you have installed -- if you even have it installed at all. I don't know what version MySQLdb needs (the documentation doesn't seem to say from a quick glance) but the easiest thing to do is just grab the latest version: http://www.egenix.com/files/python/eGenix-mx-Extensions.html#Download-mxBASE There are Linux RPMs for the latest version 2.0.5. > is this a path problem? that is python is looking at an older binary > first? If you have it installed and it's not finding it (or finding the wrong version) you could check by doing: >>> from mx import DateTime >>> DateTime.__version__ '2.0.3' (Although I have 2.0.4 installed, so maybe the version variable isn't the best ever). You can also find out where the DateTime is being imported from using __file__: >>> DateTime.__file__ '/usr/local/lib/python2.3/site-packages/mx/DateTime/__init__.pyc' Hope this helps. Brad From anunberg at oriongenomics.com Thu Aug 21 12:50:49 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Thu Aug 21 12:49:57 2003 Subject: [BioPython] building biopython in a non-default directory Message-ID: <9E066FC0-D3F7-11D7-9488-000A95A001EE@oriongenomics.com> Hi, I have a linux cluster and I was wondering how i supply a different path to install the biopython libraries on a shared mount ? Thanks --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From chapmanb at uga.edu Thu Aug 21 12:51:26 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Aug 21 12:54:36 2003 Subject: [BioPython] building biopython in a non-default directory In-Reply-To: <9E066FC0-D3F7-11D7-9488-000A95A001EE@oriongenomics.com> References: <9E066FC0-D3F7-11D7-9488-000A95A001EE@oriongenomics.com> Message-ID: <20030821165126.GB96431@evostick.agtec.uga.edu> Hi Andy; > I have a linux cluster and I was wondering how i supply a different > path to install the biopython libraries on a shared mount ? Check out the fine install documentation for the 411 on this: http://www.biopython.org/docs/install/Installation.html#htoc23 Specifically point 3b. Hopefully that helps! Brad From anunberg at oriongenomics.com Thu Aug 21 13:11:02 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Thu Aug 21 13:10:11 2003 Subject: [BioPython] Help with installing MySQLdb In-Reply-To: <20030821164151.GA96431@evostick.agtec.uga.edu> Message-ID: <7161BBB9-D3FA-11D7-8EB9-000A95A001EE@oriongenomics.com> Thanks, my DateTime has no __version__ attribute, although I can see its coming from the package I installed (it does have the __file__ attribute) Anyone else have any ideas? On Thursday, August 21, 2003, at 11:41 AM, Brad Chapman wrote: > Hey Andy; > >> I have successfully installed MySQLdb on my mac and then tried to >> install it on a red hat 7.2 machine >> I installed all the prerequisite libraries for biopyton, but when i >> try >> import MySQLdb on the redhat machine i get: >> *** You don't have the (right) mxDateTime binaries installed ! > > I don't exactly know what the problem is since I don't use red hat > and all that, but I guess I'd just listen to the error message and > look at what version of mxDateTime you have installed -- if you even > have it installed at all. > > I don't know what version MySQLdb needs (the documentation doesn't > seem to say from a quick glance) but the easiest thing to do is just > grab the latest version: > > http://www.egenix.com/files/python/eGenix-mx-Extensions.html#Download- > mxBASE > > There are Linux RPMs for the latest version 2.0.5. > >> is this a path problem? that is python is looking at an older binary >> first? > > If you have it installed and it's not finding it (or finding the > wrong version) you could check by doing: > >>>> from mx import DateTime >>>> DateTime.__version__ > '2.0.3' > > (Although I have 2.0.4 installed, so maybe the version variable > isn't the best ever). > > You can also find out where the DateTime is being imported from > using __file__: > >>>> DateTime.__file__ > '/usr/local/lib/python2.3/site-packages/mx/DateTime/__init__.pyc' > > Hope this helps. > Brad > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From chapmanb at uga.edu Thu Aug 21 13:14:54 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Aug 21 13:18:04 2003 Subject: [BioPython] Help with installing MySQLdb In-Reply-To: <7161BBB9-D3FA-11D7-8EB9-000A95A001EE@oriongenomics.com> References: <20030821164151.GA96431@evostick.agtec.uga.edu> <7161BBB9-D3FA-11D7-8EB9-000A95A001EE@oriongenomics.com> Message-ID: <20030821171454.GC96431@evostick.agtec.uga.edu> Hey Andy; > my DateTime has no __version__ attribute, although I can see its coming > from the package I installed (it does have the __file__ attribute) Then I'd expect it's really old. The only way to really know the version, then, is by querying the package organizer you are using (RPM?). The easiest solution is to just install a newer version. From the error you got and no __version__ attribute, I'd just plain assume it's too ancient. No reason not to just update to the latest version and make everything happy. Brad From anunberg at oriongenomics.com Thu Aug 21 13:25:12 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Thu Aug 21 13:24:20 2003 Subject: [BioPython] Help with installing MySQLdb In-Reply-To: <20030821171454.GC96431@evostick.agtec.uga.edu> Message-ID: <6C16CB2C-D3FC-11D7-8EB9-000A95A001EE@oriongenomics.com> well that was done after downloading the source code from the website and installing it on the machine... I havent used any of the rpm's yet On Thursday, August 21, 2003, at 12:14 PM, Brad Chapman wrote: > Hey Andy; > >> my DateTime has no __version__ attribute, although I can see its >> coming >> from the package I installed (it does have the __file__ attribute) > > Then I'd expect it's really old. The only way to really know the > version, then, is by querying the package organizer you are using > (RPM?). > > The easiest solution is to just install a newer version. From the > error you got and no __version__ attribute, I'd just plain assume > it's too ancient. No reason not to just update to the latest version > and make everything happy. > > Brad > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From chapmanb at uga.edu Thu Aug 21 13:44:21 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Aug 21 13:47:32 2003 Subject: [BioPython] Help with installing MySQLdb In-Reply-To: <6C16CB2C-D3FC-11D7-8EB9-000A95A001EE@oriongenomics.com> References: <20030821171454.GC96431@evostick.agtec.uga.edu> <6C16CB2C-D3FC-11D7-8EB9-000A95A001EE@oriongenomics.com> Message-ID: <20030821174421.GD96431@evostick.agtec.uga.edu> Hey Andy; > well that was done after downloading the source code from the website > and installing it on the machine... Well, then. Okay. You gotta be a little more verbose here, baby, help me out, now :-). I dug around in the mx extension and it looks like your error is coming from the mx extensions themselves. The "*** You don't have the (right) mxDateTime binaries installed !" message is actually in /DateTime/mxDateTime/__init__.py. So I have four guesses: 1. You didn't install the thing properly. -- how exactly did you install it? python setup.py build and python setup.py install? If you don't build the C extensions parts of the module (and just import the directory) I can get the following error: >>> from mx import DateTime *** You don't have the (right) mxDateTime binaries installed ! Traceback (most recent call last): File "", line 1, in ? File "mx/DateTime/__init__.py", line 8, in ? from DateTime import * File "DateTime.py", line 9, in ? File "/usr/local/lib/python2.3/site-packages/PIL/__init__.py", line 13, in ? ImportError: No module named mxDateTime This seems close to what you've got. 2. You are importing it from a local (non-compiled) directory when you mean to import it from the installed (compiled) directory. Does DateTime.__file__ give you the expected file (from a compiled directory)? 3. This is just guessing, but if I remember back the old versions of mxDateTime installed into a top level mxDateTime directory (instead of the current mx/DateTime). If you have these around (in site-packages or whereever) you could delete them and install fresh. 4. Your python installed is seriously messed up. In this case I can't help you out. Get a python dude 'round by you to check it out. You can get some seriously weird errors when things are totally jacked. > I havent used any of the rpm's yet If the problem is the installation one above, why not try the RPMs? I have no idea how you are administering the machine, but if the RPMs install cleanly it seems as if you can't go wrong with an already compiled package. Brad From r-spirit at sproxy03.hi-ho.ne.jp Thu Aug 21 22:54:14 2003 From: r-spirit at sproxy03.hi-ho.ne.jp (r-spirit@sproxy03.hi-ho.ne.jp) Date: Thu Aug 21 22:57:10 2003 Subject: [BioPython] Voice Message (324395940126725) Message-ID: <0HK000FJ02QE7O@sproxy03.hi-ho.ne.jp> ------ name ------ Anonymous Friend ------ address ------ Secret ------ message ------ Add expressive voice and music to your websites and emails. Use this new marketing tool in your business or just for fun!. 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Click the following link to listen to your message: http://voice-email.vze.com/?id=295697460682 Local Time: 2003/8/22/18:34 From anunberg at oriongenomics.com Mon Aug 25 16:30:48 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Mon Aug 25 16:29:51 2003 Subject: [BioPython] Game XML Message-ID: <034C84BA-D73B-11D7-88CA-000A95A001EE@oriongenomics.com> Has anyone have experience taking a seq record object and converting it to game xml for apollo viewing?? thanks --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From idoerg at burnham.org Mon Aug 25 16:47:39 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon Aug 25 16:49:22 2003 Subject: [BioPython] Enzyme module Message-ID: <3F4A75EB.4040008@burnham.org> Hi, Has anybody ever used the Enzyme module and written some sort of consumer for it? I'd like to do some very basic parsing... and steal some code :) Thanks, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From idoerg at burnham.org Mon Aug 25 18:30:06 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon Aug 25 18:31:51 2003 Subject: [BioPython] Enzyme module In-Reply-To: <3F4A75EB.4040008@burnham.org> References: <3F4A75EB.4040008@burnham.org> Message-ID: <3F4A8DEE.5070805@burnham.org> In response to myself: I am writing the consumer. Watch this space... ./I Iddo Friedberg wrote: > Hi, > > Has anybody ever used the Enzyme module and written some sort of > consumer for it? I'd like to do some very basic parsing... and steal > some code :) > > Thanks, > > Iddo > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From jchang at jeffchang.com Mon Aug 25 18:33:42 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Mon Aug 25 18:33:00 2003 Subject: [BioPython] Enzyme module In-Reply-To: <3F4A75EB.4040008@burnham.org> Message-ID: <2E0125E4-D74C-11D7-82B3-000A956845CE@jeffchang.com> Yeah, that was my code. I used it a few years ago, and did not need a consumer, so did not write one. The format was pretty simple, so it was pretty easy to write a quick throw-away consumer that just pulled out the lines I needed! Jeff On Monday, August 25, 2003, at 01:47 PM, Iddo Friedberg wrote: > Hi, > > Has anybody ever used the Enzyme module and written some sort of > consumer for it? I'd like to do some very basic parsing... and steal > some code :) > > Thanks, > > Iddo > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From ssheu at post.harvard.edu Mon Aug 25 22:01:54 2003 From: ssheu at post.harvard.edu (Shu-Hsien Sheu) Date: Mon Aug 25 22:00:59 2003 Subject: [BioPython] Windows installer for Python 2.3? Message-ID: <004e01c36b76$06416d90$9200a8c0@PowerLoom> Hi, I encountered compiler version problem (i am using C.net) when doing manual installations. Is there an installer for Python 2.3? It seems that both NumericPy and mXTexttools both have updated installers. Thanks! -Shuhsien Sheu MD, MPH From mdehoon at ims.u-tokyo.ac.jp Mon Aug 25 23:31:11 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Aug 25 23:28:16 2003 Subject: [BioPython] Windows installer for Python 2.3? In-Reply-To: <004e01c36b76$06416d90$9200a8c0@PowerLoom> References: <004e01c36b76$06416d90$9200a8c0@PowerLoom> Message-ID: <3F4AD47F.8010406@ims.u-tokyo.ac.jp> I have made a Biopython Windows installer for Python 2.3. This installer is based on Biopython 1.21 (so not on the CVS version). I will send it to Brad for inclusion in the Biopython website, and also to Shu-Hsien directly. There was one glitch with setup.py (see below); I solved this by copying those files directly. --Michiel. When running "python setup.py bdist_wininst": error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file or directory Shu-Hsien Sheu wrote: > Hi, > > I encountered compiler version problem (i am using C.net) when doing manual > installations. Is there an installer for Python 2.3? It seems that both > NumericPy and mXTexttools both have updated installers. > > Thanks! > > -Shuhsien Sheu > MD, MPH > > > _______________________________________________ > 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 letondal at pasteur.fr Tue Aug 26 04:26:19 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Tue Aug 26 04:25:21 2003 Subject: [BioPython] Enzyme module In-Reply-To: Your message of "Mon, 25 Aug 2003 13:47:39 PDT." <3F4A75EB.4040008@burnham.org> Message-ID: <200308260826.h7Q8QJvX408426@electre.pasteur.fr> Iddo Friedberg wrote: > Hi, > > Has anybody ever used the Enzyme module and written some sort of > consumer for it? I'd like to do some very basic parsing... and steal > some code :) We just have something as a serie of exercises in our online course :-) http://www.pasteur.fr/recherche/unites/sis/formation/python/ch13.html#sect_parsers (13.1.2. Exercises: building parsing classes for Enzyme: it is a progressive introduction to BioPython parser framework). So, we are interested in your feedback :-) > > Thanks, > > Iddo > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- Catherine Letondal -- Pasteur Institute Computing Center From pwilkinson at videotron.ca Tue Aug 26 09:40:29 2003 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 26 09:40:20 2003 Subject: [BioPython] Creating a parser for Quantarray data? In-Reply-To: <2E0125E4-D74C-11D7-82B3-000A956845CE@jeffchang.com> References: <3F4A75EB.4040008@burnham.org> Message-ID: <5.2.0.9.0.20030825185622.00b20a98@pop.videotron.ca> Well I have just acquired a need for some expression format parsers like QuantArray, gal, Iobion etc. I have been looking through CVS for some, and I dont see any. Is it worth creating a parser within the parser framework within biopython (Martel), or shall I build a something separately. These can be large files, and I would want to implement something that is efficient. How would Martel handle a 20M Record like a Quantarray file? When I was parsing genomic Genbank files (Bacteria), the Genbank parser's performance started to suffer ... Peter W. From ssheu at post.harvard.edu Tue Aug 26 11:42:51 2003 From: ssheu at post.harvard.edu (Shu-Hsien Sheu) Date: Tue Aug 26 11:51:56 2003 Subject: [BioPython] Windows installer for Python 2.3? References: <004e01c36b76$06416d90$9200a8c0@PowerLoom> <3F4AD47F.8010406@ims.u-tokyo.ac.jp> Message-ID: <005001c36be8$b58b5d20$d038c580@ANDIAMO> Great thanks! For some reason I did not encounter the glitch you've mentioned? Well, it's not a bath thing at all:) Hope i can contribute later on as well. -shuhsien ----- Original Message ----- From: "Michiel Jan Laurens de Hoon" To: Sent: Monday, August 25, 2003 11:31 PM Subject: Re: [BioPython] Windows installer for Python 2.3? > I have made a Biopython Windows installer for Python 2.3. This installer > is based on Biopython 1.21 (so not on the CVS version). I will send it > to Brad for inclusion in the Biopython website, and also to Shu-Hsien > directly. There was one glitch with setup.py (see below); I solved this > by copying those files directly. > > --Michiel. > > When running "python setup.py bdist_wininst": > > error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file > or directory > > > Michiel de Hoon, Assistant Professor > University of Tokyo, Institute of Medical Science > Human Genome Center > 4-6-1 Shirokane-dai, Minato-ku > Tokyo 108-8639 > Japan > http://bonsai.ims.u-tokyo.ac.jp/~mdehoon > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From andorsch at gmx.at Tue Aug 26 12:26:53 2003 From: andorsch at gmx.at (Andreas Prlic) Date: Tue Aug 26 12:25:55 2003 Subject: [BioPython] biopython 1.21 debian package In-Reply-To: <3EDD04F8-C152-11D7-989F-000A956845CE@smi.stanford.edu> References: <3EDD04F8-C152-11D7-989F-000A956845CE@smi.stanford.edu> Message-ID: <200308261826.53304.andorsch@gmx.at> Hi everybody! Does anybody provide a debian package for biopython 1.21 ? I could only find one for biopython 1.00a4 (1 year old) ... best regards, andreas From mdehoon at ims.u-tokyo.ac.jp Tue Aug 26 12:27:06 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Tue Aug 26 12:27:23 2003 Subject: [BioPython] Windows installer for Python 2.3? In-Reply-To: <005001c36be8$b58b5d20$d038c580@ANDIAMO> References: <004e01c36b76$06416d90$9200a8c0@PowerLoom> <3F4AD47F.8010406@ims.u-tokyo.ac.jp> <005001c36be8$b58b5d20$d038c580@ANDIAMO> Message-ID: <3F4B8A5A.7080503@ims.u-tokyo.ac.jp> The glitch appears only when building Biopython from source and when creating the Windows installer. I fixed the Windows installer by hand, so you shouldn't encounter any glitches when using this installer. --Michiel. Shu-Hsien Sheu wrote: > Great thanks! > > For some reason I did not encounter the glitch you've mentioned? Well, it's > not a bath thing at all:) > > Hope i can contribute later on as well. > > -shuhsien > > ----- Original Message ----- > From: "Michiel Jan Laurens de Hoon" > To: > Sent: Monday, August 25, 2003 11:31 PM > Subject: Re: [BioPython] Windows installer for Python 2.3? > > > >>I have made a Biopython Windows installer for Python 2.3. This installer >>is based on Biopython 1.21 (so not on the CVS version). I will send it >>to Brad for inclusion in the Biopython website, and also to Shu-Hsien >>directly. There was one glitch with setup.py (see below); I solved this >>by copying those files directly. >> >>--Michiel. >> >>When running "python setup.py bdist_wininst": >> >>error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file >>or directory >> >> >>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 >> >>_______________________________________________ >>BioPython mailing list - BioPython@biopython.org >>http://biopython.org/mailman/listinfo/biopython > > > _______________________________________________ > 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 dalke at dalkescientific.com Tue Aug 26 14:25:16 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue Aug 26 14:23:52 2003 Subject: [BioPython] Creating a parser for Quantarray data? In-Reply-To: <5.2.0.9.0.20030825185622.00b20a98@pop.videotron.ca> Message-ID: Peter Wilkinson: > I have been looking through CVS for some, and I dont see any. Is it > worth creating a parser within the parser framework within biopython > (Martel), or shall I build a something separately. > > These can be large files, and I would want to implement something that > is efficient. > > How would Martel handle a 20M Record like a Quantarray file? When I > was parsing genomic Genbank files (Bacteria), the Genbank parser's > performance started to suffer ... Yeah, Martel is poor that way. I've got the RecordReaders as a workaround for when a single record is small enough. Otherwise, there's about a x5 memory overhead. I've got some highly experimental code which fixes part of the problem (it ended up being a pure-python regexp engine) but it isn't usable and has problems of its own. So for this task, it's likely best you write your own parser. *sigh* Anyone want to fund me for the month or two it will take to finish up Martel. :) Andrew dalke@dalkescientific.com From dag at sonsorol.org Wed Aug 27 11:46:07 2003 From: dag at sonsorol.org (Chris Dagdigian) Date: Wed Aug 27 11:45:15 2003 Subject: [BioPython] Open-Bio server downtime and IP address changes scheduled for Tuesday September 2nd 2003 Message-ID: <3F4CD23F.8090807@sonsorol.org> Hi Everyone, Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers. Simply put -- Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone. Technically the changeover will be swift as the circuit and new routers/firewalls are already in place. Should be a matter of bringing down the old gear and lighting up the new stuff. The backbone change will have a significant affect on us though -- all of our server IP addresses will change. The change is scheduled for the evening (EST/EDT timezone) of September 2nd 2003. I'll be onsite at Wyeth in the datacenter as the change occurs so that I can bring down our servers and plug in the new IP addresses. The really nice thing is that all of our primary and secondary DNS nameservers are hosted at places other than Wyeth. This means that we can almost instantly be pushing out the new correct IP addresses for all of our open-bio.org, biojava.org etc. domain names. If I can get my act together during the day on Tuesday I'll start seeding our DNS servers with shorter TTL values which will speed up the spread of the new information. For people with 'fresh' DNS data our servers will appear back on the internet within 30 minutes or so. For people behind nameserver caches that do not refresh all that often please expect our servers to "vanish" from the internet for a period of about 8-24 hours while the new information propagates out through the internet. Regards, Chris open-bio.org -- Chris Dagdigian, BioTeam Inc. - Independent Bio-IT & Informatics consulting Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net From tt_ttt at gawab.com Thu Aug 28 09:51:26 2003 From: tt_ttt at gawab.com (Mrs. Patricia) Date: Thu Aug 28 09:51:26 2003 Subject: [BioPython] Enquire Message-ID: <200308281351.h7SDp7Ra002381@localhost.localdomain> Hello, I have contact you after due consideration and consultation to assist us in a proposition for the benefit of both parties involved (Your side and mine). We have an enormous amount of funds that we are hoping to put into a very viable venture in your country with your assistance. As soon as I receive a response from you regarding your willingness to assist us with this proposition, I will proceed immediately to provide you with further details about how we intend t o make you our overseas partner. Bear in mind, this does not have anything to do with Terrorism or Money Laundering. I will await your urgent response. Regards, Mrs. Patricia From tt_ttt at gawab.com Thu Aug 28 09:51:36 2003 From: tt_ttt at gawab.com (Mrs. Patricia) Date: Thu Aug 28 09:51:38 2003 Subject: [BioPython] Enquire Message-ID: <200308281351.h7SDpORa002414@localhost.localdomain> Hello, I have contact you after due consideration and consultation to assist us in a proposition for the benefit of both parties involved (Your side and mine). We have an enormous amount of funds that we are hoping to put into a very viable venture in your country with your assistance. As soon as I receive a response from you regarding your willingness to assist us with this proposition, I will proceed immediately to provide you with further details about how we intend to make you our overseas partner. Bear in mind, this does not have anything to do with Terrorism or Money Laundering. I will await your urgent response. Regards, Mrs. Patricia From doming at mpi-sb.mpg.de Thu Aug 28 10:45:33 2003 From: doming at mpi-sb.mpg.de (Francisco Domingues) Date: Thu Aug 28 10:46:37 2003 Subject: [BioPython] biopython 1.21 problem with Martel Message-ID: <3F4E158D.40809@mpi-sb.mpg.de> Hi, I am running SuSe Linux 8.1, I have python 2.2.1 I have installed Numerical Python and mxTextTools. I am trying to install biopython 1.21, this is a first installation of biopython in my machine. after: >python setup.py install I get *** Martel *** is either not installed or out of date. This package is required for many Biopython features. Please install it before you install Biopython. You can find Martel at http://www.biopython.org/~dalke/Martel/. According to Jeff instructions in this mailing list I went down to the Martel directory and did >python setup.py install no errors Still it fails the tests: ...biopython-1.21/Martel> python setup.py installtest running installtest ###### running tests in test_Expression ############### Traceback (most recent call last): File "setup.py", line 158, in ? File "/usr/lib/python2.2/distutils/core.py", line 138, in setup dist.run_commands() File "/usr/lib/python2.2/distutils/dist.py", line 893, in run_commands self.run_command(cmd) File "/usr/lib/python2.2/distutils/dist.py", line 913, in run_command cmd_obj.run() File "setup.py", line 139, in run File "run_tests.py", line 16, in main module = __import__(name) File "test_Expression.py", line 3, in ? from Martel import Re File "/usr/lib/python2.2/site-packages/Martel/__init__.py", line 6, in ? import Expression File "/usr/lib/python2.2/site-packages/Martel/Expression.py", line 31, in ? from xml.sax import xmlreader ImportError: No module named xml.sax Same if I do >python setup.py test I also did installation of all biopython by forcing to continue after the Martel error: *** Martel *** is either not installed or out of date. ... Do you want to continue this installation? (y/N) y It installs but running the test it gives severall errors, seem to be associated with xml.sax: > python setup.py test running test Warning: Could not import SAX for dealing with XML. This causes problems with some ParserSupport modules Skipping test because of import error: Please comment out this line to enable the tests. Skipping test because of import error: No module named MySQLdb Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named MySQLdb Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named reportlab.pdfgen Skipping test because of import error: No module named reportlab.pdfgen Skipping test because of import error: No module named reportlab.pdfgen Skipping test because of import error: No module named _KDTreec Skipping test because of import error: No module named xml.sax Skipping test because of import error: cannot import name Alignment Skipping test because of import error: cannot import name SeqRecord Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax Skipping test because of import error: No module named xml.sax I repeated the procedure severall times, but it still gives the same errors. Any Suggestions? Tanks Francisco From andreas.kuntzagk at mdc-berlin.de Thu Aug 28 11:06:35 2003 From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk) Date: Thu Aug 28 11:06:37 2003 Subject: [BioPython] biopython 1.21 problem with Martel In-Reply-To: <3F4E158D.40809@mpi-sb.mpg.de> References: <3F4E158D.40809@mpi-sb.mpg.de> Message-ID: <1062083152.9708.16.camel@sulawesi> > I am running SuSe Linux 8.1, I have python 2.2.1 Me too. > Still it fails the tests: > ...biopython-1.21/Martel> python setup.py installtest > running installtest > ###### running tests in test_Expression ############### > Traceback (most recent call last): > File "setup.py", line 158, in ? > File "/usr/lib/python2.2/distutils/core.py", line 138, in setup > dist.run_commands() > File "/usr/lib/python2.2/distutils/dist.py", line 893, in run_commands > self.run_command(cmd) > File "/usr/lib/python2.2/distutils/dist.py", line 913, in run_command > cmd_obj.run() > File "setup.py", line 139, in run > File "run_tests.py", line 16, in main > module = __import__(name) > File "test_Expression.py", line 3, in ? > from Martel import Re > File "/usr/lib/python2.2/site-packages/Martel/__init__.py", line 6, in ? > import Expression > File "/usr/lib/python2.2/site-packages/Martel/Expression.py", line 31, > in ? > from xml.sax import xmlreader > ImportError: No module named xml.sax Looks like the xml-packages are not installed. Pleas install the python-xml rpm from your installation-media and try again. HtH, Andreas From doming at mpi-sb.mpg.de Thu Aug 28 12:35:25 2003 From: doming at mpi-sb.mpg.de (Francisco Domingues) Date: Thu Aug 28 12:36:27 2003 Subject: [BioPython] biopython 1.21 problem with Martel References: <3F4E158D.40809@mpi-sb.mpg.de> <1062083152.9708.16.camel@sulawesi> Message-ID: <3F4E2F4D.4070308@mpi-sb.mpg.de> Got python-xml. Biopython installation and tests work fine now. Thanks Andreas Francisco Andreas Kuntzagk wrote: >>I am running SuSe Linux 8.1, I have python 2.2.1 >> >> > >Me too. > > > >>Still it fails the tests: >>...biopython-1.21/Martel> python setup.py installtest >>running installtest >>###### running tests in test_Expression ############### >>Traceback (most recent call last): >> File "setup.py", line 158, in ? >> File "/usr/lib/python2.2/distutils/core.py", line 138, in setup >> dist.run_commands() >> File "/usr/lib/python2.2/distutils/dist.py", line 893, in run_commands >> self.run_command(cmd) >> File "/usr/lib/python2.2/distutils/dist.py", line 913, in run_command >> cmd_obj.run() >> File "setup.py", line 139, in run >> File "run_tests.py", line 16, in main >> module = __import__(name) >> File "test_Expression.py", line 3, in ? >> from Martel import Re >> File "/usr/lib/python2.2/site-packages/Martel/__init__.py", line 6, in ? >> import Expression >> File "/usr/lib/python2.2/site-packages/Martel/Expression.py", line 31, >>in ? >> from xml.sax import xmlreader >>ImportError: No module named xml.sax >> >> > >Looks like the xml-packages are not installed. Pleas install the >python-xml rpm from your installation-media and try again. > >HtH, Andreas > > > From letondal at pasteur.fr Fri Aug 29 10:16:38 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri Aug 29 10:15:35 2003 Subject: [BioPython] Pise client In-Reply-To: Your message of "Mon, 26 Aug 2002 20:28:58 +0200." <200208261828.g7QISxLq208805@electre.pasteur.fr> Message-ID: <200308291416.h7TEGcvX469438@electre.pasteur.fr> Hi, The SAX parser (xml.sax.handler) that is used in the Pise/Python modules raises an exception, with some versions of this parser, when provided with a wrong url for the DTD. Indeed, the url provided in Pise for the XHTML DTD has changed more or less recently. So, it was quite impossible to use the Pise/Python module. Thanks to Josh Cherry for having reported the bug. Catherine Letondal wrote: > > Hi, > > I have written a Python package to run jobs on a Pise Web server from a python > program (Pise is a tool to generate user interfaces for programs running under Unix > described here: http://www.pasteur.fr/recherche/unites/sis/Pise). > > For example, the following script run a toppred job on a SeqRecord instance, displays > the standard output of this job, and save the graphical output in a file. Sequences > or alignments can be input either as Seq, SeqRecord, files or just strings. > > from Pise import PiseFactory > import Bio.Fasta > import sys > > factory = PiseFactory(email='user@domain') > program = factory.program("toppred", > graph_output=1, > profile_format="ps") > > handle = open(sys.argv[1]) > it = Bio.Fasta.Iterator(handle, Bio.Fasta.SequenceParser()) > seq = it.next() > > job = program.run(query=seq) > > if job.error(): > print job.error_message() > else: > print "url of the job: " + job.jobid() > print job.stdout() > print "Results: ", job.get_results() > job.save('.ps') > > > The package is available at: http://www.pasteur.fr/recherche/unites/sis/Pise/#pisepython > > The package is organized in 4 main classes (the package is organized about the same > way as in the bioperl API in fact): > > PiseFactory > ----------- > builds PiseApplication > instances > program() > | > | > v > > PiseApplication PiseJob PiseJobParser > --------------- ------- ------------- > object --> actual job (an xml.sax.handler) to parse > to set (methods to XHTML server output > parameters actually submit > and launch the http request > jobs via httplib, > get job state > | and results) > | > +----------------------------------------------+ > | toppred fasta hmmbuild nnssp blast2 clustalw | > | genscan tacg dnapars wublast2 ... | > | | > +----------------------------------------------+ > > > I'm aware about the Bio.Application framework, but I have understood it's more for local > run. For instance, AbstractCommandline would have been useful on a server, but > there is no such thing in the client, which does not deal with command lines. > It should be possible to wrap PiseApplication classes in Bio.Application classes though > (and ApplicationResult sub-class could re-use PiseJob methods for instance). > > > I have tried to put the minimum information in the numerous files that belongs to this > package (there is a small file for each program, and there are about 287 programs). > > > I would be very happy to get some feedback about this code! > > -- Catherine Letondal -- Pasteur Institute Computing Center From piet at clondiag.com Fri Aug 29 13:24:42 2003 From: piet at clondiag.com (Peter Slickers) Date: Fri Aug 29 13:14:59 2003 Subject: [BioPython] blast parser slows down under python2.3 Message-ID: <3F4F8C5A.8070701@clondiag.com> The biopython blast parser runs at only half of the speed seen with python2.2 when executed with python2.3. This effect is monitored best with a huge blast output file. My setup for measuring the performance is quite simple. I have used a small python script which just parses a blast file and stores the content in memory. I have started this script with the time command, and the python interpreter was explicitely specified either as python2.2 or python2.3. Each run was repeated four times. -------------------------------------------------------------- command CPU time in sec -------------------------------------------------------------- time python2.2 parser.py blastout.txt 5.11,3.58,3.98,4.15 time python2.3 parser.py blastout.txt 8.85,7.97,7.30,7.12 -------------------------------------------------------------- (with biopython 1.21) I sticked into this when running the python profiler on the blast parser. It turns out, that more than half of the CPU time was spent in the warnings module, which is part of the python standard installation (/usr/local/lib/python2.3/warnings.py). Further digging revealed that the function warn() is called each time the readline() method from class UndoHandle is executed (file site-packages/Bio/File.py). Within the readline() method the python build-in function apply() is heavily used. But since python2.3 the usage of apply() is deprecated, and therefore the warn() function is called by the interpreter each time the apply() function is used. According to the python2.3 manual, the apply() function should be substituted by the "extended call syntax" (which was introduced in python2.0). To test my hypothesis that the perfomance leck ist caused by the apply() function, I took the standard genetical approach of knock-out and complementing: I created a modified version of Bio/File.py where all occurences of apply() were replaced by "extended call syntax". After that, I run the benchmark again: -------------------------------------------------------------- command CPU time in sec -------------------------------------------------------------- time python2.2 parser.py blastout.txt 4.11,3.53,4.07,4.03 time python2.3 parser.py blastout.txt 4.94,4.96,4.54,5.24 -------------------------------------------------------------- (with modified Bio/File.py) The numbers clearly reveal that my patch successfully reconstitutes the speed of the blast parser under pythons2.3. Fazit: the "newer, better, faster" dogma is not true with python. Here is an example of what the patch looks like: old: line = apply(self._handle.readline, args, keywds) new: line = self._handle.readline(*args,**keywds) -- Peter ------------------------------------------------------------------- Peter Slickers piet@clondiag.com Clondiag Chip Technologies http://www.clondiag.com/ L?bstedter Str. 105 07749 Jena Germany Fon: 03641/5947-65 Fax: 03641/5947-20 ------------------------------------------------------------------- From jchang at jeffchang.com Fri Aug 29 15:07:48 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Fri Aug 29 15:06:50 2003 Subject: [BioPython] blast parser slows down under python2.3 In-Reply-To: <3F4F8C5A.8070701@clondiag.com> Message-ID: <14485E26-DA54-11D7-989A-000A956845CE@jeffchang.com> Hey, thanks very much for the note, and the patch (mailed separately). Python 2.3 also seems to have broken some of the regression tests. The boolean type gets printed out as "True" and "False" rather than 1 or 0 as before. I'll take a look at these over the weekend. Jeff On Friday, August 29, 2003, at 10:24 AM, Peter Slickers wrote: > The biopython blast parser runs at only half of the speed > seen with python2.2 when executed with python2.3. > > > This effect is monitored best with a huge blast output file. > My setup for measuring the performance is quite simple. > I have used a small python script which just parses a blast > file and stores the content in memory. I have started this > script with the time command, and the python interpreter > was explicitely specified either as python2.2 or python2.3. > Each run was repeated four times. > > -------------------------------------------------------------- > command CPU time in sec > -------------------------------------------------------------- > time python2.2 parser.py blastout.txt 5.11,3.58,3.98,4.15 > time python2.3 parser.py blastout.txt 8.85,7.97,7.30,7.12 > -------------------------------------------------------------- > (with biopython 1.21) > > I sticked into this when running the python profiler > on the blast parser. It turns out, that more > than half of the CPU time was spent in the warnings module, > which is part of the python standard installation > (/usr/local/lib/python2.3/warnings.py). > > Further digging revealed that the function warn() is called > each time the readline() method from class UndoHandle is > executed (file site-packages/Bio/File.py). > > Within the readline() method the python build-in function > apply() is heavily used. But since python2.3 the usage of > apply() is deprecated, and therefore the warn() function is called > by the interpreter each time the apply() function is used. > > > According to the python2.3 manual, the apply() function should be > substituted by the "extended call syntax" (which was introduced > in python2.0). > > To test my hypothesis that the perfomance leck ist caused by > the apply() function, I took the standard genetical approach > of knock-out and complementing: I created a modified version > of Bio/File.py where all occurences of apply() were replaced > by "extended call syntax". After that, I run the benchmark again: > > -------------------------------------------------------------- > command CPU time in sec > -------------------------------------------------------------- > time python2.2 parser.py blastout.txt 4.11,3.53,4.07,4.03 > time python2.3 parser.py blastout.txt 4.94,4.96,4.54,5.24 > -------------------------------------------------------------- > (with modified Bio/File.py) > > > The numbers clearly reveal that my patch successfully reconstitutes > the speed of the blast parser under pythons2.3. > > > > Fazit: the "newer, better, faster" dogma is not true with python. > > > Here is an example of what the patch looks like: > > old: line = apply(self._handle.readline, args, keywds) > new: line = self._handle.readline(*args,**keywds) > > > -- > > > Peter > ------------------------------------------------------------------- > Peter Slickers piet@clondiag.com > Clondiag Chip Technologies http://www.clondiag.com/ > L?bstedter Str. 105 > 07749 Jena > Germany > > Fon: 03641/5947-65 Fax: 03641/5947-20 > ------------------------------------------------------------------- > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From jefftc at stanford.edu Sun Aug 31 18:44:18 2003 From: jefftc at stanford.edu (Jeffrey Chang) Date: Sun Aug 31 18:43:17 2003 Subject: [BioPython] blast parser slows down under python2.3 In-Reply-To: <14485E26-DA54-11D7-989A-000A956845CE@jeffchang.com> Message-ID: I have applied the patch. Thanks very much! The regression tests now work again. For the tests that print out booleans, I am now explicitly printing out 0 or 1, for backwards compatibility. I have also gone through and changed some more instances of apply to the new call syntax. Please let me know if there appears to be any problems. Jeff On Friday, August 29, 2003, at 12:07 PM, Jeffrey Chang wrote: > Hey, thanks very much for the note, and the patch (mailed separately). > > Python 2.3 also seems to have broken some of the regression tests. > The boolean type gets printed out as "True" and "False" rather than 1 > or 0 as before. > > I'll take a look at these over the weekend. > > Jeff > > > > > On Friday, August 29, 2003, at 10:24 AM, Peter Slickers wrote: > >> The biopython blast parser runs at only half of the speed >> seen with python2.2 when executed with python2.3. >> >> >> This effect is monitored best with a huge blast output file. >> My setup for measuring the performance is quite simple. >> I have used a small python script which just parses a blast >> file and stores the content in memory. I have started this >> script with the time command, and the python interpreter >> was explicitely specified either as python2.2 or python2.3. >> Each run was repeated four times. >> >> -------------------------------------------------------------- >> command CPU time in sec >> -------------------------------------------------------------- >> time python2.2 parser.py blastout.txt 5.11,3.58,3.98,4.15 >> time python2.3 parser.py blastout.txt 8.85,7.97,7.30,7.12 >> -------------------------------------------------------------- >> (with biopython 1.21) >> >> I sticked into this when running the python profiler >> on the blast parser. It turns out, that more >> than half of the CPU time was spent in the warnings module, >> which is part of the python standard installation >> (/usr/local/lib/python2.3/warnings.py). >> >> Further digging revealed that the function warn() is called >> each time the readline() method from class UndoHandle is >> executed (file site-packages/Bio/File.py). >> >> Within the readline() method the python build-in function >> apply() is heavily used. But since python2.3 the usage of >> apply() is deprecated, and therefore the warn() function is called >> by the interpreter each time the apply() function is used. >> >> >> According to the python2.3 manual, the apply() function should be >> substituted by the "extended call syntax" (which was introduced >> in python2.0). >> >> To test my hypothesis that the perfomance leck ist caused by >> the apply() function, I took the standard genetical approach >> of knock-out and complementing: I created a modified version >> of Bio/File.py where all occurences of apply() were replaced >> by "extended call syntax". After that, I run the benchmark again: >> >> -------------------------------------------------------------- >> command CPU time in sec >> -------------------------------------------------------------- >> time python2.2 parser.py blastout.txt 4.11,3.53,4.07,4.03 >> time python2.3 parser.py blastout.txt 4.94,4.96,4.54,5.24 >> -------------------------------------------------------------- >> (with modified Bio/File.py) >> >> >> The numbers clearly reveal that my patch successfully reconstitutes >> the speed of the blast parser under pythons2.3. >> >> >> >> Fazit: the "newer, better, faster" dogma is not true with python. >> >> >> Here is an example of what the patch looks like: >> >> old: line = apply(self._handle.readline, args, keywds) >> new: line = self._handle.readline(*args,**keywds) >> >> >> -- >> >> >> Peter >> ------------------------------------------------------------------- >> Peter Slickers piet@clondiag.com >> Clondiag Chip Technologies http://www.clondiag.com/ >> L?bstedter Str. 105 >> 07749 Jena >> Germany >> >> Fon: 03641/5947-65 Fax: 03641/5947-20 >> ------------------------------------------------------------------- >> >> _______________________________________________ >> BioPython mailing list - BioPython@biopython.org >> http://biopython.org/mailman/listinfo/biopython >