From L.Pritchard at scri.sari.ac.uk Mon Sep 1 07:50:42 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Mon Sep 1 07:49:34 2003 Subject: [BioPython] Zerg BLAST parser Message-ID: <5.2.1.1.0.20030901124648.02d935d0@caird> Hi, A colleague pointed me to the Zerg BLAST parser (http://bioinfo.iq.usp.br/zerg/) which is apparently pretty quick. It only had a wrapper for Perl, so I knocked one up for Python, partly as a learning exercise in Pyrex. If you think you'll find it useful, or would like to improve on (and/or replace) it, you can find it at http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml Have fun, Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key 47B4A485: http://www.keyserver.net http://pgp.mit.edu From chapmanb at uga.edu Mon Sep 1 11:32:01 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Sep 1 11:34:35 2003 Subject: [BioPython] Zerg BLAST parser In-Reply-To: <5.2.1.1.0.20030901124648.02d935d0@caird> References: <5.2.1.1.0.20030901124648.02d935d0@caird> Message-ID: <20030901153201.GA96954@evostick.agtec.uga.edu> Hi Leighton; > A colleague pointed me to the Zerg BLAST parser > (http://bioinfo.iq.usp.br/zerg/) which is apparently pretty quick. It only > had a wrapper for Perl, so I knocked one up for Python, partly as a > learning exercise in Pyrex. If you think you'll find it useful, or would > like to improve on (and/or replace) it, you can find it at > http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml Cool! Thanks for doing this and posting it. I added the link to the ScriptCentral page (http://www.biopython.org/scriptcentral/). Thanks again! Brad From L.Pritchard at scri.sari.ac.uk Mon Sep 1 11:37:57 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Mon Sep 1 11:36:53 2003 Subject: [BioPython] Zerg BLAST parser - timings Message-ID: <5.2.1.1.0.20030901145744.02dedb28@caird> Hi, While I don't imagine Zerg will necessarily be the best option for all circumstances, running time trials with the script below (extracts all query sequence names from NCBI standalone BLAST output) gives on our Linux server: 361kb output file, 3 runs: ------------------------------------------- Module Mean StDev NCBIStandalone.Parser 0.986s 0.003s Zerg 0.032s 0.005s 367Mb output file, 3 runs: ------------------------------------------- Module Mean StDev NCBIStandalone.Parser 1461.08s 20.95s Zerg 58.29s 4.38s There are almost certainly faster ways to use the Biopython parser code (specialist consumer, perhaps?) than in the test script given below, but I couldn't think of them nearly as quickly as I could implement the quick run-though with the Zerg parser. In this simple case, the Zerg code turned out to be between 25 and 30 times faster than the Biopython code in the script below. The Zerg wrapper and build instructions can be obtained from http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml ############ import time testfile = './testBLAST2.out' print "Begin Biopython test" # BIOPYTHON from Bio.Blast import NCBIStandalone fhandle = open(testfile, 'r') parser = NCBIStandalone.BlastParser() iterator = NCBIStandalone.Iterator(fhandle, parser) biotime0 = time.time() bioquerylist = [] while 1: record = iterator.next() if record is None: break bioquerylist.append(record.query) biotime = time.time() - biotime0 print "End Biopython test" print "Begin Zerg test" # ZERG import zerg zergtime0 = time.time() zergquerylist = [] zerg.open_file(testfile) code, value = zerg.get_token() while code: if code == 2: zergquerylist.append(value) code, value = zerg.get_token() zergtime = time.time() - zergtime0 print "End Zerg test" print "Bio: %s; Zerg: %s" % (len(bioquerylist), len(zergquerylist)) print "Bio: %s; Zerg: %s" % (biotime, zergtime) ###### Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key 47B4A485: http://www.keyserver.net http://pgp.mit.edu From L.Pritchard at scri.sari.ac.uk Mon Sep 1 12:09:11 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Mon Sep 1 12:19:26 2003 Subject: [BioPython] Zerg BLAST parser In-Reply-To: <20030901153201.GA96954@evostick.agtec.uga.edu> References: <5.2.1.1.0.20030901124648.02d935d0@caird> <5.2.1.1.0.20030901124648.02d935d0@caird> Message-ID: <5.2.1.1.0.20030901170003.02d41290@caird> At 11:32 01/09/2003 -0400, you wrote: > > [...] the Zerg BLAST parser (http://bioinfo.iq.usp.br/zerg/) [...] only > > had a wrapper for Perl, so I knocked one up for Python [...] at > > http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml > >Cool! Wow, I got a 'Cool' from Brad! - that's the second really good thing to happen to me today ;) >Thanks for doing this and posting it. I added the link to the >ScriptCentral page (http://www.biopython.org/scriptcentral/). And that's the third... >Thanks again! No problem - so long as people let me know under what circumstances it stops working, and where my docs are *really* unhelpful so I can fix them. On a tangent, would anyone be interested in a publication-quality genome schematic (linear and circular genome diagram, with labels, scales and plots) drawing module? I have one that would probably benefit from public release and comment. Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key 47B4A485: http://www.keyserver.net http://pgp.mit.edu From Yves.Bastide at irisa.fr Tue Sep 2 03:42:40 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Tue Sep 2 03:41:27 2003 Subject: [BioPython] Zerg BLAST parser In-Reply-To: <5.2.1.1.0.20030901170003.02d41290@caird> References: <5.2.1.1.0.20030901124648.02d935d0@caird> <5.2.1.1.0.20030901124648.02d935d0@caird> <5.2.1.1.0.20030901170003.02d41290@caird> Message-ID: <3F5449F0.7040605@irisa.fr> Leighton Pritchard wrote: >> > [...] the Zerg BLAST parser (http://bioinfo.iq.usp.br/zerg/) [...] only >> > had a wrapper for Perl, so I knocked one up for Python [...] at >> > http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml Thanks! A minor note (I don't know Pyrex): can Zerg constants, like QUERY_NAME, be retained in pyzerg? [...] > > On a tangent, would anyone be interested in a publication-quality genome > schematic (linear and circular genome diagram, with labels, scales and > plots) drawing module? I have one that would probably benefit from > public release and comment. You bet! > > > Dr Leighton Pritchard AMRSC > PPI, Scottish Crop Research Institute > Invergowrie, Dundee, DD2 5DA, Scotland, UK > L.Pritchard@scri.sari.ac.uk > PGP key 47B4A485: http://www.keyserver.net http://pgp.mit.edu > yves From L.Pritchard at scri.sari.ac.uk Tue Sep 2 09:25:44 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Tue Sep 2 09:25:00 2003 Subject: [BioPython] Zerg BLAST parser In-Reply-To: <3F5449F0.7040605@irisa.fr> References: <5.2.1.1.0.20030901170003.02d41290@caird> <5.2.1.1.0.20030901124648.02d935d0@caird> <5.2.1.1.0.20030901124648.02d935d0@caird> <5.2.1.1.0.20030901170003.02d41290@caird> Message-ID: <5.2.1.1.0.20030902142453.00b7be60@caird> At 09:42 02/09/2003 +0200, Yves Bastide wrote: >Leighton Pritchard wrote: >>> > [...] the Zerg BLAST parser (http://bioinfo.iq.usp.br/zerg/) [...] only >>> > had a wrapper for Perl, so I knocked one up for Python [...] at >>> > http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml > >Thanks! > >A minor note (I don't know Pyrex): can Zerg constants, like QUERY_NAME, be >retained in pyzerg? Yes, and I've added this, now. You have to address them as zerg.QUERY_NAME and so on, but it works. Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key 47B4A485: http://www.keyserver.net http://pgp.mit.edu From anunberg at oriongenomics.com Tue Sep 2 10:30:11 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Tue Sep 2 10:28:45 2003 Subject: [BioPython] blast parser slows down under python2.3 In-Reply-To: Message-ID: I take it that you are applying these patches in CVS? I have only downloaded the tarball for BioPython, would you suggest i check it out from CVS and what tag should I use? Andy On Sunday, August 31, 2003, at 05:44 PM, Jeffrey Chang wrote: > 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 >> > > > _______________________________________________ > 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 guidod-2003- at gmx.de Tue Sep 2 17:35:42 2003 From: guidod-2003- at gmx.de (Guido Draheim) Date: Tue Sep 2 17:45:15 2003 Subject: [BioPython] care for an rpm spec file? Message-ID: <3F550D2E.5000704@gmx.de> attached is an rpm spec file to build biopython 1.21, it has builddependencies setup for mandrake 9.1. The chatter about "Martel" and "Reportlab" is disabled with patching setup.py - sadly, that seems necessary. btw, please fix that annoying martel install bug. While running setup, a missing "Martel" dependency is claimed - and the default is "NO", do not continue with installation, i.e. a missing required dependency. As a search through the mailinglist shows, this is simply wrong - however an innocent user will not know this since the "installation help" does not have a hint about a Martel installation dependency. Please add a paragraph on http://biopython.org/docs/install/Installation.html in section 3 - tell about what "Martel" is and that it is okay to continue. Otherwise, we should follow the setup.py recommendation, and do _not_ continue. -- have fun, guido http://google.de/search?q=guidod -------------- next part -------------- %define name biopython %define version 1.21 %define release py2.2_1mdk Summary: BioPython Name: %{name} Version: %{version} Release: %{release} Source0: %{name}-%{version}.tar.gz License: BSD-type Group: Development/Libraries BuildRoot: %{_tmppath}/%{name}-buildroot Prefix: %{_prefix} Packager: Guido Draheim Url: http://www.biopython.org BuildRequires: libpython2.2-devel BuildRequires: python-numeric-devel BuildRequires: egenix-mx-base %description "The Biopython Project" - http://www.biopython.org/ is an international association of developers of freely available Python tools for computational molecular biology. biopython.org provides an online resource for modules, scripts, and web links for developers of Python-based software for life science research. Thanks to bioperl, we can also provide web, FTP and CVS space for individuals and organizations wishing to distribute or otherwise make available standalone scripts & code. %prep %setup mv setup.py setup.py_ sed -e "s/raw_input.*/'y'/" setup.py_ >setup.py && test -s setup.py # cut out chatter about "Martel" and "Reportlab" %build env CFLAGS="$RPM_OPT_FLAGS" python2.2 setup.py build %install python2.2 setup.py install --root=%buildroot \ --record=INSTALLED_FILES --prefix=%prefix %clean rm -rf $RPM_BUILD_ROOT %files -f INSTALLED_FILES %defattr(-,root,root) %doc CONTRIB LICENSE NEWS PKG-INFO README Doc/* %_libdir/python2.2/site-packages/Bio/EUtils/DTDs/*.dtd From anunberg at oriongenomics.com Wed Sep 3 10:34:15 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Wed Sep 3 10:32:48 2003 Subject: [BioPython] blast parser slows down under python2.3 In-Reply-To: <3B7B6993-DD6D-11D7-AD5E-000A956845CE@stanford.edu> Message-ID: I was wondering if you could patch the stable branch? Reason is that some of what I do may turn into production scripts and I would rather not have it tied to bleeding edge code.. Thanks On Tuesday, September 2, 2003, at 12:45 PM, Jeffrey Chang wrote: > Yep, it's patched against the CVS. There is no tag -- just the most > recent version. We've only been tagging the releases. > > Jeff > > > On Tuesday, September 2, 2003, at 07:30 AM, Andrew Nunberg wrote: > >> I take it that you are applying these patches in CVS? >> I have only downloaded the tarball for BioPython, would you suggest i >> check it out from CVS and what tag should I use? >> >> Andy >> >> On Sunday, August 31, 2003, at 05:44 PM, Jeffrey Chang wrote: >> >>> 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 >>>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> 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 idoerg at burnham.org Wed Sep 3 11:25:31 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed Sep 3 11:27:47 2003 Subject: [BioPython] Re: [Biopython-dev] streamerror_in_local_blast.py In-Reply-To: <20030903.AAA1062582144@ggbio.com> References: <20030903.AAA1062582144@ggbio.com> Message-ID: <3F5607EB.6050308@burnham.org> Could you please provide the entire traceback? It's pretty hard to find an error without it ;) Thanks, ./I kim750@ggbio.com wrote: > Hi! > My name is Yeon-Ki. I am a novice with biopython. > Now I am tring to use local_blast.py. But the moment i typed local_blast.py I have Running blastall... > Traceback (most recent call last): and > whole bunch of "Bio/Blast/NCBIStandalone.py" errors and SyntaxError: Unexpected end of stream at the end of error message. > > I down-loaded a current version of NCBIStandalone.py --> Revision 1.49 / (as text) / (view) - annotate - [select for diffs] , Tue Sep 2 17:47:29 2003 UTC (16 hours, 11 minutes ago) by jchang. I replaced the old one in the Bio/Blast/NCBIStandalone.py with new one , but still I could not use the local_blast.py. > > Could you help me out? > > Thank you. > Yeon-Ki > > > > > > Yeon-Ki Kim, Ph.D. > Research Scientist > > GreenGene Biotech, inc. > Myongji University > 38-2 Namdong > Yongin Kyonggido 449-728 Korea > > GreenGene BioTech Inc. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- 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 chapmanb at uga.edu Wed Sep 3 14:50:38 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Sep 3 14:54:23 2003 Subject: [BioPython] blast parser slows down under python2.3 In-Reply-To: References: <3B7B6993-DD6D-11D7-AD5E-000A956845CE@stanford.edu> Message-ID: <20030903185038.GA2159@evostick.agtec.uga.edu> Hi Andy; > I was wondering if you could patch the stable branch? Reason is that > some of what I do may turn into production scripts and I would rather > not have it tied to bleeding edge code.. There is no stable branch -- or more generally, no branches at all. We work directly off the head and try to keep it working as well as possible; releases come directly off of it. So, yeah, you'll just have to work right off CVS if you want the fixes before the next release. Things are normally quite stable -- I always use CVS for my code (and consider them "production;" production for a grad student, ya know) and have never had any major complaints. Brad From SFESeminarsLtd at totalise.co.uk Wed Sep 3 22:41:59 2003 From: SFESeminarsLtd at totalise.co.uk (Robert Seviour) Date: Wed Sep 3 22:39:28 2003 Subject: [BioPython] Our next seminars dates Message-ID: <200309040239.h842dNsX016261@portal.> Selling for Engineers One-day Seminar Edinburgh Wed 3rd September 2003 Gatwick Thurs 25th September 2003 Amsterdam Fri 3rd October 2003 Belfast Wed 8th October 2003 Dublin Wed 15th October 2003 Boston Wed 29th October 2003 Chicago Mon 2nd November 2003 Dallas Thurs 6th November 2003 San Jose Wed 12th November 2003 Seattle Fri 14th November 2003 Denver Thurs 20th November 2003 Toronto Tues 25th November 2003 The Selling for Engineers seminar is a good introduction to effective sales principles for people who are new to selling, and also a useful refresher for 'old hands'. It applies to selling both technical products and intangible services. Many Sales Engineers have been learning the technical skills of their job for years but have had little formal training in selling. This course helps correct that imbalance. Typical job titles of delegates: Sales Engineer, Account Executive and Business Development Manager. Fee for this event is ?300. Telephone Sales Prospecting for Engineers One-day Workshop Leeds Mon 22nd September 2003 Belfast Thurs 9th October 2003 Dublin Thurs 16th October 2003 This event is a practical workshop teaching people in technical companies how to find new customers on the phone. It is applicable to business development for both tangible products and intangible services. The first session addresses whom to target, what to say and how to handle problems. The remainder of the day consists of live sales calls with coaching from Robert Seviour; the objective being to give delegates some positive experiences of prospecting, make sales appointments and maybe sell something! Please note that this telephone sales prospecting event is restricted to a maximum of six delegates to permit individual coaching. Fee for this event is ?300. Closing Techniques Workshop Half day workshop Edinburgh Wed 4th September 2003 Birmingham Fri 19th September 2003 Leeds Tues 23rd September 2003 Gatwick Fri 26th September 2003 Belfast Fri 10th October 2003 Dublin Fri 17th October 2003 Boston Thurs 30th October 2003 Chicago Tues 3rd November 2003 Dallas Fri 7th November 2003 San Jose Thurs 13th November 2003 Seattle Mon 17th November 2003 Denver Fri 21st November 2003 Toronto Wed 26th November 2003 What if the customer says: " " 'It's too expensive' " " 'We're happy with our present supplier' " " 'I want to think about it' Can you handle these common objections? By far the most efficient way to be more profitable is to turn more of the enquiries you receive into paid orders. For this, the ability to resolve objections is critical - either you close or you lose the sale. And if you answer 'How much discount will you give me?' with: 'I'll ask my boss', you waste profit, which could be yours with a better reply. In only half a day I will teach you techniques which overcome these objections and more. You will be able to use them immediately to win profitable orders. There is no need to lose business to your competitors or give big discounts. The price for the workshop is low, only ?145. If you have never had any formal sales training or need a refresher, don't continue to work at a disadvantage. Reservations and information Please contact Sue on: Tel: +44(0)1481 720 294 Fax: +44(0)1481 720 317 E mail robertseviour@totalise.co.uk or reply to this email with the subject "Send info" If sales training is not an issue for your company please reply to this email with the word "DELETE" in the subject line. We will remove your details promptly. From piet at clondiag.com Thu Sep 4 02:57:24 2003 From: piet at clondiag.com (Peter Slickers) Date: Thu Sep 4 02:56:12 2003 Subject: [BioPython] blast parser slows down under python2.3 In-Reply-To: References: Message-ID: <3F56E254.1080304@clondiag.com> Andrew Nunberg wrote: > I was wondering if you could patch the stable branch? Reason is that > some of what I do may turn into production scripts and I would rather > not have it tied to bleeding edge code.. > Thanks > You should not take this issue to serious. This will only affect you, if your are heavily processing huge blast output files with python2.3 and the blast parser from biopython. You can still use python2.2 for such production runs, and then there is no need to patch your local biopython code immediately. -- 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 anunberg at oriongenomics.com Thu Sep 4 11:38:39 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Thu Sep 4 11:37:12 2003 Subject: [BioPython] enabling Tkinter on Mac Message-ID: Hi, I installed the macpython 2.3 instead of building 2.3 from source, I dont seem to have Tkinter enabled, does anyone know how to do this on a Mac? I am not even sure where all the files are (Mac puts things in odd places) Thanks Andy --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From Y.Benita at pharm.uu.nl Fri Sep 5 02:28:18 2003 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Fri Sep 5 02:27:00 2003 Subject: [BioPython] enabling Tkinter on Mac In-Reply-To: Message-ID: on 4/9/03 17:38, Andrew Nunberg at anunberg@oriongenomics.com wrote: > Hi, > I installed the macpython 2.3 instead of building 2.3 from source, > I dont seem to have Tkinter enabled, does anyone know how to do this on > a Mac? > I am not even sure where all the files are (Mac puts things in odd > places) MacPython comes with a package manager. Once you launch it you can choose to install tk binaries. You can also use the Tcl/Tk aqua, available at: http://www.apple.com/downloads/macosx/unix_open_source/tcltkaqua.html Good luck, Yair -- Yair Benita Pharmaceutical Proteomics Faculty of Pharmacy Utrecht University From ms99_2000 at yahoo.de Fri Sep 5 04:56:14 2003 From: ms99_2000 at yahoo.de (Michael Schmitt) Date: Fri Sep 5 04:54:58 2003 Subject: [BioPython] Atom serial number in Bio.PDB.PDBParser Message-ID: <200309051056.14891.ms99_2000@yahoo.de> Hello. Is there a way to get the atom serial numbers in a structure I retrieved in the following way: from Bio.PDB.PDBParser import PDBParser p= PDBParser(PERMISSIVE=1) filename= 'testprotein.pdb' s= p.get_structure(testid, filename) The Atom objects have identifiers containing atom names, but I can't find the serial numbers. Thanks for help. Michael From pbouige at pasteur.fr Fri Sep 5 08:47:33 2003 From: pbouige at pasteur.fr (Philippe Bouige) Date: Fri Sep 5 08:46:15 2003 Subject: [BioPython] Widget in Tkinter ? Message-ID: <20030905144733.A272559@electre.pasteur.fr> Hello, I'm presently programming 'BioWidgets' in Python using the TKinter/Pmw module. I'd like to know whether 'BioWidgets' already exist in Python TKinter and/or Pmw, and, if they do, could you send me the related URL ? I thank you in advance for your reply. Philippe From thamelry at vub.ac.be Fri Sep 5 09:30:09 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Fri Sep 5 09:26:35 2003 Subject: [BioPython] Atom serial number in Bio.PDB.PDBParser In-Reply-To: <200309051056.14891.ms99_2000@yahoo.de> References: <200309051056.14891.ms99_2000@yahoo.de> Message-ID: <200309051327.h85DRrC9030280@sarek.skynet.be> On Friday 05 September 2003 10:56 am, Michael Schmitt wrote: > Hello. > > Is there a way to get the atom serial numbers in a structure I retrieved in > the following way: No, in fact there isn't. I didn't add it because it is so seldomly used. I'll add it during the course of this month - I expect to do some work on Bio.PDB in a couple of weeks. Best regards, -Thomas From anunberg at oriongenomics.com Fri Sep 5 11:03:27 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Fri Sep 5 11:01:53 2003 Subject: [BioPython] enabling Tkinter on Mac In-Reply-To: Message-ID: <1AE14AC8-DFB2-11D7-BF39-000A95A001EE@oriongenomics.com> Thanks, I will have to install manually, since the package manager gives me an error of unknown url when i try to install either the tk binary or Tcl/Tk Aqua, I am thinking i should just remove macpython and install python2.3 from source or via Fink.. On Friday, September 5, 2003, at 01:28 AM, Yair Benita wrote: > on 4/9/03 17:38, Andrew Nunberg at anunberg@oriongenomics.com wrote: > >> Hi, >> I installed the macpython 2.3 instead of building 2.3 from source, >> I dont seem to have Tkinter enabled, does anyone know how to do this >> on >> a Mac? >> I am not even sure where all the files are (Mac puts things in odd >> places) > > MacPython comes with a package manager. Once you launch it you can > choose to > install tk binaries. > You can also use the Tcl/Tk aqua, available at: > http://www.apple.com/downloads/macosx/unix_open_source/tcltkaqua.html > > Good luck, > Yair > -- > Yair Benita > Pharmaceutical Proteomics > Faculty of Pharmacy > Utrecht University > > _______________________________________________ > 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 kim at inb.uni-luebeck.de Fri Sep 5 11:24:15 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Fri Sep 5 11:22:56 2003 Subject: [BioPython] Widget in Tkinter ? In-Reply-To: <20030905144733.A272559@electre.pasteur.fr>; from pbouige@pasteur.fr on Fri, Sep 05, 2003 at 02:47:33PM +0200 References: <20030905144733.A272559@electre.pasteur.fr> Message-ID: <20030905172415.A9066@pc10.inb.mu-luebeck.de> On Fri, Sep 05, 2003 at 02:47:33PM +0200, Philippe Bouige wrote: > I'm presently programming 'BioWidgets' in Python using the > TKinter/Pmw module. I'd like to know whether 'BioWidgets' > already exist in Python TKinter and/or Pmw, and, if they do, > could you send me the related URL ? No, I don't know about anything called "BioWidgets" -- but, would you care to give an outline what you're working on? Greetings, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim@inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From omid9dr18 at hotmail.com Fri Sep 5 15:31:04 2003 From: omid9dr18 at hotmail.com (Omid Khalouei) Date: Fri Sep 5 15:29:46 2003 Subject: [BioPython] Discussion Group Message-ID: Hello All, I have a suggestion and I was wondering what you think about it. My suggestion is that we could have a half an hour weekly meeting in one of online discussion rooms(e.g. a yahoo private chat room), protected by password only for biopython members, and each week a relevant topic could be discussed by 2,3 field experts and at the end others could ask their questions, finally the whole session could be printed by each user for future reference. This way we can have much more interaction and even get to know each other. Please let us know what you think. Thanks Sam Khalouei Departments of Computer Science & Human Biology University of Toronto Bioinformatics Research Analyst Hospital for Sick Children, Toronto, Ontario (416)813-5569 ________________________________________________ _________________________________________________________________ Add photos to your messages with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail From guidod-2003- at gmx.de Sat Sep 6 11:48:10 2003 From: guidod-2003- at gmx.de (Guido Draheim) Date: Sat Sep 6 11:44:26 2003 Subject: [BioPython] Bio/sequtils.py annoyance Message-ID: <3F5A01BA.50004@gmx.de> $ cd Bio && python sequtils.py sequtils.py:208: SyntaxWarning: import * only allowed at module level That's for the Tkinter import... From guidod-2003- at gmx.de Sat Sep 6 12:04:23 2003 From: guidod-2003- at gmx.de (Guido Draheim) Date: Sat Sep 6 12:00:39 2003 Subject: [BioPython] Bio/xkMeans.py annoyance Message-ID: <3F5A0587.9020404@gmx.de> python xkMeans will not work, because import string, re import os, sys, commands from Tkinter import * from Numeric import * from Bio.Clustering import kMeans # <- nonexistant Module import kMeans from tkFileDialog import askopenfilename, asksaveasfilename import Pmw # <- nonexistant Module From guidod-2003- at gmx.de Sat Sep 6 12:04:28 2003 From: guidod-2003- at gmx.de (Guido Draheim) Date: Sat Sep 6 12:00:43 2003 Subject: [BioPython] Scripts/xbbtools annoyance Message-ID: <3F5A058C.8040405@gmx.de> again, we see a dependency on "Pmw" for xbb_blast.py secondly, xbbtools.py will run xbb_translations.py which does try to import Bio.Tools - a nonexistant module. I come to feel more and more uncomfortable, is the biopython project actually used and tested? From jchang at jeffchang.com Sun Sep 7 02:09:00 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sun Sep 7 02:07:35 2003 Subject: [BioPython] Scripts/xbbtools annoyance In-Reply-To: <3F5A058C.8040405@gmx.de> Message-ID: On Saturday, September 6, 2003, at 09:04 AM, Guido Draheim wrote: > again, we see a dependency on "Pmw" for xbb_blast.py > > secondly, xbbtools.py will run xbb_translations.py > which does try to import Bio.Tools - a nonexistant module. > > I come to feel more and more uncomfortable, is the > biopython project actually used and tested? Yes. Biopython is too big a project for anybody to manage. We all have day jobs, so we do what we can to keep the code up to date. Some bugs do slip through, especially on parts of the project that aren't used as much. We welcome any updates, patches, and tests! Jeff From fkauff at duke.edu Mon Sep 8 16:06:08 2003 From: fkauff at duke.edu (Frank Kauff) Date: Mon Sep 8 16:06:09 2003 Subject: [BioPython] enabling Tkinter on Mac In-Reply-To: <1AE14AC8-DFB2-11D7-BF39-000A95A001EE@oriongenomics.com> References: <1AE14AC8-DFB2-11D7-BF39-000A95A001EE@oriongenomics.com> Message-ID: <1063051637.2584.5.camel@osiris.biology.duke.edu> On Fri, 2003-09-05 at 11:03, Andrew Nunberg wrote: > Thanks, > I will have to install manually, since the package manager gives me an > error of unknown url when i try to install either the tk binary or > Tcl/Tk Aqua, > > I am thinking i should just remove macpython and install python2.3 from > source or via Fink.. > > On Friday, September 5, 2003, at 01:28 AM, Yair Benita wrote: > > > on 4/9/03 17:38, Andrew Nunberg at anunberg@oriongenomics.com wrote: > > > >> Hi, > >> I installed the macpython 2.3 instead of building 2.3 from source, > >> I dont seem to have Tkinter enabled, does anyone know how to do this > >> on > >> a Mac? > >> I am not even sure where all the files are (Mac puts things in odd > >> places) > > > > MacPython comes with a package manager. Once you launch it you can > > choose to > > install tk binaries. > > You can also use the Tcl/Tk aqua, available at: > > http://www.apple.com/downloads/macosx/unix_open_source/tcltkaqua.html > > > > Good luck, > > Yair > > -- > > Yair Benita > > Pharmaceutical Proteomics > > Faculty of Pharmacy > > Utrecht University > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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 From karin.lagesen at labmed.uio.no Wed Sep 10 09:51:15 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Wed Sep 10 09:50:33 2003 Subject: [BioPython] installation problems relating to mxTextTools Message-ID: <20030910135115.GB17295@uracil.uio.no> Hi! I am trying to install biopython on my machine which is running Redhat 7.3. The version of python I have is 2.2.1. I installed Numeric as specified without a problem: gunzip Numeric-23.1.tar.gz tar -xvpf Numeric-23.1.tar cd Numeric-23.1 python setup.py build python setup.py install I also rpmd mxTextTools in without any complaints: rpm -i egenix-mx-base-2.0.5-py2.2_1.src.rpm I then try to install biopython: tar -xzvpf biopython-1.21.tar.gz cd biopython-1.21 python setup.py install And the result I get is: running install *** mxTextTools *** 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 mxTextTools at http://www.lemburg.com/files/python/mxExtensions.html. Do you want to continue this installation? (y/N) I am just wondering where/what went wrong? TIA, Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From fkauff at duke.edu Wed Sep 10 11:07:47 2003 From: fkauff at duke.edu (Frank Kauff) Date: Wed Sep 10 11:07:48 2003 Subject: [BioPython] Alignment distribution from NCBIWWW Message-ID: <1063206537.2044.19.camel@osiris.biology.duke.edu> Hi all, when doing a web blast with NCBIWWW.blast, the htlm returned looks pretty much like the normal www output when blasting directly at the ncbi website. However, that little grpahical distribution overview at the beginning that shows the color-coded alignments is missing. Is there a possibility to get that? tia, Frank -- Frank Kauff Dept. of Biology Duke University Box 90338 Durham, NC 27708 USA Phone 919-660-7382 Fax 919-660-7293 From piet at clondiag.com Wed Sep 10 11:57:40 2003 From: piet at clondiag.com (Peter Slickers) Date: Wed Sep 10 11:56:18 2003 Subject: [BioPython] installation problems relating to mxTextTools In-Reply-To: <20030910135115.GB17295@uracil.uio.no> References: <20030910135115.GB17295@uracil.uio.no> Message-ID: <3F5F49F4.4010606@clondiag.com> Karin Lagesen wrote: > > The version of python I have is 2.2.1. > > rpm -i egenix-mx-base-2.0.5-py2.2_1.src.rpm > Maybe there is a mismatch between your python2.2.1 and your rpm, which seems to be suited for python2.2 only. Please check, if mx was installed successfully. Just start python and type in these two commands: python >>> import mx >>> print mx.__version__ If this test fails, you should try to install mx directly from the tar archive using 'python setup.py install'. This is the same procedure as you have used for Numeric. Good luck, -- 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 jpg at research.dfci.harvard.edu Wed Sep 10 13:19:13 2003 From: jpg at research.dfci.harvard.edu (JP Glutting) Date: Wed Sep 10 13:17:42 2003 Subject: [BioPython] New User problem with GenBank References: <3F05E2F5.6050804@yahoo.com> <200307221808.56253.Peter.Bienstman@ugent.be> Message-ID: <3F5F5D11.40409@research.dfci.harvard.edu> I am having some trouble with a script that I wrote to retrieve GenBank data. If I run this (I am just inserting a known GI [33413925]) for a protein I ran this on a few months ago: >>> from Bio import GenBank >>> gi = 33413925 >>> record_parser = GenBank.FeatureParser() >>> ncbi_dict = GenBank.NCBIDictionary(database="Protein") >>> ncbi_parse_dict = GenBank.NCBIDictionary(database="Protein", parser=record_parser) >>> gb_record = ncbi_dict[gi] Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1538, in __getitem__ raise KeyError, x KeyError: ERROR, possibly because id not available? Any idea why this happens, and if there is a work-around? Thanks, JP Peter Bienstman wrote: > FYI, I've confirmed that the parsing errors don't occur with the current CVS > version, so the fix should be in the upcoming new release. > > Cheers, > > Peter From jpg at research.dfci.harvard.edu Wed Sep 10 13:30:15 2003 From: jpg at research.dfci.harvard.edu (JP Glutting) Date: Wed Sep 10 13:28:44 2003 Subject: [BioPython] New User problem with GenBank References: <3F05E2F5.6050804@yahoo.com> <200307221808.56253.Peter.Bienstman@ugent.be> <3F5F5D11.40409@research.dfci.harvard.edu> Message-ID: <3F5F5FA7.6070700@research.dfci.harvard.edu> I should have mentioned that this is a new install of biopython 1.21 and Martel. I am running Debian Stable (Woody), and python2.2. Cheers, JP JP Glutting wrote: > I am having some trouble with a script that I wrote to retrieve GenBank > data. > > If I run this (I am just inserting a known GI [33413925]) for a protein > I ran this on a few months ago: > > >>> from Bio import GenBank > >>> gi = 33413925 > >>> record_parser = GenBank.FeatureParser() > >>> ncbi_dict = GenBank.NCBIDictionary(database="Protein") > >>> ncbi_parse_dict = GenBank.NCBIDictionary(database="Protein", > parser=record_parser) > >>> gb_record = ncbi_dict[gi] > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line > 1538, in __getitem__ > raise KeyError, x > KeyError: ERROR, possibly because id not available? > > Any idea why this happens, and if there is a work-around? > > Thanks, > > JP > From jchang at jeffchang.com Wed Sep 10 13:41:59 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Wed Sep 10 13:40:25 2003 Subject: [BioPython] New User problem with GenBank In-Reply-To: <3F5F5D11.40409@research.dfci.harvard.edu> Message-ID: <14569E9B-E3B6-11D7-BA7A-000A956845CE@jeffchang.com> Try doing: >>> ncbi_dict = GenBank.NCBIDictionary(database="Protein", format="gp") The code that chooses the proper format for the database needs to be fixed... Jeff On Wednesday, September 10, 2003, at 10:19 AM, JP Glutting wrote: > I am having some trouble with a script that I wrote to retrieve > GenBank data. > > If I run this (I am just inserting a known GI [33413925]) for a > protein I ran this on a few months ago: > > >>> from Bio import GenBank > >>> gi = 33413925 > >>> record_parser = GenBank.FeatureParser() > >>> ncbi_dict = GenBank.NCBIDictionary(database="Protein") > >>> ncbi_parse_dict = GenBank.NCBIDictionary(database="Protein", > parser=record_parser) > >>> gb_record = ncbi_dict[gi] > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", > line 1538, in __getitem__ > raise KeyError, x > KeyError: ERROR, possibly because id not available? > > Any idea why this happens, and if there is a work-around? > > Thanks, > > JP > > Peter Bienstman wrote: >> FYI, I've confirmed that the parsing errors don't occur with the >> current CVS version, so the fix should be in the upcoming new >> release. >> Cheers, >> Peter > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From jchang at jeffchang.com Wed Sep 10 14:20:25 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Wed Sep 10 14:18:50 2003 Subject: [BioPython] Alignment distribution from NCBIWWW In-Reply-To: <1063206537.2044.19.camel@osiris.biology.duke.edu> Message-ID: <73053F78-E3BB-11D7-BA7A-000A956845CE@jeffchang.com> Do you know which parameter this is controlled by? Is it SHOW_OVERVIEW, or something else? Jeff On Wednesday, September 10, 2003, at 08:08 AM, Frank Kauff wrote: > Hi all, > > when doing a web blast with NCBIWWW.blast, the htlm returned looks > pretty much like the normal www output when blasting directly at the > ncbi website. However, that little grpahical distribution overview at > the beginning that shows the color-coded alignments is missing. Is > there > a possibility to get that? > > tia, > Frank > > -- > Frank Kauff > Dept. of Biology > Duke University > Box 90338 > Durham, NC 27708 > USA > > Phone 919-660-7382 > Fax 919-660-7293 > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From fkauff at duke.edu Wed Sep 10 14:49:42 2003 From: fkauff at duke.edu (Frank Kauff) Date: Wed Sep 10 14:49:42 2003 Subject: [BioPython] Alignment distribution from NCBIWWW In-Reply-To: <73053F78-E3BB-11D7-BA7A-000A956845CE@jeffchang.com> References: <73053F78-E3BB-11D7-BA7A-000A956845CE@jeffchang.com> Message-ID: <1063219855.2044.45.camel@osiris.biology.duke.edu> On Wed, 2003-09-10 at 14:20, Jeffrey Chang wrote: > Do you know which parameter this is controlled by? Is it > SHOW_OVERVIEW, or something else? > > Jeff > I also thought show_overview would be the one, but is set to 'on' by default. show_overview='yes' makes no difference. All the other options don't seem to be related to it. Frank > > On Wednesday, September 10, 2003, at 08:08 AM, Frank Kauff wrote: > > > Hi all, > > > > when doing a web blast with NCBIWWW.blast, the htlm returned looks > > pretty much like the normal www output when blasting directly at the > > ncbi website. However, that little grpahical distribution overview at > > the beginning that shows the color-coded alignments is missing. Is > > there > > a possibility to get that? > > > > tia, > > Frank > > > > -- > > Frank Kauff > > Dept. of Biology > > Duke University > > Box 90338 > > Durham, NC 27708 > > USA > > > > Phone 919-660-7382 > > Fax 919-660-7293 > > > > _______________________________________________ > > 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 From karin.lagesen at labmed.uio.no Thu Sep 11 05:33:12 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Thu Sep 11 05:31:43 2003 Subject: [BioPython] installation problems relating to mxTextTools In-Reply-To: <3F5F49F4.4010606@clondiag.com> References: <20030910135115.GB17295@uracil.uio.no> <3F5F49F4.4010606@clondiag.com> Message-ID: <20030911093312.GD17295@uracil.uio.no> On Wed, Sep 10, 2003 at 05:57:40PM +0200, Peter Slickers wrote: > Karin Lagesen wrote: > Please check, if mx was installed successfully. > Just start python and type in these two commands: > > python > > >>> import mx > >>> print mx.__version__ > > If this test fails, you should try to install mx directly > from the tar archive using 'python setup.py install'. This is > the same procedure as you have used for Numeric. You were right, this was the problem. However, I now have a different problem: bash-2.05a# python setup.py install running install *** 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/. Do you want to continue this installation? (y/N) I did not see any package called Martel under the required list on the biopython download page, and the link doesn't work. Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From kim at inb.uni-luebeck.de Thu Sep 11 06:16:25 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Thu Sep 11 06:14:55 2003 Subject: [BioPython] installation problems relating to mxTextTools In-Reply-To: <20030911093312.GD17295@uracil.uio.no>; from karin.lagesen@labmed.uio.no on Thu, Sep 11, 2003 at 11:33:12AM +0200 References: <20030910135115.GB17295@uracil.uio.no> <3F5F49F4.4010606@clondiag.com> <20030911093312.GD17295@uracil.uio.no> Message-ID: <20030911121625.B27942@pc10.inb.mu-luebeck.de> On Thu, Sep 11, 2003 at 11:33:12AM +0200, Karin Lagesen wrote: > You were right, this was the problem. However, I now have a different > problem: > > bash-2.05a# python setup.py install > running install > *** Martel *** is either not installed or out of date. Just run ``python setup.py install'' a second time. The first installation will, in fact, have already installed Martel, but it seems it does not know about this itself. I speculate that the python process running the setup script would have to rehash its list of modules available for import, but it doesn't. Greetings from Luebeck, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim@inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From karin.lagesen at labmed.uio.no Fri Sep 12 08:16:28 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Fri Sep 12 08:15:03 2003 Subject: [BioPython] installation problems relating to mxTextTools In-Reply-To: <3F5F49F4.4010606@clondiag.com> References: <20030910135115.GB17295@uracil.uio.no> <3F5F49F4.4010606@clondiag.com> Message-ID: <20030912121628.GB12279@uracil.uio.no> I got help from somebody on the list with the Martel problem. However, I am now (again) encountering a new problem: bash-2.05a# python setup.py install running install *** Numerical Python *** is either not installed or out of date. This package is optional, which means it is only used in a few specialized modules in Biopython. You probably don't need this is you are unsure. You can ignore this requirement, and install it later if you see ImportErrors. You can find Numerical Python at http://numpy.sourceforge.net/. Do you want to continue this installation? (Y/n) And this is now the third time this happens during the install. And I have installed numpy. Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From jchang at jeffchang.com Fri Sep 12 11:45:48 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Fri Sep 12 11:44:08 2003 Subject: [BioPython] installation problems relating to mxTextTools In-Reply-To: <20030912121628.GB12279@uracil.uio.no> Message-ID: <2E12F50F-E538-11D7-99B4-000A956845CE@jeffchang.com> On Friday, September 12, 2003, at 05:16 AM, Karin Lagesen wrote: > I got help from somebody on the list with the Martel problem. However, > I am now (again) encountering a new problem: > > bash-2.05a# python setup.py install > running install > *** Numerical Python *** is either not installed or out of date. > > This package is optional, which means it is only used in a few > specialized modules in Biopython. You probably don't need this is you > are unsure. You can ignore this requirement, and install it later if > you see ImportErrors. > You can find Numerical Python at http://numpy.sourceforge.net/. > > Do you want to continue this installation? (Y/n) > > > And this is now the third time this happens during the install. And I > have installed numpy. That is odd. If you execute python: [sophie:~] jchang% python Python 2.3b2 (#1, Jul 3 2003, 22:26:38) [GCC 3.1 20020420 (prerelease)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric Does it complain? Jeff From hlapp at gnf.org Tue Sep 16 17:15:31 2003 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Sep 16 17:13:36 2003 Subject: [BioPython] Re: [BioSQL-l] Problem with example in python_biosql_basic.txt In-Reply-To: <3F61EEC1.60803@irisa.fr> Message-ID: Jeff/Brad or anybody else who can comment: is there anything more precise that we can tell people inquiring about biopython supporting the singapore version of biosql? -hilmar On Friday, September 12, 2003, at 09:05 AM, Yves Bastide wrote: > Robert Roth wrote: >> Hi, >> I am completly new to Biopython and BioSQL so my problems might arise >> from something trivial that I have missed. After installing MySQL, >> Biopython, MySQLdb and BioSQL I loaded the scheme for BioSQL into the >> database and everything is in place. The machine is running WinXP and >> python 2.3. >> But when I try to follow the simple example in the documentation for >> using Biopython with BioSQL that is described in >> biosql/biosql-schema/doc/python_biosql_basic.txt it chokes (see >> below). >> ----- >>>>> import MySQLdb >>>>> from BioSQL import BioSeqDatabase >>>>> server = BioSeqDatabase.open_database(driver = "MySQLdb", user = >>>>> "test", passwd = "biopython", host = "localhost", db = "bioseqdb") >>>>> db = server.new_database("cold") >>>>> from Bio import GenBank >>>>> parser = GenBank.FeatureParser() >>>>> iterator = GenBank.Iterator(open("cor6_6.gb"), parser) >>>>> db.load(iterator) > > [snip] > >> When looking at Loader.py there is a call to MySQL (snippet above). >> But when I look at the ERD for BioSQL I cant find either binomial or >> variant in the taxon table. Am I completely of here (as I said I'm a >> complete newbie) or is this the reason its choking? >> Any help on what is going wrong would be greatly appreciated. >> Thanks in advance, > > Biopython is still using an old version of the schema. This should > change in the not-too-far future... > >> Robert > > yves > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From chapmanb at uga.edu Tue Sep 16 17:36:01 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Sep 16 17:39:22 2003 Subject: [BioPython] Re: [BioSQL-l] Problem with example in python_biosql_basic.txt In-Reply-To: References: <3F61EEC1.60803@irisa.fr> Message-ID: <20030916213601.GA24804@evostick.agtec.uga.edu> Hilmar and Robert; > Jeff/Brad or anybody else who can comment: is there anything more > precise that we can tell people inquiring about biopython supporting > the singapore version of biosql? Yves Bastide kindly sent updates to the Biopython BioSQL code to the dev list last week: http://www.biopython.org/pipermail/biopython-dev/2003-September/001485.html This should bring it up to date with the current SQL. I haven't had a chance to integrate this yet but was hoping to Thursday night. Hopefully it will then make it into the new release that Jeff has planned for real-soon-now. If things need to be up and running sooner then that the SQL that the Biopython code works with can be found in the Tests/BioSQL directory. Sorry to have been slack on this. I have been feelin' really bad about not having time to get it in, if that is any consolation for anyone :-). But Thursday, Thursday... Brad > On Friday, September 12, 2003, at 09:05 AM, Yves Bastide wrote: > > >Robert Roth wrote: > >>Hi, > >>I am completly new to Biopython and BioSQL so my problems might arise > >>from something trivial that I have missed. After installing MySQL, > >>Biopython, MySQLdb and BioSQL I loaded the scheme for BioSQL into the > >>database and everything is in place. The machine is running WinXP and > >>python 2.3. > >>But when I try to follow the simple example in the documentation for > >>using Biopython with BioSQL that is described in > >>biosql/biosql-schema/doc/python_biosql_basic.txt it chokes (see > >>below). > >>----- > >>>>>import MySQLdb > >>>>>from BioSQL import BioSeqDatabase > >>>>>server = BioSeqDatabase.open_database(driver = "MySQLdb", user = > >>>>>"test", passwd = "biopython", host = "localhost", db = "bioseqdb") > >>>>>db = server.new_database("cold") > >>>>>from Bio import GenBank > >>>>>parser = GenBank.FeatureParser() > >>>>>iterator = GenBank.Iterator(open("cor6_6.gb"), parser) > >>>>>db.load(iterator) > > > >[snip] > > > >>When looking at Loader.py there is a call to MySQL (snippet above). > >>But when I look at the ERD for BioSQL I cant find either binomial or > >>variant in the taxon table. Am I completely of here (as I said I'm a > >>complete newbie) or is this the reason its choking? > >>Any help on what is going wrong would be greatly appreciated. > >>Thanks in advance, > > > >Biopython is still using an old version of the schema. This should > >change in the not-too-far future... > > > >>Robert > > > >yves > > > >_______________________________________________ > >BioSQL-l mailing list > >BioSQL-l@open-bio.org > >http://open-bio.org/mailman/listinfo/biosql-l > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From karin.lagesen at labmed.uio.no Thu Sep 18 04:54:26 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Thu Sep 18 04:52:46 2003 Subject: [BioPython] biopython installation problem (cont.) Message-ID: <20030918085426.GA1602@uracil.uio.no> I have now discovered why I had such big problems installing biopython, site_packages gets overwritten every night by the sysadmins disting python to me. I have because of this installed Numeric-23.1 and egenix-mx-base-2.0.5 (using --home="..") in a directory called /site/python_packages. I now set PYTHONPATH to point at /site/python_packages, but I cannot import the packages. uracil:10:49> export PYTHONPATH=/site/python_packages/ uracil:10:52> python Python 2.2.1 (#1, May 31 2002, 19:17:21) [GCC egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import mx Traceback (most recent call last): File "", line 1, in ? ImportError: No module named mx >>> import Numeric Traceback (most recent call last): File "", line 1, in ? ImportError: No module named Numeric >>> I am obiously doing something weird here, could somebody tell me what, so I can get around to doing some actual _work_...:) TIA, and thanks for your patience. Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From fkauff at duke.edu Thu Sep 18 14:13:14 2003 From: fkauff at duke.edu (Frank Kauff) Date: Thu Sep 18 14:13:16 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output Message-ID: <1063908901.2030.207.camel@osiris.biology.duke.edu> Hi folks, does anybody know which is the correct value for format_type in NCBIWWW.blast() to get a plain text output? It's 'html' by default, and I tried format_type='txt'/'text'/'plain'/'plaintext' and even 'ascii', but still it returns html. And maybe I'm blind, but is there any place in the web which lists exactly the different options? Thanks, Frank PS: and the show_overview question is still open... :-) -- Frank Kauff Dept. of Biology Duke University Box 90338 Durham, NC 27708 USA Phone 919-660-7382 Fax 919-660-7293 From sbassi at asalup.org Thu Sep 18 15:10:52 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Sep 18 15:11:47 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output In-Reply-To: <1063908901.2030.207.camel@osiris.biology.duke.edu> References: <1063908901.2030.207.camel@osiris.biology.duke.edu> Message-ID: <3F6A033C.7060107@asalup.org> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Frank Kauff wrote: | does anybody know which is the correct value for format_type in | NCBIWWW.blast() to get a plain text output? It's 'html' by default, and | I tried format_type='txt'/'text'/'plain'/'plaintext' and even 'ascii', | but still it returns html. And maybe I'm blind, but is there any place | in the web which lists exactly the different options? I use NCBIStandalone.blastall function and the last parameter is "html=T" or "html=F". | | PS: and the show_overview question is still open... :-) Don't remember that question. - -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// ~ http://Bioinformatica.info -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAj9qAzsACgkQ6lc7ixf6gKooHACeKVIzpeUr5h286f2sOFGq2t6P UNcAn1JPfNB2B9JypwodtFgz8910lFr6 =ermr -----END PGP SIGNATURE----- From fkauff at duke.edu Thu Sep 18 15:33:33 2003 From: fkauff at duke.edu (Frank Kauff) Date: Thu Sep 18 15:33:34 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output In-Reply-To: <3F6A033C.7060107@asalup.org> References: <1063908901.2030.207.camel@osiris.biology.duke.edu> <3F6A033C.7060107@asalup.org> Message-ID: <1063913719.4124.9.camel@osiris.biology.duke.edu> On Thu, 2003-09-18 at 15:10, Sebastian Bassi wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Frank Kauff wrote: > > | does anybody know which is the correct value for format_type in > | NCBIWWW.blast() to get a plain text output? It's 'html' by default, and > | I tried format_type='txt'/'text'/'plain'/'plaintext' and even 'ascii', > | but still it returns html. And maybe I'm blind, but is there any place > | in the web which lists exactly the different options? > > I use NCBIStandalone.blastall function and the last parameter is > "html=T" or "html=F" Yes, that works fine with NCBIStandalone.blastall(), but for the www interface some options differ (for whatever reason). There's no option html= in ncbiwww.blast(), instead format_type is used. At least that's what I think. > > | > | PS: and the show_overview question is still open... :-) > > Don't remember that question. > Posted some days ago: when doing a web blast with NCBIWWW.blast, the htlm returned looks pretty much like the normal www output when blasting directly at the ncbi website. However, that little grpahical distribution overview at the beginning that shows the color-coded alignments is missing. Is there a possibility to get that? show_overview seems to do this at the website, but has no effect when used in a script? Frank > - -- > Best regards, > > //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ > \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// > //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ > \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// > > ~ http://Bioinformatica.info > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.6 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAj9qAzsACgkQ6lc7ixf6gKooHACeKVIzpeUr5h286f2sOFGq2t6P > UNcAn1JPfNB2B9JypwodtFgz8910lFr6 > =ermr > -----END PGP SIGNATURE----- > > _______________________________________________ > 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 From peter.maxwell at anu.edu.au Thu Sep 18 20:43:03 2003 From: peter.maxwell at anu.edu.au (Peter Maxwell) Date: Thu Sep 18 20:41:11 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output In-Reply-To: <1063908901.2030.207.camel@osiris.biology.duke.edu> Message-ID: <3A5253B0-EA3A-11D7-BE18-000A9573A794@anu.edu.au> On Friday, September 19, 2003, at 04:15 AM, Frank Kauff wrote: > does anybody know which is the correct value for format_type in > NCBIWWW.blast() to get a plain text output? 'Text' , but last time I tried (a long while ago) NCBIWWW.blast() lost it somewhere along the way, which one reason why I wrote http://www.biolateral.com.au/download/NCBI.py. BTW if tempted to use my version as-is change the rate at which it polls for the result (time.sleep(5) to time.sleep(30) or something). The web server log watchers at NCBI don't like excessive polling. > but still it returns html. And maybe I'm blind, but is there any place > in the web which lists exactly the different options? http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html Cheers, -- Peter Maxwell From anunberg at oriongenomics.com Fri Sep 19 17:51:12 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Fri Sep 19 17:49:21 2003 Subject: [BioPython] how to send a seq object to an outgoing Fasta stream Message-ID: <62B42F6C-EAEB-11D7-B132-000A95A001EE@oriongenomics.com> stillnew to biopython and i am coming from the other biop project.. If i have a seq object or a seqrecord object and I want to then print it in FASTA format, what should I do? I noticed that the Fasta.Record object does not take any arguments when intialized and I cant seem to find a way to define an outward going FASTA stream(or do you even do this in pythone) like in bioperl : $out=Bio::SeqIO->new(-format=>'fasta); $out->write_seq($seq_obj) What is the equiv in biopython? Thanks --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com From development at cifrosoft.com Sat Sep 20 08:45:42 2003 From: development at cifrosoft.com (Vitaly Demin) Date: Sat Sep 20 08:44:03 2003 Subject: [BioPython] Partnering Enquiry from CifroSoft LLC (Russia) Message-ID: Dear colleagues, We are a software development company from Tomsk, Russia. We have been working on the Russian IT market for quite a long time and completed many projects. Now we plan to work with western software companies to become its outsourcing partner here in Russia. As you know such corporations as IBM and SUN Microsystems cooperate with Russian companies because it greatly reduces their costs as the labour force in Russia is a lot cheaper than in the west. Moreover Russian programmers are in high demand worldwide. We found your company rather professional in software development and if you are interested we are ready to become your partner in developing any kind of software. Actually there are two ways we can cooperate. 1. We can work with project components or entire projects of any scale. That is we'll be doing offshore programming for you on the terms we'll have discussed or 2. We can become your affiliate where our programmers we'll be working. It's up to you to make your choice. Below you can see a detailed list of our abilities and professional skills: Programming Languages C++ (Visual C++ 6.0/NET) Java (Java2) Technologies and Standards Win32 API Microsoft DNA (DCOM/COM+) DirectX, OpenGL, GDI+ TCP/IP protocols Java2 Enterprise Edition (Servlets, JSP, EJB, etc) ADO, DAO, BDE, JDBC, ODBC, etc Databases MS SQL Server Microsoft Access Sybase Oracle (PL/SQL, OCI) Software Engineering Tools Rational ROSE ErWin Power Designer All this information and all details about our company you can find at www.cifrosoft.com. We would be very glad to hear back from you. We will consider any kind of business cooperation offer from you if you are interested in our partnering. Please, write to us any time convenient for you. Sincerely Vitaly Demin Development Manager CifroSoft LLC From obaro777 at indiatimes.com Sun Sep 21 02:21:18 2003 From: obaro777 at indiatimes.com (chief obaro o. obaro) Date: Sat Sep 20 18:15:51 2003 Subject: [BioPython] (no subject) Message-ID: <200309202215.h8KMFfMg006428@portal.open-bio.org> HIEF OBARO & CO CHAMBERS ATTORNEYS AT LAW BARRISTERS Office. State House Annex.Ikoyi-Lagos Fax 234 1 7595789 Attn. Managing Director/CEO For the purpose of introduction, I am the private attorney to GENERAL ISHAYA BAMAYI, the former chief of army staff during the regime of late general Sani Abacha, who was the former head of state. As you may know, General Bamayi is presently in detention over some activities that took place when he was in government and the matter in court right now. Last year, the present civilian government set up a truth and reconciliation panel which was, CODE Name OPUTAL PANEL .If you are aware of this and probably you followed the proceeding on CNN, you would have seen in one occasion how one another retired military officer, General Sabo testified how all the generals looted billion of dollars. One specific case is the US$90.5m given to the late head of state for safe keeping by the oil companies in Nigeria for his campaign as he was planning to succeed himself but unfortunately he died shortly after the money was given and this money was taken by my client and deposit it a Security Company in Europe for safe keeping. Now that the matter has been made know, my client wants the money to be moved from where it is and be lodged in a bank account that will carry a foreigner’s name. This is the reason why I am contacting you. If you can handle this, please get back to me urgently so that I can arrange to send you documents with which the consignment was deposited and also arrange for you to travel to Europe where arrangement has been conclude to move the money and do something about it. This is TOP SECRET and must be treated as such.Please fax me on my direct fax number .234 1 7595789 for further info. Thanks for your understanding, kind consideration and cooperation my best regards to you and your family. Please let me have your private phone and fax numbers. Chief obaro O. obaro (SAN From L.Pritchard at scri.sari.ac.uk Mon Sep 22 04:16:45 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Mon Sep 22 04:59:50 2003 Subject: [BioPython] how to send a seq object to an outgoing Fasta stream In-Reply-To: <62B42F6C-EAEB-11D7-B132-000A95A001EE@oriongenomics.com> Message-ID: <5.2.1.1.0.20030922090425.0310bd40@caird> Hi Andrew, There's an analogous SeqIO module in BioPython, which contains a FASTA format writer, which can be used like this: from Bio.SeqIO.FASTA import FastaWriter from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq outfile = open('test.fas', 'w') writer = FastaWriter(outfile) record = SeqRecord(Seq('ACGTACGTACGTACGT'), id='Test sequence') writer.write(record) hope this helps... At 16:51 19/09/2003 -0500, you wrote: >stillnew to biopython and i am coming from the other biop project.. > >If i have a seq object or a seqrecord object and I want to then print it >in FASTA format, what should I do? >I noticed that the Fasta.Record object does not take any arguments when >intialized and I cant seem to find a way to define an outward going FASTA >stream(or do you even do this in pythone) like in bioperl : >$out=Bio::SeqIO->new(-format=>'fasta); >$out->write_seq($seq_obj) > >What is the equiv in biopython? >Thanks > >--------------------------------------------------- >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 Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key FEFC205C: http://www.keyserver.net http://pgp.mit.edu From letondal at pasteur.fr Mon Sep 22 06:04:26 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon Sep 22 06:02:34 2003 Subject: [BioPython] End-User Development Survey Message-ID: <200309221004.h8MA4QlQ351512@electre.pasteur.fr> Hi, An european End-User Development network (http://giove.cnuce.cnr.it/eud-net.htm) has started 1 year ago. Its aim is to develop and promote development and tailoring of software tools by their users, which I think is of major importance in our field. By "users", they mean not only "end-user" - I don't really like this term but it's the common adopted one - but also people who, while being professional of a domain (i.e bioinformatics) and thus not being "professional" computer scientists, do participate in the development of software tools. I thought that it might be interesting for this network to get some input from real "practicionners" by asking to the biopythoners to answer the survey questionnaire that is online : http://www.lri.fr/~letondal/Bib/eud_survey.html Answers are sent by email to the organizers of the network and are fully anonymous (no record of the sending machine is made, nobody has access to the log files etc...). The questionnaire tests show that it should take about 10 minutes to fill. Thanks to all of you, -- Catherine Letondal -- Pasteur Institute Computing Center From karin.lagesen at labmed.uio.no Thu Sep 18 07:14:23 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Mon Sep 22 07:33:40 2003 Subject: [BioPython] biopython installation problem (cont.) In-Reply-To: <3F698589.4080907@clondiag.com> References: <20030918085426.GA1602@uracil.uio.no> <3F698589.4080907@clondiag.com> Message-ID: <20030918111422.GB1602@uracil.uio.no> On Thu, Sep 18, 2003 at 12:14:33PM +0200, Peter Slickers wrote: [snipped sys.path stuff] > Please check if directory '/site/python_packages' is in the list. It is. > Second: > > Within directory '/site/python_packages' you need a '*.pth' file. > If this file is missing, python will not search any subdirectories > of '/site/python_packages'. This file can be easily create > by the following command: > > > cd /site/python_packages > find . -type d -maxdepth 1 | awk '{ if($0 !~ /CVS/) {print substr($0,3)}}' > > packages.pth > > cat packages.pth > > As you can see the path file just contains the names of all > subdirectories (since I assume that every subdirectory contains > a python package.) Please recreate 'packages.pth' each time > you install in new package in '/site/python_packages'. Hmm... I created this file, however, the result of installing both Numeric and the mxTextTools package there is this: uracil:13:08> ls /site/python_packages/*/*/* /site/python_packages/lib/python/Numeric.pth /site/python_packages/include/python/Numeric: arrayobject.h f2c.h ranlib.h ufuncobject.h /site/python_packages/lib/python/Numeric: ArrayPrinter.py MLab.pyc RNG lapack_lite.so ArrayPrinter.pyc Matrix.py RandomArray.py multiarray.so FFT Matrix.pyc RandomArray.pyc numeric_version.py LinearAlgebra.py Numeric.py UserArray.py numeric_version.pyc LinearAlgebra.pyc Numeric.pyc UserArray.pyc ranlib.so MA Precision.py _numpy.so umath.so MLab.py Precision.pyc arrayfns.so /site/python_packages/lib/python/mx: BeeBase Doc Log.pyc NewBuiltins.py Proxy TextTools __init__.pyc COPYRIGHT LICENSE Log.pyo NewBuiltins.pyc Queue Tools __init__.pyo DateTime Log.py Misc NewBuiltins.pyo Stack __init__.py uracil:13:09> I.e, in /site/python_packages I don't have either mx nor Numeric. I tried instead setting PYTHONPATH to /site/python_packages/lib/python, and then I could import mx but not Numeric. Curiouser and curiouser... Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From yadanasiru at indiatimes.com Tue Sep 23 09:21:44 2003 From: yadanasiru at indiatimes.com (Yada Nasiru) Date: Tue Sep 23 09:19:44 2003 Subject: [BioPython] Honest!!!!!!! Message-ID: <200309231319.h8NDJYMg016398@portal.open-bio.org> Dear Sir As you read this, I dont want you to feel sorry for me, because, I believe everyone will die someday. My name is MR Yada Nasiru, a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer which was discovered very late, due to my laxity in carrying for my health. It has defiled all forms of medicine, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone not even myself but my business. Though I am very rich, I was never generous,I was always hostile to people and only focus on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world.I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my properties and assets to my immediate and extended family members and as well as a few close friends. I want God to be merciful to me and accept my soul and so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this my self any more. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of twenty four million dollars that I have with a security company.I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 20% for you for your time and patience.please reply to God be with you. MR Yada Nasiru From sbassi at asalup.org Tue Sep 23 10:10:48 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Tue Sep 23 10:11:40 2003 Subject: [BioPython] Honest!!!!!!! In-Reply-To: <200309231319.h8NDJYMg016398@portal.open-bio.org> References: <200309231319.h8NDJYMg016398@portal.open-bio.org> Message-ID: <3F705468.2020108@asalup.org> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Yada Nasiru wrote: | Dear Sir | | As you read this, I dont want you to feel sorry for me, because, I believe This kind of scam is getting funnier over time :) - -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// ~ http://Bioinformatica.info -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAj9wVFcACgkQ6lc7ixf6gKohkQCgkaS/Z/SNWHcXjetIFArEJl17 uz0AoJN7PT0KeDYA4OuS1mHmzdiU/lXW =8/4k -----END PGP SIGNATURE----- From karin.lagesen at labmed.uio.no Tue Sep 23 10:19:21 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Tue Sep 23 10:17:30 2003 Subject: [BioPython] reading large sequence files Message-ID: <20030923141921.GA13177@uracil.uio.no> Hi! I am working on whole (procaryote) genomes, and due to this I need to work with whole genomes at the time. I am for instance reading in the ecoli genome like this: ecoliDir = genomePath + ecoli ecoliFiles = os.listdir(ecoliDir) ecoliFile = fnmatch.filter(ecoliFiles, '*.fna') ecoliFile = open(os.path.join(ecoliDir, ecoliFile[0]), 'r') iterator = Fasta.Iterator(ecoliFile, parser) fileContents = iterator.next() ecoliSeq = fileContents.sequence ecoliFile.close() where genomePath tells the program where the genome files are, and ecoli just gives the genome name. All genome files end in .fna However, when I do it this way it takes a looooooooong time to read in the genome, it currently takes almost 10 minutes. Is there some way I can make this go faster? I need to work with alltogether 13 genomes, and it would be nice if this part of it wasn't the bottleneck. Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From L.Pritchard at scri.sari.ac.uk Tue Sep 23 10:57:07 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Tue Sep 23 10:55:20 2003 Subject: [BioPython] reading large sequence files In-Reply-To: <20030923141921.GA13177@uracil.uio.no> Message-ID: <5.2.1.1.0.20030923155216.03046df0@caird> Hi Karin, Guessing that you have one .fna sequence file containing the whole sequence (or each chromosome/plasmid), then you can use quick_FASTA_reader from SeqUtils in a manner similar to: from Bio.SeqUtils import quick_FASTA_reader name, seq = quick_FASTA_reader(genome_file)[0] The quick_FASTA_reader reads in (name, sequence) tuples without doing anything too clever or time-consuming like parsing sequences as SeqRecords. It's *much* faster than using the Fasta.Iterator class. Hope this helps, At 16:19 23/09/2003 +0200, Karin Lagesen wrote: >Hi! > >I am working on whole (procaryote) genomes, and due to this I need to >work with whole genomes at the time. I am for instance reading in the >ecoli genome like this: > >ecoliDir = genomePath + ecoli >ecoliFiles = os.listdir(ecoliDir) >ecoliFile = fnmatch.filter(ecoliFiles, '*.fna') >ecoliFile = open(os.path.join(ecoliDir, ecoliFile[0]), 'r') >iterator = Fasta.Iterator(ecoliFile, parser) >fileContents = iterator.next() >ecoliSeq = fileContents.sequence >ecoliFile.close() > >where genomePath tells the program where the genome files are, and >ecoli just gives the genome name. All genome files end in .fna > >However, when I do it this way it takes a looooooooong time to read in >the genome, it currently takes almost 10 minutes. Is there some way I >can make this go faster? I need to work with alltogether 13 genomes, >and it would be nice if this part of it wasn't the bottleneck. > > >Karin >-- >Karin Lagesen, PhD student >karin.lagesen@labmed.uio.no >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key FEFC205C: http://www.keyserver.net http://pgp.mit.edu From Cath.Lawrence at anu.edu.au Tue Sep 23 21:24:24 2003 From: Cath.Lawrence at anu.edu.au (Cath Lawrence) Date: Tue Sep 23 21:21:15 2003 Subject: [BioPython] mmCIF parser? Message-ID: So is anyone working on this? I'm just barely beginning to learn what it's all about. cheers C Cath Lawrence, Cath.Lawrence@anu.edu.au Senior Scientific Programmer, Centre for Bioinformation Science, John Curtin School of Medical Research (room 4088) Australian National University, Canberra ACT 0200 ph: (02) 61257959 mobile: 0421-902694 fax: (02) 61252595 From dalke at dalkescientific.com Tue Sep 23 22:19:31 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue Sep 23 22:16:35 2003 Subject: [BioPython] mmCIF parser? In-Reply-To: Message-ID: <881318FC-EE35-11D7-90C0-000393C92466@dalkescientific.com> [Cath Lawrence asked about mmCIF] Try Jay Painter's PyMMLib, at http://pymmlib.sourceforge.net/ Andrew dalke@dalkescientific.com From thamelry at vub.ac.be Wed Sep 24 02:17:59 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Wed Sep 24 03:23:37 2003 Subject: [BioPython] mmCIF parser? In-Reply-To: References: Message-ID: <200309240817.59295.thamelry@vub.ac.be> On Wednesday 24 September 2003 03:24 am, Cath Lawrence wrote: > So is anyone working on this? I'm just barely beginning to learn what > it's all about. Bio.PDB only deals with PDB files. However, I do have some code lying around that deals with mmCIF files, (lex generated C code + python bindings) but I didn't add it to Bio.PDB because (a) I don not use mmCIF and (b) no one asked for it - until now that is :-). What do you need it for? I might be tempted to add mmCIF support after all. OTOH, as Andrew pointed out, PyMMLib indeed comes with mmCIF support, so that's an out-of-the-box solution for you. Regards, --- Thomas Hamelryck COMO-ULTR Vrije Universiteit Brussel (VUB) Belgium http://homepages.vub.ac.be/~thamelry From karin.lagesen at labmed.uio.no Wed Sep 24 03:28:28 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Wed Sep 24 03:26:38 2003 Subject: [BioPython] reading large sequence files In-Reply-To: <5.2.1.1.0.20030923155216.03046df0@caird> References: <20030923141921.GA13177@uracil.uio.no> <5.2.1.1.0.20030923155216.03046df0@caird> Message-ID: <20030924072828.GA24597@uracil.uio.no> On Tue, Sep 23, 2003 at 03:57:07PM +0100, Leighton Pritchard wrote: > Hi Karin, > > Guessing that you have one .fna sequence file containing the whole sequence > (or each chromosome/plasmid), then you can use quick_FASTA_reader from > SeqUtils in a manner similar to: > > from Bio.SeqUtils import quick_FASTA_reader > > name, seq = quick_FASTA_reader(genome_file)[0] > > > The quick_FASTA_reader reads in (name, sequence) tuples without doing > anything too clever or time-consuming like parsing sequences as > SeqRecords. It's *much* faster than using the Fasta.Iterator class. > > Hope this helps, So do I...:) However, I have come upon a weird thing: My sequence file looks like this: >gi|16127994|ref|NC_000913.1| Escherichia coli K12, complete genome AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC and so on. When I try to load in this genome it crashes: File "gene.py", line 11, in __readFastaFile print quick_FASTA_reader(file)[0] File "/site/python_packages//lib/python/Bio/SeqUtils/__init__.py", line 281, in quick_FASTA_reader name,seq= entry.split('\n',1) ValueError: unpack list of wrong size The way I call it is as follows: def __readFastaFile(self, file): title, seq = quick_FASTA_reader(file)[0] return title, seq Where file is a string containing the absolute file name. I am reasonably new to python, so please excuse me if I am doing something obviously wrong/idiotic...:) Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no From L.Pritchard at scri.sari.ac.uk Wed Sep 24 04:16:04 2003 From: L.Pritchard at scri.sari.ac.uk (Leighton Pritchard) Date: Wed Sep 24 04:20:42 2003 Subject: [BioPython] reading large sequence files In-Reply-To: <20030924072828.GA24597@uracil.uio.no> References: <5.2.1.1.0.20030923155216.03046df0@caird> <20030923141921.GA13177@uracil.uio.no> <5.2.1.1.0.20030923155216.03046df0@caird> Message-ID: <5.2.1.1.0.20030924090211.058bbc20@caird> Hi Karin, There doesn't look to be anything wrong with your code at first glance, except that 'file' is already used as a keyword in Python, so it's best to avoid using it as a variable name. I'm guessing (again) that you're using the file NC_000913.fna from NCBI (or your favourite download source). I've tried to replicate your error with that file and your code (substituting 'filename' for 'file'), and it works fine for me. Have you already tried loading that file in interactive mode with quick_FASTA_reader and the absolute filename as an argument? Let me know how you get on, At 09:28 24/09/2003 +0200, Karin Lagesen wrote: >On Tue, Sep 23, 2003 at 03:57:07PM +0100, Leighton Pritchard wrote: > > Hi Karin, > > > > Guessing that you have one .fna sequence file containing the whole > sequence > > (or each chromosome/plasmid), then you can use quick_FASTA_reader from > > SeqUtils in a manner similar to: > > > > from Bio.SeqUtils import quick_FASTA_reader > > name, seq = quick_FASTA_reader(genome_file)[0] > > Hope this helps, > >So do I...:) > >However, I have come upon a weird thing: >[...] >When I try to load in this genome it crashes: > > File "gene.py", line 11, in __readFastaFile > print quick_FASTA_reader(file)[0] > File "/site/python_packages//lib/python/Bio/SeqUtils/__init__.py", >line 281, in quick_FASTA_reader > name,seq= entry.split('\n',1) >ValueError: unpack list of wrong size > >The way I call it is as follows: > > def __readFastaFile(self, file): > title, seq = quick_FASTA_reader(file)[0] > return title, seq > >Where file is a string containing the absolute file name. > >I am reasonably new to python, so please excuse me if I am doing >something obviously wrong/idiotic...:) Dr Leighton Pritchard AMRSC PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK L.Pritchard@scri.sari.ac.uk PGP key FEFC205C: http://www.keyserver.net http://pgp.mit.edu From sbassi at asalup.org Wed Sep 24 11:09:37 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Wed Sep 24 11:11:04 2003 Subject: [BioPython] [Fwd: [blast-announce] [BLAST-Announce #036]: Discontinuation of old BLAST web service.] Message-ID: <3F71B3B1.1040103@asalup.org> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'd like to know if this change is going to affect the functionality of any component of biopython. For the mainteiner of Blast module, please read this: - -------- Original Message -------- From: Mcginnis, Scott (NIH/NLM/NCBI) To: 'blast-announce@ncbi.nlm.nih.gov' Date: Wed, 24 Sep 2003 10:34:03 -0400 [BLAST-Announce #036]: Discontinuation of old BLAST web service. NCBI will be discontinuing an older and outdated BLAST web server. It will be turned off at or about October 24, 2003. This is the old BLAST web service can be distinguished by the URL which contains "/cgi-bin/BLAST/nph-blast_report". The removal of old, outdated services free up resources to allow NCBI to continue providing new features and optimize BLAST performance. This change should not effect the BLAST web pages as they were migrated to the new system a few years ago. However, this change may effect old third party applications and some custom scripts. Third party applications should now use the BLAST URL API documentation which is located here: http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html. Several companies have already migrated their software to the new BLAST servers. If you use an older, third party program (e.g. GCG) you should contact the manufacturer to inquire about updates for these programs. Users of older forms of these programs will no longer be able to perform BLAST searches once the old service is removed. If you have any questions regarding this or other BLAST services, please contact us at blast-help@ncbi.nlm.nih.gov. - -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// ~ http://Bioinformatica.info -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAj9xs7AACgkQ6lc7ixf6gKoWLQCgxiytWHKSl4eNiaqzERcRckBb amwAoJeR52huNwVnKf/KNrC/4UlD/Cuz =BfcI -----END PGP SIGNATURE----- From jchang at smi.stanford.edu Wed Sep 24 11:32:45 2003 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Wed Sep 24 11:22:45 2003 Subject: [BioPython] [Fwd: [blast-announce] [BLAST-Announce #036]: Discontinuation of old BLAST web service.] In-Reply-To: <3F71B3B1.1040103@asalup.org> References: <3F71B3B1.1040103@asalup.org> Message-ID: <20030924153245.GC48736@springfield.stanford.edu> Yes, this will affect the NCBIWWW.blasturl function, since that uses this web service. Since it doesn't look like NCBI is going to replace it with anything, this function will be deprecated. Is this going to affect anyon? It seems like people use NCBIWWW.blast instead anyway (or at least, those are the bugs I hear about). Jeff On Wed, Sep 24, 2003 at 12:09:37PM -0300, Sebastian Bassi wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > I'd like to know if this change is going to affect the functionality of > any component of biopython. > For the mainteiner of Blast module, please read this: > > - -------- Original Message -------- > From: Mcginnis, Scott (NIH/NLM/NCBI) > To: 'blast-announce@ncbi.nlm.nih.gov' > Date: Wed, 24 Sep 2003 10:34:03 -0400 > > [BLAST-Announce #036]: Discontinuation of old BLAST web service. > > NCBI will be discontinuing an older and outdated BLAST web server. It > will be turned off at or about October 24, 2003. This is the old BLAST > web service can be distinguished by the URL which contains > "/cgi-bin/BLAST/nph-blast_report". The removal of old, outdated services > free up resources to allow NCBI to continue providing new features and > optimize BLAST performance. > > This change should not effect the BLAST web pages as they were migrated > to the new system a few years ago. However, this change may effect old > third party applications and some custom scripts. Third party > applications should now use the BLAST URL API documentation which is > located here: > http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html. Several companies > have already migrated their software to the new BLAST servers. > > If you use an older, third party program (e.g. GCG) you should contact > the manufacturer to inquire about updates for these programs. Users of > older forms of these programs will no longer be able to perform BLAST > searches once the old service is removed. > > If you have any questions regarding this or other BLAST services, please > contact us at > blast-help@ncbi.nlm.nih.gov. > > > > - -- > Best regards, > > //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ > \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// > //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ > \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// > > ~ http://Bioinformatica.info > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.6 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAj9xs7AACgkQ6lc7ixf6gKoWLQCgxiytWHKSl4eNiaqzERcRckBb > amwAoJeR52huNwVnKf/KNrC/4UlD/Cuz > =BfcI > -----END PGP SIGNATURE----- > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From dalke at dalkescientific.com Wed Sep 24 14:33:43 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Wed Sep 24 14:30:49 2003 Subject: [BioPython] biopython.com domain about to expire In-Reply-To: <3F71D824.7080700@sonsorol.org> Message-ID: After ISMB 2001, I bought the biopython.com domain with the hopes of setting up a site listing companies which used Python in biology, with a preference for ones which encouraged open source. I bought it in my company's name so I could set the policy -- I felt that if it was done under the OBF umbrella then the site would need a stronger open-source leaning, and I figured that biopython.org's own web site is sufficient for that. The domain is set to expire, in ... 3 days. I've been putting off renewing it since it turns out I haven't done much biology programming the last few years. Most of my income has come from doing chemistry software instead, and I expect it to stay that way for at least another year or more. (But if you have money, make me an offer ;) Before it lapses back to general availability, I wondered if anyone here wanted to develop and maintain a biopython.com site? Given my opinion above, I don't think it's right for the OBF to do it, and given the work involved I suspect no one wants to volunteer for it. But I thought I'ld make the offer. Andrew dalke@dalkescientific.com -- Need usable, robust software for bioinformatics or chemical informatics? Want to integrate your different tools so you can do more science in less time? Contact us! http://www.dalkescientific.com/ From Cath.Lawrence at anu.edu.au Wed Sep 24 20:00:38 2003 From: Cath.Lawrence at anu.edu.au (Cath Lawrence) Date: Wed Sep 24 19:57:32 2003 Subject: [BioPython] mmCIF parser? In-Reply-To: <200309240817.59295.thamelry@vub.ac.be> Message-ID: <4BBC9383-EEEB-11D7-A915-00039390F614@anu.edu.au> On Wednesday, September 24, 2003, at 04:17 PM, Thomas Hamelryck wrote: > On Wednesday 24 September 2003 03:24 am, Cath Lawrence wrote: >> So is anyone working on this? I'm just barely beginning to learn what >> it's all about. > Bio.PDB only deals with PDB files. However, I do have some code lying > around that deals with mmCIF files, (lex generated C code + python > bindings) > but I didn't add it to Bio.PDB because (a) I don not use mmCIF and (b) > no one > asked for it - until now that is :-). > What do you need it for? I might be tempted to add mmCIF support after > all. > OTOH, as Andrew pointed out, PyMMLib indeed comes with mmCIF support, > so > that's an out-of-the-box solution for you. Well, the PDB data uniformity project is rebuilding PDB with mmCIF format files. And a RDBMS but that's in alpha now. We've registered as potential beta testers but that won't be until maybe December. Meanwhile, the mmCIF files in the uniformity project are better curated, and the format is less flaky. As you no doubt know, the PDB parser breaks on quite a few of the PDB files - for various reasons to do with data quality, not poor coding, I hasten to add. And I want all the files I can get - my local mathematician wants bulk stats on amino acid distances. I'm looking at PyMMLib now - thanks to Andrew for the reference. So far it builds and the test runs. Now for some larger tests... cheers Cath Cath Lawrence, Cath.Lawrence@anu.edu.au Senior Scientific Programmer, Centre for Bioinformation Science, John Curtin School of Medical Research (room 4088) Australian National University, Canberra ACT 0200 ph: (02) 61257959 mobile: 0421-902694 fax: (02) 61252595 From jchang at jeffchang.com Mon Sep 22 13:24:28 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Thu Sep 25 01:47:36 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output In-Reply-To: <3A5253B0-EA3A-11D7-BE18-000A9573A794@anu.edu.au> Message-ID: <9EEBD60A-ED21-11D7-B868-000A956845CE@jeffchang.com> On Thursday, September 18, 2003, at 05:43 PM, Peter Maxwell wrote: > On Friday, September 19, 2003, at 04:15 AM, Frank Kauff wrote: >> does anybody know which is the correct value for format_type in >> NCBIWWW.blast() to get a plain text output? > > 'Text' , but last time I tried (a long while ago) NCBIWWW.blast() lost > it somewhere along the way, which one reason why I wrote > http://www.biolateral.com.au/download/NCBI.py. Can you double check to see if NCBIWWW.blast was/is losing options? It would be a pretty serious error, but I cannot see where that might be happening. Thanks, Jeff From peter.maxwell at anu.edu.au Thu Sep 25 03:16:23 2003 From: peter.maxwell at anu.edu.au (Peter Maxwell) Date: Thu Sep 25 03:14:15 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output In-Reply-To: <9EEBD60A-ED21-11D7-B868-000A956845CE@jeffchang.com> Message-ID: <2B0B3A62-EF28-11D7-BE18-000A9573A794@anu.edu.au> On Tuesday, September 23, 2003, at 03:24 AM, Jeffrey Chang wrote: > Can you double check to see if NCBIWWW.blast was/is losing options? > It would be a pretty serious error, but I cannot see where that might > be happening. Sorry, NCBIWWW.blast is obsolete for me so I can't find any motivation to go testing it! See http://biopython.org/pipermail/biopython/2002-August/001015.html for my thoughts at the time. -- Peter From fkauff at duke.edu Thu Sep 25 09:22:03 2003 From: fkauff at duke.edu (Frank Kauff) Date: Thu Sep 25 09:22:05 2003 Subject: [BioPython] NCBIWWW.blast(): how to get text formatted output In-Reply-To: <9EEBD60A-ED21-11D7-B868-000A956845CE@jeffchang.com> References: <9EEBD60A-ED21-11D7-B868-000A956845CE@jeffchang.com> Message-ID: <1064496244.2031.9.camel@osiris.biology.duke.edu> On Mon, 2003-09-22 at 13:24, Jeffrey Chang wrote: > On Thursday, September 18, 2003, at 05:43 PM, Peter Maxwell wrote: > > > On Friday, September 19, 2003, at 04:15 AM, Frank Kauff wrote: > >> does anybody know which is the correct value for format_type in > >> NCBIWWW.blast() to get a plain text output? > > > > 'Text' , but last time I tried (a long while ago) NCBIWWW.blast() lost > > it somewhere along the way, which one reason why I wrote > > http://www.biolateral.com.au/download/NCBI.py. > > Can you double check to see if NCBIWWW.blast was/is losing options? It > would be a pretty serious error, but I cannot see where that might be > happening. It seems the options are not lost. If I print the options just before they are passed to the Entrez handle in Bio.WWW.NCBI._open(), I get SERVICE=plain&QUERY_FROM=&NCBI_GI=on&CMD=Put&PROGRAM=blastn&DESCRIPTIONS=100 &FORMAT_OBJECT=alignment&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=on&QUERY_TO= &SHOW_OVERVIEW=yes&ENTREZ_QUERY=%28none%29&EXPECT=10&I_THRESH=0.001 &FORMAT_TYPE=html&LAYOUT=OneWindow&DATABASE=nr&GENETIC_CODE=1&FILTER=L &CLIENT=web&CDD_SEARCH=on&WORD_SIZE=11 &QUERY=%3EABUL1x%0ATGGC.....GGT%0A&ALIGNMENTS=500&PAGE=Nucleotides with default options and if I call it with bres=NCBIWWW.blast('blastn','nr',record,format_type='Text') I get SERVICE=plain&QUERY_FROM=&NCBI_GI=on&CMD=Put&PROGRAM=blastn&DESCRIPTIONS=100 &FORMAT_OBJECT=alignment&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=on&QUERY_TO= &SHOW_OVERVIEW=yes&ENTREZ_QUERY=%28none%29&EXPECT=10&I_THRESH=0.001 &FORMAT_TYPE=Text&LAYOUT=OneWindow&DATABASE=nr&GENETIC_CODE=1&FILTER=L &CLIENT=web&CDD_SEARCH=on&WORD_SIZE=11 &QUERY=%3EABUL1x%0ATGGC...GGT&ALIGNMENTS=50&PAGE=Nucleotides Frank > > Thanks, > Jeff > > _______________________________________________ > 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 From bogus@does.not.exist.com Fri Sep 26 14:05:30 2003 From: bogus@does.not.exist.com () Date: Fri Sep 26 14:00:25 2003 Subject: [BioPython] =?iso-8859-1?q?Controle_de_Processos_Jur=EDdicos?= Message-ID: <200309261800.h8QI0Ldb012009@portal.open-bio.org> Conhe?a o mais novo produto do Bonijuris ( p r O f f i c i u m ) Controle de Processos "prOfficium" Profissional e Empresarial clique aqui http://www.bonijuris.com.br Controle at? 50 processos gratuitamente. From bogus@does.not.exist.com Fri Sep 26 15:17:08 2003 From: bogus@does.not.exist.com () Date: Fri Sep 26 15:12:05 2003 Subject: [BioPython] =?iso-8859-1?q?Promo=E7=E3o_BANCO_DE_CONTRATOS_e_PET?= =?iso-8859-1?q?I=C7=D5ES?= Message-ID: <200309261911.h8QJBwdb016426@portal.open-bio.org> Visite sem compromisso http://www.agilicom.com.br Programa com; 3500 Modelos de Peti??es 2000 Modelos de Contratos Atualizados pelo novo C?digo Civil. Lan?amento Nacional. From anunberg at oriongenomics.com Tue Sep 30 18:36:59 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Tue Sep 30 18:34:50 2003 Subject: [BioPython] help with mx installation on redhat Message-ID: <9AE1D738-F396-11D7-B71D-000A95A001EE@oriongenomics.com> Hi, I installed the egenix mx module on a redhat 7,2 machine. i can import mx but cannot import TexTools when i try from mx import TextTools i get: Traceback (most recent call last): File "", line 1, in ? File "/usr/local/lib/python2.3/site-packages/mx/TextTools/__init__.py", line 8, in ? File "/usr/local/lib/python2.3/site-packages/mx/TextTools/TextTools.py", line 13, in ? File "/usr/local/lib/python2.3/site-packages/mx/TextTools/mxTextTools/ __init__.py", line 8, in ? ImportError: No module named mxTextTools I take it i did not install themodule correctly or is it some permission issue? Thanks --------------------------------------------------- Andrew Nunberg Ph.D Bioinfomagician Orion Genomics 4041 Forest Park St Louis, MO 314-615-6989 anunberg@oriongenomics.com www.oriongenomics.com