From brmyers at dink.foretune.co.jp Thu Jul 1 07:40:38 2004 From: brmyers at dink.foretune.co.jp (brmyers@dink.foretune.co.jp) Date: Thu Jul 1 07:46:33 2004 Subject: [BioPython] software In-Reply-To: <5E13675C8KHAA28L@biopython.org> References: <5E13675C8KHAA28L@biopython.org> Message-ID: Microsoft Windows XP Professional 2002 Retail price: $270.99 Our low Price: $50.00 You Save: $220.00 Adobe Photoshop 7.0 Retail price: $609.99 Our low Price: $60.00 You Save: $550.00 Microsoft Office XP Professional 2002 Retail price: $579.99 Our low Price: $60.00 You Save: $510.00 Adobe Illustrator 10 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Corel Draw Graphics Suite 11 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Delphi 7 Retail price: $404.99 Our low Price: $60.00 You Save: $335.00 And more!!! Our site is http://WcRke.cnhdcdai.info/?h0jSj2hQWRoG3NNtY Why so cheap? All the software is OEM- Meaning that you don't get the box and the manual with your software. 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Direct Mail(???????? ???????? ????????) ????????. 1. ?????? ????? ?????????? ? ???????? ?????? ???? ?????? ??? ??????????? ??? ? ??????? ???; 2. ???????????? ????????; 3. ?????? ???????? ? ???????? ?????????? ??????; 4. ??????? ????? ?????????;???????? ????? ?????????; 5. ??????????? ??????????????? ? ??????????? ????; 6. ?????? ??? ?????????? ????????. ? ??????? ???????! ?? ?????? ??????, ???????? ? ???? ??? ???? ???????? ???????? ?? ????? ????????. ? ???????? ?? ?????? ?????????????? ???????? "???? ????" (095)-540-09-80-????? From lise at deneg.net Sat Jul 3 18:29:30 2004 From: lise at deneg.net (=?Windows-1251?B?xOjs6PLw6Okgw+Xt8Oj17uLo9w==?=) Date: Sat Jul 3 20:37:45 2004 Subject: [BioPython] =?windows-1251?b?xOv/IMLg8SDu8iDF4u/w4Orx6P8gz+jy?= =?windows-1251?b?6PDo7O7i7eA=?= Message-ID: <121305097.20040703223430@> Hello ???????? ?????????? ??????????? ? ????? ???????? ? ???????, ??????????? ????? ????????????, ???? ?????????? ??? ???? ?????? ? ??????????? Direct Mail(???????? ???????? ????????) ????????. 1. ????? ?????????? ? ???????? ?????? ???? ?????? ??? ??????????? ??? ? ?????????? ???; 2. ?????? ??? ????????; 3. ?????? ???????? ? ???????? ?????????? ??????; 4. ??????? ????? ?????????;???????? ????? ?????????; 5. ??????????? ??????????????? ? ??????????? ????; 6. ?????? ??? ?????????? ????????. ? ??????? ???????! ?? ?????? ??????, ???????? ? ???? ??? ???? ???????? ???????? ?? ????? ????????. ? ???????? ?? ???????????? ?????????????? ???????? "???? ????" (095)-107-26-31-?????? From nabil at seznam.cz Sun Jul 4 14:04:47 2004 From: nabil at seznam.cz (monika) Date: Sun Jul 4 14:13:29 2004 Subject: [BioPython] =?windows-1251?b?4eXr/OU=?= Message-ID: <200407041813.i64IDMKr020627@portal.open-bio.org> ??? ???? ????????? ??????????? ????? ?? ????? http://www.mypresent.ru. ??????? ????? ???????? ? ????????. From jessitienda at freemail.nl Sun Jul 4 16:07:29 2004 From: jessitienda at freemail.nl (jessitienda@freemail.nl) Date: Sun Jul 4 18:06:58 2004 Subject: [BioPython] xanax valium codine vicodin Message-ID: xanax valium codine vicodin No prior script needed http://hereleavegone.com/phfo/pharm.html Rem0ve on site or write to PO box 42 Maenam Post Office Surathani, Ko Samui 84330 Thailand From ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za Mon Jul 5 05:55:57 2004 From: ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za (ssalie_lab_staff_health_med_uct@mail.med.uct.ac.za) Date: Mon Jul 5 06:06:29 2004 Subject: [BioPython] Huge problems with examples Message-ID: <1089021357.40e925ad1277b@webmail.uct.ac.za> Hi, I've downloaded Biopython onto windows XP and trying examples...quite a few error messages popping up when trying to run C:\>C:\Python23\examples\fasta_iterator.py Traceback (most recent call last): File "C:\Python23\examples\fasta_iterator.py", line 29, in ? all_species = extract_organisms("ls_orchid.fasta") File "C:\Python23\examples\fasta_iterator.py", line 7, in extract_organisms file = open(file_to_parse, 'r') IOError: [Errno 2] No such file or directory: 'ls_orchid.fasta' C:\>C:\Examples\query_entrez.py Traceback (most recent call last): File "C:\Examples\query_entrez.py", line 24, in ? doptcmdl = return_format) File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 51, in query return _open(cgi, variables) File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 191, in _open handle = urllib.urlopen(fullcgi) File "C:\Python23\lib\urllib.py", line 76, in urlopen return opener.open(url) File "C:\Python23\lib\urllib.py", line 181, in open return getattr(self, name)(url) File "C:\Python23\lib\urllib.py", line 297, in open_http h.endheaders() File "C:\Python23\lib\httplib.py", line 712, in endheaders self._send_output() File "C:\Python23\lib\httplib.py", line 597, in _send_output self.send(msg) File "C:\Python23\lib\httplib.py", line 564, in send self.connect() File "C:\Python23\lib\httplib.py", line 548, in connect raise socket.error, msg IOError: [Errno socket error] (10060, 'Operation timed out') C:\>C:\Python23\examples\fasta_consumer.py Traceback (most recent call last): File "C:\Python23\examples\fasta_consumer.py", line 35, in ? all_species = extract_organisms("ls_orchid.fasta", 94) File "C:\Python23\examples\fasta_consumer.py", line 21, in extract_organisms scanner = Fasta._Scanner() AttributeError: 'module' object has no attribute '_Scanner' C:\>C:\Python23\examples\getgene.py Traceback (most recent call last): File "C:\Python23\examples\getgene.py", line 36, in ? import gdbm ImportError: No module named gdbm From ebwhfz at geocities.com Mon Jul 5 22:26:34 2004 From: ebwhfz at geocities.com (Malinda Harmon) Date: Mon Jul 5 21:32:24 2004 Subject: [BioPython] Windows XP xa Professional Message-ID: <8650749703.07938@hotpop.com> mxyogmvpm High-quality software at lowest possible price. 50-60 USD: Windows XP Professional Microsoft Office 2003 Professional Adobe Photoshop MacroMedia Studio MX MS SQL Server 2000 Enterprise Save your company thousands of dollars when it needs software That promotion just got closer... wait there is more, Software packages you can save big on: Windows XP Professional Adobe Photoshop 7.0 Microsoft Office XP Professional Microsoft Office 2003 Professional Microsoft Money 2004 Microsoft 2000 Professional Adobe Photoshop CS Adobe Pagemaker 7.0 Adobe Illustrator 10 Corel Draw Graphics Suite 11 Adobe Acrobat 6.0 Professional Borland Delphi 7 Professional Visual Studio.Net Enterprise Architecht MS SQL Server 2000 Enterprise MS Windows Server 2003 Enterprise MS Windows 2000 Server And this is only the top of the list http://www.rjjh.ph.jzond.dmblmiff.info/?Cl8H8TCIIGJfmqCfii why it could never be more than a toy. No man of money even thought ofstrength of the road. I do know that in the reorganization of 1914 theturnover of labour and our present force we should have to hire at the lqigk lluom fjhebzl I wish don't recive this anymore. http://avutjub.IHJJFJDF.info/cehtm?ETaJapEKeIfNUsEqtwvx disease. I think that if an industrial institution is to fill its wholeThe man who does not get a certain satisfaction out of his day's work isthe most important factors was the Detroit, Toledo, & Irontonthe manufacturers were in such a hurry to obtain something to sell thatdoubtless discover other changes that will have to be made in our From ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za Tue Jul 6 09:51:46 2004 From: ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za (ssalie_lab_staff_health_med_uct@mail.med.uct.ac.za) Date: Tue Jul 6 10:02:15 2004 Subject: [BioPython] IOError: [Errno socket error] (10060, 'Operation timed out') Message-ID: <1089121906.40eaae72b07c1@webmail.uct.ac.za> Hi Genius, I have tried to run this on my laptop and works without a glitch. However on my work PC I have this error message...Please help! C:\>C:\Python23\biopython-1.30\examples\query_entrez.py Traceback (most recent call last): File "C:\Python23\biopython-1.30\examples\query_entrez.py", line 24, in ? doptcmdl = return_format) File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 51, in query return _open(cgi, variables) File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 191, in _open handle = urllib.urlopen(fullcgi) File "C:\Python23\lib\urllib.py", line 76, in urlopen return opener.open(url) File "C:\Python23\lib\urllib.py", line 181, in open return getattr(self, name)(url) File "C:\Python23\lib\urllib.py", line 297, in open_http h.endheaders() File "C:\Python23\lib\httplib.py", line 712, in endheaders self._send_output() File "C:\Python23\lib\httplib.py", line 597, in _send_output self.send(msg) File "C:\Python23\lib\httplib.py", line 564, in send self.connect() File "C:\Python23\lib\httplib.py", line 548, in connect raise socket.error, msg IOError: [Errno socket error] (10060, 'Operation timed out') From ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za Tue Jul 6 10:04:23 2004 From: ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za (ssalie_lab_staff_health_med_uct@mail.med.uct.ac.za) Date: Tue Jul 6 10:14:53 2004 Subject: [BioPython] IOError:[Errno 2]No such file or directory:'ls_orchid.fasta' Message-ID: <1089122663.40eab16733484@webmail.uct.ac.za> CLASSPATH=C:\Python23\biopython-1.30\examples I tried to run this script always the same error Please Help! C:\>C:\Python23\biopython-1.30\examples\fasta_iterator.py Traceback (most recent call last): File "C:\Python23\biopython-1.30\examples\fasta_iterator.py", line 29, in ? all_species = extract_organisms("ls_orchid.fasta") File "C:\Python23\biopython-1.30\examples\fasta_iterator.py", line 7, in extra ct_organisms file = open(file_to_parse, 'r') IOError: [Errno 2] No such file or directory: 'ls_orchid.fasta' From mdehoon at ims.u-tokyo.ac.jp Tue Jul 6 10:39:15 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Tue Jul 6 10:40:13 2004 Subject: [BioPython] IOError:[Errno 2]No such file or directory:'ls_orchid.fasta' In-Reply-To: <1089122663.40eab16733484@webmail.uct.ac.za> References: <1089122663.40eab16733484@webmail.uct.ac.za> Message-ID: <40EAB993.20307@ims.u-tokyo.ac.jp> Try going through Section 2.4 in the Biopython tutorial. You'll create the ls_orchid.fasta file when you run the examples there. --Michiel. ssalie_lab_staff_health_med_uct@mail.med.uct.ac.za wrote: > IOError: [Errno 2] No such file or directory: 'ls_orchid.fasta' -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From idoerg at burnham.org Tue Jul 6 11:58:48 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue Jul 6 12:01:04 2004 Subject: [BioPython] Huge problems with examples In-Reply-To: <1089021357.40e925ad1277b@webmail.uct.ac.za> References: <1089021357.40e925ad1277b@webmail.uct.ac.za> Message-ID: <40EACC38.2020109@burnham.org> Thanks for doing this, sorry about your problems. I am running the Linux version, so I am not sure about your use of examples, Does the Windows version come with an "examples" directory, or did you just cut & paste stuff from the Tutorial/Cookbook? I'll assume there is no such directory, and that you tried to run the examples from 2.4 in the T/C. ssalie_lab_staff_health_med_uct@mail.med.uct.ac.za wrote: > Hi, I've downloaded Biopython onto windows XP and trying examples...quite a > few error messages popping up when trying to run > > C:\>C:\Python23\examples\fasta_iterator.py > Traceback (most recent call last): > File "C:\Python23\examples\fasta_iterator.py", line 29, in ? > all_species = extract_organisms("ls_orchid.fasta") > File "C:\Python23\examples\fasta_iterator.py", line 7, in extract_organisms > file = open(file_to_parse, 'r') > IOError: [Errno 2] No such file or directory: 'ls_orchid.fasta' > > Sounds like it cannot find the ls_orchid.fasta file. You're supposed to create it by download from ncbi. See 2.4.2 in the manual. > > C:\>C:\Examples\query_entrez.py > Traceback (most recent call last): > File "C:\Examples\query_entrez.py", line 24, in ? > doptcmdl = return_format) > File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 51, in query > return _open(cgi, variables) > File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 191, in _open > handle = urllib.urlopen(fullcgi) > File "C:\Python23\lib\urllib.py", line 76, in urlopen > return opener.open(url) > File "C:\Python23\lib\urllib.py", line 181, in open > return getattr(self, name)(url) > File "C:\Python23\lib\urllib.py", line 297, in open_http > h.endheaders() > File "C:\Python23\lib\httplib.py", line 712, in endheaders > self._send_output() > File "C:\Python23\lib\httplib.py", line 597, in _send_output > self.send(msg) > File "C:\Python23\lib\httplib.py", line 564, in send > self.connect() > File "C:\Python23\lib\httplib.py", line 548, in connect > raise socket.error, msg > IOError: [Errno socket error] (10060, 'Operation timed out') > This looks like your connection to NCBI is bad. Either that machine was not on the net, or you have some sort of connection problem. Generally, if you can get to NCBI using your browser, you should be able to run this code. If it is on the net, and you can get to NCBI via your browser, I would check first for proxy settings, which is usually the problem in such timeouts. > > C:\>C:\Python23\examples\fasta_consumer.py > Traceback (most recent call last): > File "C:\Python23\examples\fasta_consumer.py", line 35, in ? > all_species = extract_organisms("ls_orchid.fasta", 94) > File "C:\Python23\examples\fasta_consumer.py", line 21, in extract_organisms > scanner = Fasta._Scanner() > AttributeError: 'module' object has no attribute '_Scanner' Documentation is outdated. Thanks for the catch. This will be amended soon. If you want to see how the Bio.Fasta module works now, "look under the hood" in the source file (Fasta/__init__.py) The following bit of code (a bit later in the manual) should work: >>> from Bio import Fasta >>> parser = Fasta.RecordParser() >>> file = open("ls_orchid.fasta") >>> iterator = Fasta.Iterator(file, parser) (Provided you have the "ls_orchid.fasta" file, of course :) > > > C:\>C:\Python23\examples\getgene.py > Traceback (most recent call last): > File "C:\Python23\examples\getgene.py", line 36, in ? > import gdbm > ImportError: No module named gdbm > > This module provides an interface to the GNU DBM (GDBM) library, which you probably do not have since it is not a standard on Windows. Which bit in the T/C did you get this from? > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- 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) 713 9930 http://ffas.ljcrf.edu/~iddo From dtefft at case.edu Wed Jul 7 10:38:31 2004 From: dtefft at case.edu (David Tefft) Date: Wed Jul 7 10:40:41 2004 Subject: [BioPython] Newbie Message-ID: <40EC0AE7.8010406@case.edu> Can someone point me in the direction of some documentation and/or examples that are a bit more comprehensive than the Tutorial and Cookbook available at Biopython.org. Thanks, Dave From crocha at dc.uba.ar Wed Jul 7 12:18:12 2004 From: crocha at dc.uba.ar (Cristian S. Rocha) Date: Wed Jul 7 12:20:28 2004 Subject: [BioPython] About pfam parsing. Message-ID: <1089217092.21561.19.camel@numero2> Hi, I'm trying to parse hmmsearch results. I saw the Bio.expressions.hmmpfam module but it look unfinished. Somebody can tell me how it should work? Does a TODO file exist? Perhaps I could help to finish it. Thanks, Cristian. -- Cristian S. Rocha Universidad de Buenos Aires From idoerg at burnham.org Wed Jul 7 12:31:18 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed Jul 7 12:33:27 2004 Subject: [BioPython] Newbie In-Reply-To: <40EC0AE7.8010406@case.edu> References: <40EC0AE7.8010406@case.edu> Message-ID: <40EC2556.6040305@burnham.org> Hi David, You can try the online course notes that are on the documentation pages. Katherine & Katja's course would be something you might find particualrly useful: http://www.pasteur.fr/recherche/unites/sis/formation/python/ Cheers, Iddo David Tefft wrote: > Can someone point me in the direction of some documentation and/or > examples that are a bit more comprehensive than the Tutorial and > Cookbook available at Biopython.org. > Thanks, > Dave > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- 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) 713 9930 http://ffas.ljcrf.edu/~iddo From daia at nerdfarm.org Thu Jul 8 07:34:08 2004 From: daia at nerdfarm.org (daia@nerdfarm.org) Date: Thu Jul 8 07:39:37 2004 Subject: [BioPython] software In-Reply-To: References: Message-ID: <7D557B98L68846CI@nerdfarm.org> Microsoft Windows XP Professional 2002 Retail price: $270.99 Our low Price: $50.00 You Save: $220.00 Adobe Photoshop 7.0 Retail price: $609.99 Our low Price: $60.00 You Save: $550.00 Microsoft Office XP Professional 2002 Retail price: $579.99 Our low Price: $60.00 You Save: $510.00 Adobe Illustrator 10 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Corel Draw Graphics Suite 11 Retail price: $270.99 Our low Price: $60.00 You Save: $210.00 Delphi 7 Retail price: $404.99 Our low Price: $60.00 You Save: $335.00 And more!!! Our site is http://OpHTylW.nfkiijl.info/?NwjmjyhQWRoG3hhTxYt Why so cheap? 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"??????" ???? ?????????? ??? ???? ??????????? ????????-????????????? ????????? ?????????????? ??? ?????? ??????????????? ? ??? ??????????????-???????, ?????????? ? ????: ?????? ???????, ???????????, ??????????, ???, LAN ? ?.?. ??????? ????? ? ????????? ?????? ????. www: http://www.armadacable.ru/cables.html E-mail: sales@armadacable.ru ???. +7-(095)543-5937, +7-(095)517-7203 ???????? ? ????? ????? ??????. From carol at backpackers.net Fri Jul 9 01:39:44 2004 From: carol at backpackers.net (=?Windows-1251?B?yOPt4PIgy+7j4+jt7uLo9w==?=) Date: Fri Jul 9 03:46:18 2004 Subject: [BioPython] Direct Mail Message-ID: <1109818911.20040709054444@> (095)-540-09-80-????? ???? ????! ????????? ??????? ?????????????? ??????? ????????????? ?????? ?????? ? ????????? ????????? ???? ??????????? ????? ?????????. ??? ??????? ??????? ???????. ??? ????? ???????? ??????????. ??? ???????? ???????? ? ?????? ???????. ???? ?????????? ??????? ???????? ????. ??? ?????????? ???????-??????????. ???? ?????????? ???? ????????! ?? ??? ?? ???????? ?? ??????? ?????? ??? ???????, ?? ??????? ?????????? ?????????? ?????? ? ?????????? ?? ? ????????, ?? ?????????? ???????? ? ??????????? ?? ?????? ?????, ?? ?????????? ???????? ???????? ?????, ?? ????? ?????? ?? ????? ? ???? ??????????? ??????? ??? ??????????? ???? ??????? ? ??????????? ?????????? ????????? ?????????, ? ?????????????? ????? ???????? ??? ??? ??? ???????????? ? ???????? ?????? ?? ????????? ???????? ???????????????. ?????????? ????? ???????? ??????? ??? ?? ???! ???? ?????????????? ? ?????????????! 8-(095)-107--27--56--??????? From amos at seznam.cz Fri Jul 9 08:21:07 2004 From: amos at seznam.cz (madhu) Date: Fri Jul 9 08:29:43 2004 Subject: [BioPython] =?windows-1251?b?zuHn7vAg4PDh6PLw4Obt7ukg7/Dg6vLo?= =?windows-1251?b?6ugu?= Message-ID: <200407091229.i69CTXKr002401@portal.open-bio.org> ??????????????? ?????, ?????????? ????????????? ???????????, ???????, ?????????? ??????????, ? ????? ?? ?????????? ? ???????????? ?? ????????? ???????? ?????????-??????????? -------------------------------------------------------------------------------- 19 ???? 2004 ???? ?????? ??????????? ???????? ?? ???????????? ????????? ????????? ??????? ??? ????????? ? ??????????? ??? ????? ?? ?????? ?????, ??? ???????? ??????? ?????????, ?? ? ??????????? ????? ???????? ?????????? ??? ??? ???? ?????, ???????, ?? ??????? ??????? ???????? ???????? ? ??? ???????? ???????? ??????. ????? ????, ???????? ??????????? ? ????????? ??? ?? 2002 ?????????? ????????? ???????, ?????????? ?????????? ???????? ????? ??????????? ?????, ? ????????? ????? ?? ?????????? ???????? ????? ? ??????? ???????. ? ?????? ??????? ???????? ??????????????? ??????? ???? ?????????? ??? ??, ??????????? ??????, ??????????? ????? ?? ?????? ? ??. ????????? ????????: - ?????????? ???? ???????????? ??????????????? ??????? ??, ???????????? ??????????????? ??????? ?? ??? ?????????? ????????????? ??????????. - ?????????????????? ? ??????????? ??????. - ???????? ?????????? ????????? ????? ??????????????? ???. - ??????????? ???????????? ? ????????? ???????????????? ??? ??????????? ??????? ???, ?????????? ?????????????? ?????? ??????????? ???????. - ??????? ????????? ?????????????. ??????????????? ?? ???????????? ????????? ?????????????. - ?????????????? ?????? ??? ?? ?? 24.07.2003 ???? N 72 ?????? ???????? ???????? ???????????? ?????? ??? ?? ??????????? ????? ?? ??????, ????????? ? ?????????? ?????? ??????. - ????? ????????? ?? ??????????? ?????? ???????????? ????????. (???????? ?.?.) - ?????? ????????? ????????????? ??????? ??????? ???????????? ???? ?? ?? 18.11.2003 ???? N 19 ?? ????????? ???????? ?????????? ???????????? ?????? ??? ??????????? ??????????. ????????? ??????? ? ???????? ? 3 900 ??????, ? ?????? ???. -------------------------------------------------------------------------------- 20 ???? 2004 ???? ????????? ??????????????? ???????????? ??????????????? ??????? ??. ??????? ??????? ???????? ???????? ?? ??????????????? ????????????? ?????? ???? ?????????? ?????????? ???? ? ????????? ???????????????, ??? ???? ?????????? ?????????? ???????????????? ????????? ?????????, ??????????? ?? ????? ?? ?????????? ???????????? ???????? ???? (??. 183 ??? ??), ??? ?????????? ??? ??????????? ??? ????????? ??? ?????? ? ??????? ??????? ???????? ?????, ?????????? ? ???????? ????. ?????? ?? ??? ? ?????? ??????? ?? ?????? ???? ????? ??????????? ? ?????? ???????????? ?????????. ????????? ????????: - ??????? ???????????? ? ???? ?????? ?????????. ??????? ? ???????????? ????????? ???????. ????? ? ??????????????? ? ??????????? ???????????? ?? ????. ???????? ????????? ?????????? ???? ??? ????????. - ???????? ?????? ???? ??????????? ? ?????????????? ???????????????? ??? ???????????? ???????????? ?????? ??? ?? ???????????????? ???????????????. - ??????????? ??????????? ? ????????????? ?????. ?????? ????????????. - ?????????? ???????? ????? ??????????? ?????. ??????????? ???? ??? ?? 2002 ???? ? ?? ??? ?????????????? ?????????????. - ????????? ? ??????? ??????????? ????????, ??????????? ???????? ?????????. - ????????? ????????? ?? ????????? ???????? (????????????, ?????? ??????, ??????????? ?????????????). - ??????? ????????? ? ??????????? ????????. ????????? ??????? ? ???????? ? 3 900 ??????, ? ?????? ???. -------------------------------------------------------------------------------- ????? ?????? ????? (???????? ??? ???????????). ? ????????? ??????: ??????? ? ?????? ????????, ??????????? ????????, ????-?????, ???? ? ?????????. ??? ??????????? ?? ??? ????????, ? ????? ??? ??????? ???? ?????????????? ?? ????????, ??????????????? ?????? ? 10 %. ?? ????????? ????????? ????????????? ??????? ???????????? ???? ??. ???????? ???????? ? ?????? (?. ?????????????). ?????? - ? 9.30 , ????????? ? 17.30. ??????????? ?????????? ???????????. ??? ??????????? ?????????? ???????? ????????? ??????: ???????????? ???????????, ???, ??????????? ?????, ???????, ????, ?.?.?. ??????????, ?????????? ????. ?????????? ???????: + 7 (095) 7 887 328 From saroj at adexec.com Fri Jul 9 08:49:26 2004 From: saroj at adexec.com (=?Windows-1251?B?3vHy6O0gy+7j4+jt7uLo9w==?=) Date: Fri Jul 9 08:59:13 2004 Subject: [BioPython] =?windows-1251?b?zuPw7uzt++kg4vvh7vAg6CDt5eL78e7q?= =?windows-1251?b?6OUg9uXt+y4=?= Message-ID: <143010577.20040709125426@> ????? "?????? ?????????? ??? ?????? ??????????? ????????-????????????? ????????? ???????????? ??? ?????? ??????????????? ? ??? ??????????????-???????, ?????????? ? ????: ?????? ???????, ???????????, ??????????, ???, LAN ? ?.?. ??????? ??????????? ? ????????? ????????? ????. www: http://www.armadacable.ru/cables.html E-mail: sales@armadacable.ru ???. +7-(095)543-5937, +7-(095)517-7203 ???????? ?? ??????. From boon-hwe at geocities.com Sun Jul 11 14:26:48 2004 From: boon-hwe at geocities.com (=?Windows-1251?B?zeDz7CDS6Ozu9OXl4uj3?=) Date: Sun Jul 11 14:39:21 2004 Subject: [BioPython] =?windows-1251?b?zvLr6Pft++kg8OXs7u3yIOv+4fv1IOri?= =?windows-1251?b?4PDy6PAg7vIg7/Du8fLu6SDq7vHs5fLo6ugg5O4gwvvx+OXj7iDw4Ofw?= =?windows-1251?b?/+Tg?= Message-ID: <195954224.20040711183148@> (095) 504-8116 (095) 772-0647 ??????? ?????? ????? ?????? ?? ???????? ?? ??????? ????? ?. ?.?.: ??????? ??????????? ????????? ??? ????? ??????? ?????????? ????????? ??????????? ????????? ?????? ????????????? ??? ????? ?????????? ??????? ??????????? - ???????? ?????? ???????? ?????????? ?? ??????? ?? ??????? ?????? ?????? ??????????????? ????????? ???? ??????????? ????? ?????? ????????? ???? ? ???????? (095) 504-8116 (095) 772-0647 From Hegedus.Tamas at mayo.edu Wed Jul 7 10:42:23 2004 From: Hegedus.Tamas at mayo.edu (Hegedus, Tamas .) Date: Sun Jul 11 16:33:13 2004 Subject: [BioPython] SProtCrack Message-ID: Hi, As I needed to parse the newest SwissProt release dat file, I had to make some modification in the SProt.py file (see header for modifications). That was my first crack in my life (if this is what is called crack): I liked it, since it was a pritty clean code to find out what to do. I think it is working well, but if you would like to use it, please, check it... Best regards, Tamas <> -------------- next part -------------- A non-text attachment was scrubbed... Name: SProt.py Type: application/octet-stream Size: 34710 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040707/8fa609ee/SProt-0001.obj From syl_schupp at yahoo.fr Fri Jul 9 05:29:48 2004 From: syl_schupp at yahoo.fr (=?iso-8859-1?q?Sylvain=20Sch=FCpp?=) Date: Sun Jul 11 16:33:19 2004 Subject: [BioPython] GenBank and index_file Message-ID: <20040709092948.71903.qmail@web21123.mail.yahoo.com> Hi, I try to use the GenBank package to manage GenBank files from NCBI. For that, I'm following the cookbook I found on BioPython. There, the authors proposed me to create an iterator to naviguate through my file. I tried with a genbank from a plasmide : that works perfectly. I tried with a complete genome : that bugs perfectly, cause Pythin seems not to be able to manage big file. The funniest point is that the error I obtain happen after the end of my file. If somebody have an idea, I'm still there. Thanks gb_file = "h:\\viewer_fcgi.gb" gb_handle = open(gb_file,'r') feature_parser = GenBank.FeatureParser() gb_iterator = GenBank.Iterator(gb_handle, feature_parser) while 1 : cur_record = gb_iterator.next() if cur_record is None: break print cur_record.features[1] Traceback (most recent call last): File "H:\SylSch\genbank\configGenbank.py", line 9, in -toplevel- cur_record = gb_iterator.next() File "C:\sschupp\Python23\Lib\site-packages\Bio\GenBank\__init__.py", line 129, in next return self._parser.parse(File.StringHandle(data)) File "C:\sschupp\Python23\Lib\site-packages\Bio\GenBank\__init__.py", line 219, in parse self._scanner.feed(handle, self._consumer) File "C:\sschupp\Python23\Lib\site-packages\Bio\GenBank\__init__.py", line 1259, in feed self._parser.parseFile(handle) File "C:\sschupp\Python23\lib\site-packages\Martel\Parser.py", line 328, in parseFile self.parseString(fileobj.read()) File "C:\sschupp\Python23\lib\site-packages\Martel\Parser.py", line 356, in parseString self._err_handler.fatalError(result) File "C:\sschupp\Python23\lib\xml\sax\handler.py", line 38, in fatalError raise exception ParserPositionException: error parsing at or beyond character 988544 Pour suivre mes aventures su?doises : www.marschupp.fr.st --------------------------------- Cr?ez gratuitement votre Yahoo! Mail avec 100 Mo de stockage ! Cr?ez votre Yahoo! Mail Dialoguez en direct avec vos amis gr?ce ? Yahoo! Messenger ! From postmaster at ebi.ac.uk Mon Jul 12 04:53:43 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Mon Jul 12 04:55:42 2004 Subject: [BioPython] Warning: E-mail containing attachment(s) blocked Message-ID: <200407120853.i6C8rh89018339@madeiro.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: birney@ebi.ac.uk Subject: Re: A!p$ghsa Date: Mon Jul 12 09:53:42 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: (important.zip) -- MailScanner Email Virus Scanner www.mailscanner.info From h.j.tipney at stud.man.ac.uk Mon Jul 12 10:34:27 2004 From: h.j.tipney at stud.man.ac.uk (h.j.tipney@stud.man.ac.uk) Date: Mon Jul 12 10:36:31 2004 Subject: [BioPython] python newbies blast problem Message-ID: Hi I'm hoping someone can help me. I'm very new to programming and even newer to python, so I apologise in advance if this is a simple problem with an obvious solution but there are no python programmers near to help me. Anyway, I inherited the script below and have been using it on and off as part of a larger workflow. It has been running fine, but I ran it again last week and it didn't give the output I expected - it returned the 'your results will be updated in X seconds' page rather than the actual results. It has been a while since I had used this program and both blast and biopython had been updated so I've now got the new biopython release (1.30) but I still get the 'wrong' output. I'm using python 2.3.3 on solaris, if that helps. Any help would be greatly appreciated! Thank you in advance Hannah Tipney #!/opt/cs/bin/python from Bio import Fasta from Bio.Blast import NCBIWWW import sys import getopt opts, args = getopt.getopt(sys.argv[1:],"",['program=','database=','format=','entrez_query=']) print sys.argv print opts if len(args)==0: print "no file given" sys.exit(2) program = "blastn" database = "nr" format = "Text" #"Homo sapiens [ORGN]" short_query="" for o,a in opts: print o,a if o == "--program": program = a if o == "--database": database = a if o == "--format": format = a if o == "--entrez_query": short_query = a if short_query=="human": query="Homo sapiens [ORGN]" else: query="" print "program = %s , database = %s, query = %s" % (program,database,query) file_for_blast = open(args[0], 'r') f_iterator = Fasta.Iterator(file_for_blast) f_record = f_iterator.next() file_for_blast.close() b_results = NCBIWWW.blast(program, database, f_record,format_type=format, entrez_query=query,timeout=60) blast_results = b_results.read() sys.stdout.write(blast_results) ------------------------------------------ Hannah Tipney Manchester University, Academic Unit of Medical Genetics, St Mary's Hospital, Hathersage Road, Manchester. M13 0JH. UK tel: +44 (0)161 276 6602 fax: +44 (0)161 276 6606 From fkauff at duke.edu Mon Jul 12 10:54:18 2004 From: fkauff at duke.edu (Frank Kauff) Date: Mon Jul 12 10:56:20 2004 Subject: [BioPython] python newbies blast problem In-Reply-To: References: Message-ID: <1089644058.2068.36.camel@osiris.biology.duke.edu> Yep, same happened to me recently with a script that was actually running fine for quite a while. Did NCBI maybe change some format so that the parser gets confused? Frank On Mon, 2004-07-12 at 10:34, h.j.tipney@stud.man.ac.uk wrote: > Hi > I'm hoping someone can help me. I'm very new to programming and > even newer to python, so I apologise in advance if this is a simple > problem with an obvious solution but there are no python > programmers near to help me. > Anyway, I inherited the script below and have been using it on and > off as part of a larger workflow. It has been running fine, but I ran it > again last week and it didn't give the output I expected - it returned > the 'your results will be updated in X seconds' page rather than the > actual results. It has been a while since I had used this program and > both blast and biopython had been updated so I've now got the new > biopython release (1.30) but I still get the 'wrong' output. > I'm using python 2.3.3 on solaris, if that helps. > Any help would be greatly appreciated! > Thank you in advance > Hannah Tipney > > #!/opt/cs/bin/python > from Bio import Fasta > from Bio.Blast import NCBIWWW > import sys > import getopt > > opts, args = getopt.getopt(sys.argv[1:],"",['program=','database=','format=','entrez_query=']) > > print sys.argv > print opts > > if len(args)==0: > print "no file given" > sys.exit(2) > > program = "blastn" > database = "nr" > format = "Text" > #"Homo sapiens [ORGN]" > > short_query="" > > for o,a in opts: > print o,a > if o == "--program": > program = a > if o == "--database": > database = a > if o == "--format": > format = a > if o == "--entrez_query": > short_query = a > > if short_query=="human": > query="Homo sapiens [ORGN]" > else: > query="" > > print "program = %s , database = %s, query = %s" % (program,database,query) > > file_for_blast = open(args[0], 'r') > f_iterator = Fasta.Iterator(file_for_blast) > > f_record = f_iterator.next() > file_for_blast.close() > b_results = NCBIWWW.blast(program, database, f_record,format_type=format, > entrez_query=query,timeout=60) > > blast_results = b_results.read() > sys.stdout.write(blast_results) > > ------------------------------------------ > Hannah Tipney > Manchester University, > Academic Unit of Medical Genetics, > St Mary's Hospital, > Hathersage Road, > Manchester. M13 0JH. > UK > > tel: +44 (0)161 276 6602 > fax: +44 (0)161 276 6606 > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- Frank Kauff Dept. of Biology Duke University Box 90338 Durham, NC 27708 USA Phone 919-660-7382 Fax 919-660-7293 Web http://www.lutzonilab.net/member/frankkauff.shtml From h.j.tipney at stud.man.ac.uk Mon Jul 12 11:41:27 2004 From: h.j.tipney at stud.man.ac.uk (h.j.tipney@stud.man.ac.uk) Date: Mon Jul 12 11:43:32 2004 Subject: [BioPython] python newbies blast problem In-Reply-To: <1089644058.2068.36.camel@osiris.biology.duke.edu> References: Message-ID: The newest blast release (2.2.9) came out 12th May, the newest BioPython two days later so I had hoped any changes would have been already accounted for. Have tried to mail Blast people but the address bounces : ( Frank - did you come up with a solution?? Hannah ------------------------------------------ Hannah Tipney Manchester University, Academic Unit of Medical Genetics, St Mary's Hospital, Hathersage Road, Manchester. M13 0JH. UK tel: +44 (0)161 276 6602 fax: +44 (0)161 276 6606 From pappas at t-online.de Tue Jul 13 14:04:19 2004 From: pappas at t-online.de (minnie) Date: Tue Jul 13 14:11:50 2004 Subject: [BioPython] =?windows-1251?b?0fPv5fAg+O7w8vsgUG93ZXIgR1lN?= Message-ID: <200407131811.i6DIBKKr007770@portal.open-bio.org> ???????????? ??? ????? ? ??????????? ???? ??????????? ???? ??????, ????????? ????? ??? ? ?????? ???????? ????? ????, ???????? ???????? !! ??????????????? !!! ???????? ????????? ????!!! ??????? ??????????? ?? ????? ?????: http://www.pokupki.net From swon9 at itsa.ucsf.edu Tue Jul 13 19:37:50 2004 From: swon9 at itsa.ucsf.edu (Sergio E. Wong) Date: Tue Jul 13 19:39:56 2004 Subject: [BioPython] Problem with Superimposer Message-ID: Hi; I am trying to superimpose two crystal structures using the Bio.PDB.Superimposer, following the example in the biopython FAQ document where it explains how to do this. For the purposes of testing, I am only using 5 atoms in the atoms lists. Below I show the two atom lists and the error I get when I try to use the set_atoms method. >>> ebg_res1 [, , , , ] >>> ebh_res1 [, , , , ] >>> sup.set_atoms( ebg_res1, ebh_res1) Traceback (most recent call last): File "", line 1, in ? TypeError: unbound method set_atoms() must be called with Superimposer instance as first argument (got list instance instead) Does anyone have any idea of why this is happening? Thanks -Sergio From ho-shyan at t-online.de Tue Jul 13 21:29:08 2004 From: ho-shyan at t-online.de (asad) Date: Tue Jul 13 21:37:14 2004 Subject: [BioPython] =?windows-1251?b?wujk5e7x5ezo7eDw+yDv7iDT0c0=?= Message-ID: <200407140137.i6E1awKr011033@portal.open-bio.org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rom fkauff at duke.edu Thu Jul 15 09:51:11 2004 From: fkauff at duke.edu (Frank Kauff) Date: Thu Jul 15 09:53:10 2004 Subject: [BioPython] Re: [Biopython-dev] python newbies blast problem In-Reply-To: <893C92DD-D548-11D8-8676-000A956845CE@stanfordalumni.org> References: <893C92DD-D548-11D8-8676-000A956845CE@stanfordalumni.org> Message-ID: <1089899471.2065.7.camel@osiris.biology.duke.edu> Thanks, Jeff! It woorks fine with my scripts. Frank On Tue, 2004-07-13 at 23:47, Jeffrey Chang wrote: > Hello, > > This is because the NCBI website is not really meant to be queried by > computer scripts. It looks like a recent change has broken the > NCBIWWW.blast function. Fortunately, NCBI does have a computer > friendly BLAST API called QBLAST. I added an interface to QBLAST into > biopython called NCBIWWW.qblast. Please get the updated version of the > NCBIWWW.py from CVS, and replace NCBIWWW.blast with NCBIWWW.qblast in > your script, and see if that fixes things. > > The anonymous CVS is at: > http://cvs.biopython.org/ > > Jeff > > > > > On Jul 13, 2004, at 9:56 AM, h.j.tipney@stud.man.ac.uk wrote: > > > Hi > > I posted this to the other mailing list and got no response so I'm > > hoping you guys can help me. I'm very new to programming and > > even newer to python, so I apologise in advance if this is a simple > > problem with an obvious solution but there are no python > > programmers > > near to help me. Anyway, I inherited the script below and have been > > using it on and off as part of a larger workflow. It has been running > > fine, but I ran it again last week and it didn't give the output I > > expected - it returned the 'your results will be updated in X seconds' > > page rather than the actual results. It has been a while since I had > > used this program and both blast and biopython had been updated > > so > > I've now got the new biopython release (1.30) but I still get the > > 'wrong' output. I'm using python 2.3.3 on solaris, if that helps. Any > > help would be greatly appreciated! Thank you in advance Hannah > > Tipney > > > > #!/opt/cs/bin/python > > from Bio import Fasta > > from Bio.Blast import NCBIWWW > > import sys > > import getopt > > > > opts, args = > > getopt.getopt(sys.argv[1:],"",['program=','database=','format=','e > > ntrez_query=']) > > > > print sys.argv > > print opts > > > > if len(args)==0: > > print "no file given" > > sys.exit(2) > > > > program = "blastn" > > database = "nr" > > format = "Text" > > #"Homo sapiens [ORGN]" > > > > short_query="" > > > > for o,a in opts: > > print o,a > > if o == "--program": > > program = a > > if o == "--database": > > database = a > > if o == "--format": > > format = a > > if o == "--entrez_query": > > short_query = a > > > > if short_query=="human": > > query="Homo sapiens [ORGN]" > > else: > > query="" > > > > print "program = %s , database = %s, query = %s" % > > (program,database,query) > > > > file_for_blast = open(args[0], 'r') > > f_iterator = Fasta.Iterator(file_for_blast) > > > > f_record = f_iterator.next() > > file_for_blast.close() > > b_results = NCBIWWW.blast(program, database, > > f_record,format_type=format, entrez_query=query,timeout=60) > > > > blast_results = b_results.read() > > sys.stdout.write(blast_results) > > > > ------- End of forwarded message ------- > > ------------------------------------------ > > Hannah Tipney > > Manchester University, > > Academic Unit of Medical Genetics, > > St Mary's Hospital, > > Hathersage Road, > > Manchester. M13 0JH. > > UK > > > > tel: +44 (0)161 276 6602 > > fax: +44 (0)161 276 6606 > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- Frank Kauff Dept. of Biology Duke University Box 90338 Durham, NC 27708 USA Phone 919-660-7382 Fax 919-660-7293 Web http://www.lutzonilab.net/member/frankkauff.shtml From h.j.tipney at stud.man.ac.uk Thu Jul 15 09:53:39 2004 From: h.j.tipney at stud.man.ac.uk (h.j.tipney@stud.man.ac.uk) Date: Thu Jul 15 09:55:58 2004 Subject: [BioPython] Re: [Biopython-dev] python newbies blast problem In-Reply-To: <1089899471.2065.7.camel@osiris.biology.duke.edu> References: <893C92DD-D548-11D8-8676-000A956845CE@stanfordalumni.org> Message-ID: Thank you all for your help - my scripts are all up and running again now - phew! Cheers Hannah Subject: Re: [Biopython-dev] python newbies blast problem From: Frank Kauff To: biopython@biopython.org Organization: Duke University Date sent: Thu, 15 Jul 2004 09:51:11 -0400 > Thanks, Jeff! It woorks fine with my scripts. > > Frank > > On Tue, 2004-07-13 at 23:47, Jeffrey Chang wrote: > > Hello, > > > > This is because the NCBI website is not really meant to be queried > > by computer scripts. It looks like a recent change has broken the > > NCBIWWW.blast function. Fortunately, NCBI does have a computer > > friendly BLAST API called QBLAST. I added an interface to QBLAST > > into biopython called NCBIWWW.qblast. Please get the updated > > version of the NCBIWWW.py from CVS, and replace NCBIWWW.blast with > > NCBIWWW.qblast in your script, and see if that fixes things. > > > > The anonymous CVS is at: > > http://cvs.biopython.org/ > > > > Jeff > > > > > > > > > > On Jul 13, 2004, at 9:56 AM, h.j.tipney@stud.man.ac.uk wrote: > > > > > Hi > > > I posted this to the other mailing list and got no response so I'm > > > hoping you guys can help me. I'm very new to programming and even > > > newer to python, so I apologise in advance if this is a simple > > > problem with an obvious solution but there are no python > > > programmers near to help me. Anyway, I inherited the script below > > > and have been using it on and off as part of a larger workflow. It > > > has been running fine, but I ran it again last week and it didn't > > > give the output I expected - it returned the 'your results will be > > > updated in X seconds' page rather than the actual results. It has > > > been a while since I had used this program and both blast and > > > biopython had been updated so I've now got the new biopython > > > release (1.30) but I still get the 'wrong' output. I'm using > > > python 2.3.3 on solaris, if that helps. Any help would be greatly > > > appreciated! Thank you in advance Hannah Tipney > > > > > > #!/opt/cs/bin/python > > > from Bio import Fasta > > > from Bio.Blast import NCBIWWW > > > import sys > > > import getopt > > > > > > opts, args = > > > getopt.getopt(sys.argv[1:],"",['program=','database=','format= > > > ','e ntrez_query=']) > > > > > > print sys.argv > > > print opts > > > > > > if len(args)==0: > > > print "no file given" > > > sys.exit(2) > > > > > > program = "blastn" > > > database = "nr" > > > format = "Text" > > > #"Homo sapiens [ORGN]" > > > > > > short_query="" > > > > > > for o,a in opts: > > > print o,a > > > if o == "--program": > > > program = a > > > if o == "--database": > > > database = a > > > if o == "--format": > > > format = a > > > if o == "--entrez_query": > > > short_query = a > > > > > > if short_query=="human": > > > query="Homo sapiens [ORGN]" > > > else: > > > query="" > > > > > > print "program = %s , database = %s, query = %s" % > > > (program,database,query) > > > > > > file_for_blast = open(args[0], 'r') > > > f_iterator = Fasta.Iterator(file_for_blast) > > > > > > f_record = f_iterator.next() > > > file_for_blast.close() > > > b_results = NCBIWWW.blast(program, database, > > > f_record,format_type=format, entrez_query=query,timeout=60) > > > > > > blast_results = b_results.read() > > > sys.stdout.write(blast_results) > > > > > > ------- End of forwarded message ------- > > > ------------------------------------------ > > > Hannah Tipney > > > Manchester University, > > > Academic Unit of Medical Genetics, > > > St Mary's Hospital, > > > Hathersage Road, > > > Manchester. M13 0JH. > > > UK > > > > > > tel: +44 (0)161 276 6602 > > > fax: +44 (0)161 276 6606 > > > _______________________________________________ > > > Biopython-dev mailing list > > > Biopython-dev@biopython.org > > > http://biopython.org/mailman/listinfo/biopython-dev > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > -- > Frank Kauff > Dept. of Biology > Duke University > Box 90338 > Durham, NC 27708 > USA > > Phone 919-660-7382 > Fax 919-660-7293 > Web http://www.lutzonilab.net/member/frankkauff.shtml > ------------------------------------------ Hannah Tipney Manchester University, Academic Unit of Medical Genetics, St Mary's Hospital, Hathersage Road, Manchester. M13 0JH. UK tel: +44 (0)161 276 6602 fax: +44 (0)161 276 6606 From Hegedus.Tamas at mayo.edu Thu Jul 15 14:58:18 2004 From: Hegedus.Tamas at mayo.edu (Hegedus, Tamas .) Date: Thu Jul 15 15:07:21 2004 Subject: [BioPython] ModBioSQL release 0.12 Message-ID: Dear All, Since I used Python and BioPython in my Modular BioSQL packege, my site would be interesting for you: http://www.biomembrane.hu/~hegedus/modbiosql/ Best regards, Tamas -- Tamas Hegedus, Research Fellow | phone: 480-301-6041 Mayo Clinic Scottsdale | fax: 480-301-7017 13000 E. Shea Blvd | mailto:hegedus.tamas@mayo.edu Scottsdale, AZ, 85259 | http://www.biomembrane.hu/~hegedus From nores at e-ticket-marketing.com Thu Jul 15 15:40:09 2004 From: nores at e-ticket-marketing.com (Sean M) Date: Thu Jul 15 22:25:55 2004 Subject: [BioPython] why your computer is running slow Message-ID: <20040715154009.ohguqbseka@bluecomcast.com> Hello, Have you noticed your computer running slower than ever? The reason for that may have to do with online advertisers adding SpyWare or AdWare to your computer without your knowledge. "Spyware" is a common term for files that are installed on your system without your knowledge that allow companies to monitor your Internet activity. "AdWare" is software that will show you popup ads over and over. What they don't tell you, however, is how these files can be extremely dangerous to your PC and could cause major problems with your PC. We are offering every computer owner, including yourself, the opportunity to scan your computer to see how many "SpyWare" infections your PC has free of charge. To scan your computer for free, click here: http://bluecomcast.com/dbm83/l.php?959&31327204&riceez420/trekblue8 Our goal is to put an end to shady online advertising so that Internet users can enjoy the World Wide Web without having their privacy intruded upon. We urge you to run the free scan! Click Here To Begin Scan: http://bluecomcast.com/dbm83/l.php?959&31327204&riceez420/trekblue8 PLACE URL HERE Thank you for your time, and we hope that we have been of some help. -------------------------------------------- We hope you enjoyed receiving this email, but if you no longer wish to receive our emails please respond here: http://bluecomcast.com/dbm83/un.php?738&31327204 To Remove by Mail e-ticket-marketing.com PO Box 9 Irvine Ca 92650 tcjxfry From crocha at dc.uba.ar Fri Jul 16 10:11:33 2004 From: crocha at dc.uba.ar (Cristian S. Rocha) Date: Fri Jul 16 10:13:35 2004 Subject: [BioPython] Question about featues genbank standars and SeqFeature class. Message-ID: <1089987093.8258.8.camel@numero2> Hi, I'm working to parse the hmmsearch output to append recognized patterns to sequences features. My question is about if exists an standard way to store this kind of information in the SeqFeature class. Thanks, Cristian. -- Cristian S. Rocha Universidad de Buenos Aires From nomy2020 at yahoo.com Fri Jul 16 21:34:00 2004 From: nomy2020 at yahoo.com (Bzy Bee) Date: Fri Jul 16 21:35:49 2004 Subject: [BioPython] Blast parser missing first record In-Reply-To: <200406011953.i51JrPKt012453@portal.open-bio.org> Message-ID: <20040717013400.47204.qmail@web51803.mail.yahoo.com> Hi everyone My program that uses NCBI standalone blast parser works just fine, well almost! The only problem is that it misses first record (i.e. all the details and hits of first query sequence) and starts from the second query. Has anyone come across this one before? Below is a sample code: ------------------------------------ from Bio.Blast import NCBIStandalone import sys,os,string in_file = 'myblast.txt' def testp(blast_res): bf = open(blast_res) parser = NCBIStandalone.BlastParser() iter = NCBIStandalone.Iterator(bf, parser) myrec = parser.parse(bf) while 1: myrec = iter.next() if myrec is None: break for alignment in myrec.alignments: hsps = alignment.hsps num_hsp = len(alignment.hsps) al_tit = alignment.title[1:40] i=0 hsp_i = alignment.hsps[i] if num_hsp > 1: print myrec.query[0:40],',', myrec.query_letters, ',', al_tit,',',\ num_hsp,",", alignment.length,",", hsp_i.strand[1] # Main testp(in_file) ----------------------------------------------- I am running Blast 2.2.9 and the output is just a normal output. Here is the sample output of my standalone Blast. ================================================ BLASTN 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= test_seq1 (1563 letters) Database: mydb.seq 24,211 sequences; 12,519,432 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Sequence1,...................................................... 2557 0.0 >sequence1: this is just a test sequence Length = 701 Score = 184 bits (93), Expect = 1e-45 Identities = 171/197 (86%) Strand = Plus / Plus Query: 346 accatggactctgtgcgctcggggcctttcgggcagatcttcaggccggacaactttgtc 405 |||||||||||||| ||||| || ||||| || ||||||||||| || ||||||||||| Sbjct: 350 accatggactctgttcgctcaggtccttttggtcagatcttcagaccagacaactttgtt 409 Query: 406 ttcggtcagagcggtgccgggaacaactgggccaagggacactacacggaaggggcggag 465 || |||||| ||| || || ||||||||||||||||| ||||| || || || || ||| Sbjct: 410 tttggtcagtccggggcaggcaacaactgggccaagggccactatacagagggagccgag 469 Query: 466 ctcgtcgactcggtgctggatgtcgtgaggaaggaggccgagagctgtgactgcctgcag 525 || || |||||||| |||||||| || |||||||||||||||||||||||||||||||| Sbjct: 470 ctggttgactcggtcctggatgtggttcggaaggaggccgagagctgtgactgcctgcag 529 Query: 526 ggcttccagctgaccca 542 ||||||||||||||||| Sbjct: 530 ggcttccagctgaccca 546 Score = 153 bits (77), Expect = 4e-36 Identities = 146/169 (86%) Strand = Plus / Plus Query: 57 atgagggagatcgtgcacctgcaggccggccagtgcggcaaccagatcggcgccaagttt 116 |||||||| ||||||||| | |||||||| ||||| ||||| |||||||| |||||||| Sbjct: 137 atgagggaaatcgtgcacatccaggccggtcagtgtggcaatcagatcggtgccaagttc 196 Query: 117 tgggaggtgatcagcgacgagcatggcatcgaccccaccggcacctaccacggggacagc 176 |||||||| ||||| || || |||||||||||||||||||||||||| || ||||||||| Sbjct: 197 tgggaggtaatcagtgatgaacatggcatcgaccccaccggcacctatcatggggacagc 256 Query: 177 gacctgcagctggagcgaatcaacgtgtactacaacgaggccaccggtg 225 ||||| || ||||| || ||| |||||||||||| || ||||| |||| Sbjct: 257 gacctacaactggaccgcatctccgtgtactacaatgaagccacaggtg 305 Database: mydb.seq Posted date: Sep 21, 1998 11:19 AM Number of letters in database: 12,519,432 Number of sequences in database: 24,211 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 130 Number of Sequences: 24211 Number of extensions: 132 Number of successful extensions: 111 Number of sequences better than 1.0e-20: 13 Number of HSP's better than 0.0 without gapping: 12 Number of HSP's successfully gapped in prelim test: 1 Number of HSP's that attempted gapping in prelim test: 147 Number of HSP's gapped (non-prelim): 59 length of query: 1563 length of database: 12,519,432 effective HSP length: 18 effective length of query: 1545 effective length of database: 11,343,111 effective search space: 211578144 effective search space used: 211578144 T: 0 A: 0 X1: 6 (11.9 bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 52 (103.6 bits) BLASTN 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= seq2 (1352 letters) Database: mydb.seq 24,211 sequences; 12,519,432 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Sequence2,...................................................... 737 0.0 >sequence2 this is just a test sequence Length = 1523 Score = 737 bits (372), Expect = 0.0 Identities = 502/544 (92%), Gaps = 1/544 (0%) Strand = Plus / Plus Query: 540 taagtcatcagacagttcatactggagagaaaccttacaaatgtgatgagtgtggcgagg 599 |||||||| ||| | ||||||||||||||| ||||||||||||||||||||||||| ||| Sbjct: 440 taagtcataagagatttcatactggagagagaccttacaaatgtgatgagtgtggcaagg 499 Query: 600 cctttcgtctaaagtcaacccttttaagtcatcagacggttcatactggtgataaacctt 659 |||||||| ||||||||| |||||||||||||||||| ||||||||||| || ||||||| Sbjct: 500 cctttcgtgtaaagtcaatccttttaagtcatcagacagttcatactggagagaaacctt 559 Query: 660 acaagtgtgatgagtgtggaaaagtctttggtcgaaaaccacatcttcaacttcactgga 719 |||| || |||||||||||||||||||| |||| |||||||||||||| ||||||||||| Sbjct: 560 acaaatgcgatgagtgtggaaaagtcttcggtcaaaaaccacatcttcgacttcactgga 619 Query: 720 gaattcataatggagagagacctttcagatgtaatgagtgtggcaagttcttcagtcaaa 779 ||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| || Sbjct: 620 gaattcatactggagagagacctttcaaatgtaatgagtgtggcaagttcttcagtcgaa 679 Query: 780 attcacaccttaaaaaacattggagaatacatatagagaaacctttcaaatgtttcaagt 839 |||||||||||| || ||| |||||||||||||||||||||||||||| |||||| ||| Sbjct: 680 attcacaccttacaagtcatcggagaatacatatagagaaacctttcaagtgtttcgagt 739 Query: 840 gtggaaaatcctttattcaggtctcagcactcactaaacatcagaaaatccatacatgag 899 ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| Sbjct: 740 gtggaaaatcctttactcaggtctcagcactcactaaacatcagaaaatccatacatgag 799 Query: 900 agaaactcatgtgaatgtcatatatggtagaactctt-gaaatttaaagttcaaaattca 958 |||||||||||||||||| ||||||||||| |||| ||||| ||||||||||||||| Sbjct: 800 agaaactcatgtgaatgtggaatatggtagaagtcttcaaaattcaaagttcaaaattca 859 Query: 959 caccctacagttgctcagagaattcatcttactgaaaaaccatacaaatatcatgagtgt 1018 |||||||| |||| |||||||||||| |||||| ||||||||||||||||| |||||| Sbjct: 860 caccctactgttggtcagagaattcacactactgagaaaccatacaaatatcacgagtgt 919 Query: 1019 ggcaacatcttaggcttcatgagaaaattcatactggatagaagggagatataaatgtat 1078 |||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||| Sbjct: 920 ggcaacatcttaggcttcatgagaaaattcatactggatagaagccagatatatatgtat 979 Query: 1079 ttat 1082 |||| Sbjct: 980 ttat 983 Score = 327 bits (165), Expect = 9e-89 Identities = 180/185 (97%) Strand = Plus / Plus Query: 1133 ctcacatctcaccagtagtatcagagtatttatcctggagaaaacacacagcagtgtaat 1192 ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| Sbjct: 1076 ctcacatctcaccagtagtatcagagtatttatcctggagaaaacacacagcaatgtaat 1135 Query: 1193 gtgtgtggcaaggatcttacccaaaagtcacaagataggaatatagtggagccatacttc 1252 ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| Sbjct: 1136 gtgtgtggcaaggatcttacccaaaagtcacaagacaggaatatagtggagccatacttc 1195 Query: 1253 ccagactcagtggtggtggcaaatcctttacctttttcactctatggattctctgatgac 1312 |||||||||||||| |||||||||||||||||||||||||| |||| ||||||||||||| Sbjct: 1196 ccagactcagtggttgtggcaaatcctttacctttttcactatatgtattctctgatgac 1255 Query: 1313 tttag 1317 ||||| Sbjct: 1256 tttag 1260 Database: mydb.seq Posted date: Sep 21, 1998 11:19 AM Number of letters in database: 12,123,335 Number of sequences in database: 24,211 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 130 Number of Sequences: 24211 Number of extensions: 132 Number of successful extensions: 111 Number of sequences better than 1.0e-20: 13 Number of HSP's better than 0.0 without gapping: 12 Number of HSP's successfully gapped in prelim test: 1 Number of HSP's that attempted gapping in prelim test: 147 Number of HSP's gapped (non-prelim): 59 length of query: 1563 length of database: 12,519,432 effective HSP length: 18 effective length of query: 1545 effective length of database: 11,343,111 effective search space: 211578144 effective search space used: 211578144 T: 0 A: 0 X1: 6 (11.9 bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 52 (103.6 bits) BLASTN 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= seq3 (768 letters) Database: mydb.seq 24,211 sequences; 12,519,432 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Sequence3,...................................................... 305 2e-82 >Sequence3 this is just a test sequence Length = 1523 Score = 305 bits (154), Expect = 2e-82 Identities = 199/214 (92%) Strand = Plus / Plus Query: 304 ttcatgctggagagaaacgttacaaatgtgatgagtgtggtgaggcctttcctgaaaagt 363 ||||| ||||||||| || ||||||||||||||||||||| ||||||||| || ||||| Sbjct: 455 ttcatactggagagagaccttacaaatgtgatgagtgtggcaaggcctttcgtgtaaagt 514 Query: 364 caacccttttaaggcatcagacagttcatactggtgagaaagcttacaaatgtgatgagt 423 ||| ||||||||| |||||||||||||||||||| |||||| |||||||||| ||||||| Sbjct: 515 caatccttttaagtcatcagacagttcatactggagagaaaccttacaaatgcgatgagt 574 Query: 424 gtggataagtcttcggtcaaaaaccacatcttcaacttcactggagaattcatactggag 483 ||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||||| Sbjct: 575 gtggaaaagtcttcggtcaaaaaccacatcttcgacttcactggagaattcatactggag 634 Query: 484 agagacctttcagatgtaatgagtgtggcaagtt 517 |||||||||||| ||||||||||||||||||||| Sbjct: 635 agagacctttcaaatgtaatgagtgtggcaagtt 668 Score = 232 bits (117), Expect = 2e-60 Identities = 139/145 (95%), Gaps = 1/145 (0%) Strand = Plus / Plus Query: 519 ggagaatacatatagagaaacctttcaa-tgtttcgagtgtggaaaatccttttctcagg 577 |||||||||||||||||||||||||||| |||||||||||||||||||||||| |||||| Sbjct: 701 ggagaatacatatagagaaacctttcaagtgtttcgagtgtggaaaatcctttactcagg 760 Query: 578 tctcagcactcactaaacatcaaaaaatccatacgtgagagaaactcaggtgaatgtggt 637 |||||||||||||||||||||| ||||||||||| ||||||||||||| |||||||||| Sbjct: 761 tctcagcactcactaaacatcagaaaatccatacatgagagaaactcatgtgaatgtgga 820 Query: 638 atatggtagaagtcttcaaaattca 662 ||||||||||||||||||||||||| Sbjct: 821 atatggtagaagtcttcaaaattca 845 Database: mydb.seq Posted date: Sep 21, 1998 11:19 AM Number of letters in database: 12,519,432 Number of sequences in database: 24,211 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 130 Number of Sequences: 24211 Number of extensions: 132 Number of successful extensions: 111 Number of sequences better than 1.0e-20: 13 Number of HSP's better than 0.0 without gapping: 12 Number of HSP's successfully gapped in prelim test: 1 Number of HSP's that attempted gapping in prelim test: 147 Number of HSP's gapped (non-prelim): 59 length of query: 1563 length of database: 12,519,432 effective HSP length: 18 effective length of query: 1545 effective length of database: 11,343,111 effective search space: 211578144 effective search space used: 211578144 T: 0 A: 0 X1: 6 (11.9 bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 52 (103.6 bits) BLASTN 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= seq4 (1100 letters) Database: mydb.seq 24,211 sequences; 12,519,432 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value sequence4,..................................................... 1237 0.0 >seqeunce4 this is just a test sequence Length = 782 Score = 1237 bits (624), Expect = 0.0 Identities = 624/624 (100%) Strand = Plus / Plus Query: 357 ctgatctgcagaatgatgaagtagcatttagaaaattcaagctaattactgaggatgttc 416 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 159 ctgatctgcagaatgatgaagtagcatttagaaaattcaagctaattactgaggatgttc 218 Query: 417 agggcaaaaactgcctgactaactttcatggtatggatcttacccgtgacaaaatgtgct 476 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 219 agggcaaaaactgcctgactaactttcatggtatggatcttacccgtgacaaaatgtgct 278 Query: 477 ccatggtcaaaaaatggcagaccatgattgaagctcacgtagacgtcaagactaccgatg 536 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 279 ccatggtcaaaaaatggcagaccatgattgaagctcacgtagacgtcaagactaccgatg 338 Query: 537 gttacttgcttcgtctgttctgtgtgggttttactaaaaagcgcaacaatcagattcgga 596 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 339 gttacttgcttcgtctgttctgtgtgggttttactaaaaagcgcaacaatcagattcgga 398 Query: 597 agacctcttacgcccagcaccagcaggtgcgccagatccgcaagaagatgatggagatca 656 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 399 agacctcttacgcccagcaccagcaggtgcgccagatccgcaagaagatgatggagatca 458 Query: 657 tgacccgagaggtgcagaccaacgacctgaaagaggtggtcaataaactgattccagata 716 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 459 tgacccgagaggtgcagaccaacgacctgaaagaggtggtcaataaactgattccagata 518 Query: 717 gcattggaaaagacatagaaaaggcttgccaatctatttatccactccatgatgtcttcg 776 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 519 gcattggaaaagacatagaaaaggcttgccaatctatttatccactccatgatgtcttcg 578 Query: 777 ttagaaaagtaaaaatgctgaagaagcccaaatttgaattgggaaaactcatggagctac 836 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 579 ttagaaaagtaaaaatgctgaagaagcccaaatttgaattgggaaaactcatggagctac 638 Query: 837 atggtgaaggtagtagttctggaaaagctactggggatgagacaggtgctaaagttgaac 896 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 639 atggtgaaggtagtagttctggaaaagctactggggatgagacaggtgctaaagttgaac 698 Query: 897 gagctgatggatacgagccaccagtccaagaatcggtttaaaatgcagactcttaatggt 956 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 699 gagctgatggatacgagccaccagtccaagaatcggtttaaaatgcagactcttaatggt 758 Query: 957 gacaaataaaagatcttatttgtg 980 |||||||||||||||||||||||| Sbjct: 759 gacaaataaaagatcttatttgtg 782 Score = 192 bits (97), Expect = 3e-48 Identities = 97/97 (100%) Strand = Plus / Plus Query: 137 ggcaccatggcggtcggcaagaacaagcgccttacgaaaggaggcaaaaagggagccaag 196 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 1 ggcaccatggcggtcggcaagaacaagcgccttacgaaaggaggcaaaaagggagccaag 60 Query: 197 aagaaagtggttgacccattttctaaaaaagattggt 233 ||||||||||||||||||||||||||||||||||||| Sbjct: 61 aagaaagtggttgacccattttctaaaaaagattggt 97 Database: mydb.seq Posted date: Sep 21, 1998 11:19 AM Number of letters in database: 12,519,432 Number of sequences in database: 24,211 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 130 Number of Sequences: 24211 Number of extensions: 132 Number of successful extensions: 111 Number of sequences better than 1.0e-20: 13 Number of HSP's better than 0.0 without gapping: 12 Number of HSP's successfully gapped in prelim test: 1 Number of HSP's that attempted gapping in prelim test: 147 Number of HSP's gapped (non-prelim): 59 length of query: 1563 length of database: 12,519,432 effective HSP length: 18 effective length of query: 1545 effective length of database: 11,343,111 effective search space: 211578144 effective search space used: 211578144 T: 0 A: 0 X1: 6 (11.9 bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 52 (103.6 bits) ================================================ Any help would be great. regards JA __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/ From jeffrey_chang at stanfordalumni.org Fri Jul 16 23:33:04 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Fri Jul 16 23:35:00 2004 Subject: [BioPython] Blast parser missing first record In-Reply-To: <20040717013400.47204.qmail@web51803.mail.yahoo.com> References: <20040717013400.47204.qmail@web51803.mail.yahoo.com> Message-ID: <0308B2B9-D7A2-11D8-826B-000A956845CE@stanfordalumni.org> On Jul 16, 2004, at 9:34 PM, Bzy Bee wrote: > Hi everyone > > My program that uses NCBI standalone blast parser > works just fine, well almost! > > The only problem is that it misses first record (i.e. > all the details and hits of first query sequence) and > starts from the second query. Has anyone come across > this one before? Below is a sample code: > > ------------------------------------ > from Bio.Blast import NCBIStandalone > import sys,os,string > > > in_file = 'myblast.txt' > > def testp(blast_res): > bf = open(blast_res) > parser = NCBIStandalone.BlastParser() > iter = NCBIStandalone.Iterator(bf, parser) > myrec = parser.parse(bf) Get rid of this line. You're parsing the results from the first query sequence... > while 1: > myrec = iter.next() > if myrec is None: > break ... and then immediately discarding it by assigning the second record to the same variable. Jeff From swon9 at itsa.ucsf.edu Sat Jul 17 15:55:25 2004 From: swon9 at itsa.ucsf.edu (Sergio E. Wong) Date: Sat Jul 17 15:57:16 2004 Subject: [BioPython] Problem superimposing structures Message-ID: Dear sirs.. I posted an inquiry several days ago, but haven't gotten any response. I am reposting and asking the same question, perhaps in a different way to see if anyone can help me. I'm trying to superimpose two crystal structures. I have successfully installed Numeric.py module and the Bio module. My python version is 2.2. Has anyone been succesful in doing this? and if so, can you tell me how to do it? As explained below, I've tried the documentation, but it hasn't worked. I am trying to superimpose two crystal structures using the Bio.PDB.Superimposer, following the example in the biopython FAQ document where it explains how to do this. For the purposes of testing, I am only using 5 atoms in the atoms lists. Below I show the two atom lists and the error I get when I try to use the set_atoms method. >>> ebg_res1 [, , , , ] >>> ebh_res1 [, , , , ] >>> sup.set_atoms( ebg_res1, ebh_res1) Traceback (most recent call last): File "", line 1, in ? TypeError: unbound method set_atoms() must be called with Superimposer instance as first argument (got list instance instead) Does anyone have any idea of why this is happening? Does anyone know of a work around? Perhaps using some other module?? Thanks -Sergio From e.picardi at unical.it Tue Jul 20 07:21:12 2004 From: e.picardi at unical.it (Ernesto) Date: Tue Jul 20 08:38:21 2004 Subject: [BioPython] hydrofobic index Message-ID: <007a01c46e4d$cfb41800$572561a0@Travelmate> Hi all, do you know if there is a biopython function to calculate the Kyte-Doolittle hydrofobic index? (Just the score for each site, not the plot) Many thanks Ernesto From idoerg at burnham.org Tue Jul 20 12:39:19 2004 From: idoerg at burnham.org (Iddo) Date: Tue Jul 20 12:41:05 2004 Subject: [BioPython] hydrofobic index In-Reply-To: <007a01c46e4d$cfb41800$572561a0@Travelmate> References: <007a01c46e4d$cfb41800$572561a0@Travelmate> Message-ID: <40FD4AB7.5010300@burnham.org> (When going after your question, I actually found a bug in ProtParam. So please check it out of the CVS). The module you should use is: Bio.SeqUtils.ProtParam.py Try this: from Bio.SeqUtils import ProtParam my_seq="MAEGEITTFTALTEKFNLPPGNYKKPKLLY" pa = ProtParam.ProteinAnalysis(my_seq) print "GRAVY", pa.gravy print "K&D along the protein": for i in pa.protein_scale(ProtParamData.kd, 9, 0.4): print "%.3f" % i HTH, Iddo Ernesto wrote >Hi all, >do you know if there is a biopython function to calculate the Kyte-Doolittle hydrofobic index? (Just the score for each site, not the plot) > >Many thanks > >Ernesto > > >------------------------------------------------------------------------ > >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From idoerg at burnham.org Tue Jul 20 14:31:15 2004 From: idoerg at burnham.org (Iddo) Date: Tue Jul 20 14:33:08 2004 Subject: [BioPython] hydrofobic index In-Reply-To: <40FD4AB7.5010300@burnham.org> References: <007a01c46e4d$cfb41800$572561a0@Travelmate> <40FD4AB7.5010300@burnham.org> Message-ID: <40FD64F3.10901@burnham.org> Iddo wrote: If I didn't make it clear, I fixed the bug, so the new ProtParam should be checked out of CVS. Also, please correct line 4 in the code I gave to: print "GRAVY", pa.gravy() > > (When going after your question, I actually found a bug in ProtParam. > So please check it out of the CVS). > > The module you should use is: Bio.SeqUtils.ProtParam.py > > > Try this: > > from Bio.SeqUtils import ProtParam > my_seq="MAEGEITTFTALTEKFNLPPGNYKKPKLLY" > pa = ProtParam.ProteinAnalysis(my_seq) > > print "GRAVY", pa.gravy > > print "K&D along the protein": > for i in pa.protein_scale(ProtParamData.kd, 9, 0.4): > print "%.3f" % i > > > HTH, > > Iddo > > > Ernesto wrote > >> Hi all, >> do you know if there is a biopython function to calculate the >> Kyte-Doolittle hydrofobic index? (Just the score for each site, not >> the plot) >> >> Many thanks >> >> Ernesto >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioPython mailing list - BioPython@biopython.org >> http://biopython.org/mailman/listinfo/biopython >> >> > > -- 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) 713 9930 http://ffas.ljcrf.edu/~iddo From nores at e-ticket-marketing.com Tue Jul 20 09:40:09 2004 From: nores at e-ticket-marketing.com (Redmanbroadcasting) Date: Tue Jul 20 18:59:28 2004 Subject: [BioPython] Get Paid To Shop & Eat! Message-ID: <20040720094009.sekatcjxfr@whitebroadcasting.com> Get paid to shop, eat in restaurants, play golf, take cruises and more! Visit our site for all of the details concerning this fantastic program! http://whitebroadcasting.com/dbm83/l.php?1043&31327204&riceez420/shopuyd -------------------------------------------- We hope you enjoyed receiving this email, but if you no longer wish to receive our emails please respond here: http://whitebroadcasting.com/dbm83/un.php?763&31327204 To Remove by Mail Removal Department PO Box 9 Irvine Ca 92650 ylmpinz From kael at sonic.net Tue Jul 20 19:39:19 2004 From: kael at sonic.net (Kael Fischer) Date: Tue Jul 20 19:41:01 2004 Subject: [BioPython] GenBank.NCBIDictionary broken? Message-ID: <6.1.1.1.2.20040720162614.020857d0@pop.sonic.net> Sometime in the past few weeks GenBank.NCBIDictionary seems to have stopped working. Typical traceback follows. I don't see anything promising in the CVS heads. This may be a problem in Bio.db or EUtils, I suppose. Does anyone have more information about this. Any ideas about where one would start digging around? >>> from Bio import GenBank >>> gb = GenBank.NCBIDictionary('nucleotide','fasta') >>> gb['28201044'] Traceback (most recent call last): File "", line 1, in ? File "/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/GenBank/__init__.py", line 1361, in __getitem__ handle = self.db[id] File "/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/DBRegistry.py", line 89, in __getitem__ return self._get(key) File "/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/_support.py", line 107, in __call__ return self.fn(*args, **keywds) File "/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/DBRegistry.py", line 372, in _get handle = self._check_for_errors(handle, self.failure_cases) File "/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/DBRegistry.py", line 246, in _check_for_errors raise KeyError, errormsg KeyError: "I got HTML and shouldn't have" TIA, Kael -- Kael Fischer, Ph.D. DeRisi Lab, University of California San Francisco http://derisilab.ucsf.edu Desk: 415-514-4320 kael@derisilab.ucsf.edu DSA key found on many key servers and http://kael.net/kael.gpg Fingerprint: DEE9 DD59 6081 B776 1704 54C9 AAD2 AA66 3828 More: http://kael.net From kael at sonic.net Tue Jul 20 20:06:34 2004 From: kael at sonic.net (Kael Fischer) Date: Tue Jul 20 20:08:19 2004 Subject: [BioPython] GenBank.NCBIDictionary broken? In-Reply-To: <6.1.1.1.2.20040720162614.020857d0@pop.sonic.net> References: <6.1.1.1.2.20040720162614.020857d0@pop.sonic.net> Message-ID: <6.1.1.1.2.20040720170454.02115490@pop.sonic.net> Ignore that... Somebody must have been doing something bad, because the HTML the parser was complaining about was a message saying we were banned from the ncbi website. Kael -- Kael Fischer, Ph.D. DeRisi Lab, University of California San Francisco http://derisilab.ucsf.edu Desk: 415-514-4320 kael@derisilab.ucsf.edu DSA key found on many key servers and http://kael.net/kael.gpg Fingerprint: DEE9 DD59 6081 B776 1704 54C9 AAD2 AA66 3828 More: http://kael.net From docwebmaster at cerline.com Wed Jul 21 23:31:38 2004 From: docwebmaster at cerline.com (docwebmaster@cerline.com) Date: Wed Jul 21 23:29:25 2004 Subject: [BioPython] New O E M software site In-Reply-To: References: Message-ID: <6F44D4502F6I99L3@cerline.com> Huge of O E M Software! You will find everything you need on our site http://ldeege.biz Microsoft Windows XP Professional Retail price: $299.00 Our low Price: $50.00 You Save: $249.00 Adobe Photoshop CS V 8.0 PC Retail price: $609.99 Our low Price: $80.00 You Save: $529.99 Microsoft Office XP Professional Retail price: $499.95 Our low Price: $100.00 You Save: $399.95 Microsoft Windows 2000 Professional Retail price: $320.00 Our low Price: $50.00 You Save: $270.00 Adobe Pagemaker V 7.0 PC Retail price: $599.95 Our low Price: $80.00 You Save: $519.95 Adobe Illustrator CS V 11.0 PC Retail price: $599.95 Our low Price: $80.00 You Save: $519.95 CorelDraw Graphics Suite V 12 PC Retail price: $349.95 Our low Price: $100.00 You Save: $249.95 Microsoft SQL Server 2000 Retail price: $1450.00 Our low Price: $90.00 You Save: $1360.00 Symantec Norton Antivirus 2004 Professional Retail price: $69.95 Our low Price: $15.00 You Save: $54.95 RedHat Linux 9.0 Retail price: $79.99 Our low Price: $60.00 You Save: $19.99 or site is http://gabydg.biz From syl_schupp at yahoo.fr Thu Jul 22 10:20:12 2004 From: syl_schupp at yahoo.fr (=?iso-8859-1?q?Sylvain=20Sch=FCpp?=) Date: Thu Jul 22 10:23:47 2004 Subject: [BioPython] Drawing tree Message-ID: <20040722142012.5623.qmail@web21107.mail.yahoo.com> Hello, I'm using the Clustal class from BioPython to align genomic data. I have no problem to obtain a PHYLIP tree file. But it's not very easy to read. So I'd like to use a program to draw the tree, like NJPlot or Retree. But I don't find any information about command line for these programs. I someone have already wrote a script in this way, I'm really interesting. Thanks Sylvain Pour suivre mes aventures su?doises : www.marschupp.fr.st --------------------------------- Cr?ez gratuitement votre Yahoo! Mail avec 100 Mo de stockage ! Cr?ez votre Yahoo! Mail Yahoo! Messenger : dialoguez instantan?ment avec vos amis - c'est gratuit ! From sbassi at asalup.org Thu Jul 22 10:41:31 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Jul 22 10:43:35 2004 Subject: [BioPython] CG content and random sequence Message-ID: <40FFD21B.2020100@asalup.org> Hello, I did some scripts that I could turn into function to add into Biopython if there is some interest. 1) Calculate CG content of all the sequences contained on a FASTA file. 2) Generate N random sequence with a given CG content. This one is based on Ashleigh work he gave me in this list on 6/16. But I added a new parameter, CG content. His work is like mine but with a fixed 50% probability of CG. In my script, you set the CG content. -- 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 From aaron at ocelot-atroxen.dyndns.org Thu Jul 22 19:30:21 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Thu Jul 22 19:32:01 2004 Subject: [BioPython] BLAST/tutorial problems Message-ID: <1958E8C6-DC37-11D8-A355-003065706E3A@atroxen.com> I recently started having my program hang during the part that does BLAST queries. I traced the problem to this section of my code: -------- b_results = NCBIWWW.blast('blastp', 'nr', f_record, format_type = "HTML") save_file = open(data_path_prefix + file_unique_id + 'blast', 'w') -------- which was pretty much taken verbatim from the tutorial. However instead of getting my results back in a usable format, I get the HTML below saved to a file. My server logs just say 'unexpected end of stream' (this is running as part of a CGI script) has anyone encountered an error like this before? thanks in advance, Aaron Zschau -------- Header of the page
WAITING

Request ID 1090538237-8571-194036110105.BLASTQ4
StatusSearching
Submitted atThu Jul 22 19:17:17 2004
Current timeThu Jul 22 19:18:15 2004

This page will be automatically updated in 12 seconds until search is done
From jeffrey_chang at stanfordalumni.org Thu Jul 22 20:35:48 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Thu Jul 22 20:37:28 2004 Subject: [BioPython] BLAST/tutorial problems In-Reply-To: <1958E8C6-DC37-11D8-A355-003065706E3A@atroxen.com> References: <1958E8C6-DC37-11D8-A355-003065706E3A@atroxen.com> Message-ID: <3DFCF7F5-DC40-11D8-911F-000A956845CE@stanfordalumni.org> On Jul 22, 2004, at 7:30 PM, Aaron Zschau wrote: > I recently started having my program hang during the part that does > BLAST queries. Yes, NCBI has recently changed their BLAST server, and broke the Biopython code. It has been fixed now in the CVS version, which you can retrieve at: http://cvs.biopython.org/ Please grab the latest NCBIWWW.py file from there, and save it over the older version. The major change in this version is that this blast code has been deprecated in favor of the NCBI QBlast API, which should be more stable. Thus, after you install the new file, change the NCBIWWW.blast call to NCBIWWW.qblast in your code. Jeff From aaron at ocelot-atroxen.dyndns.org Fri Jul 23 22:34:48 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Fri Jul 23 22:36:29 2004 Subject: [BioPython] BLAST/tutorial problems In-Reply-To: <6E8C2F4D-DCDF-11D8-B349-000A956845CE@stanfordalumni.org> References: <1958E8C6-DC37-11D8-A355-003065706E3A@atroxen.com> <3DFCF7F5-DC40-11D8-911F-000A956845CE@stanfordalumni.org> <6E8C2F4D-DCDF-11D8-B349-000A956845CE@stanfordalumni.org> Message-ID: <08603FA9-DD1A-11D8-A355-003065706E3A@atroxen.com> I just did some tracing back and made sure I was up to date with the current CVS versions of all of biopython and my BLAST searches all seem to be working again, however the problem I was getting from my last email seems to be a problem in parsing my fasta file generated by my genbank query. The code as follows: -------------- file_for_blast = open(data_path_prefix + file_unique_id + 'fasta', 'r') f_iterator = Fasta.Iterator(file_for_blast) f_record = f_iterator.next() -------------- should work according to the cook book, however when I call f_record = f_iterator.next() I get the following error: -------------- Traceback (most recent call last): File "cluster-debug.py", line 110, in ? sys.stdout.flush() File "/usr/lib/python2.2/site-packages/Bio/Fasta/__init__.py", line 72, in next result = self._iterator.next() File "/home/zschamm/bioinfo/biopython-1.30/build/lib.linux-i586-2.2/Martel/ IterParser.py", line 152, in iterateFile File "/home/zschamm/bioinfo/biopython-1.30/build/lib.linux-i586-2.2/Martel/ Parser.py", line 361, in parseString File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserIncompleteException: error parsing at or beyond character 0 (unparsed text remains) -------------- if I simply replace the last line with a protein direct sequence entry in the above code, my program continues along just fine and the BLAST portions now run. f_record = "MNKRGKYTTLNLEEKMKVLSRIEAGRSLKSVMDEFGISKSTFYDIKKNKKLILDFVLKQDMPLVGAEKRKR TTGAKYGDVDDAVYMWYQQKRSAGVPVRGVELQAAAERFARCFGRTDFKASTGWLFRFRNRHAIGNRKGCGE QVLSSVSENVEPFRQKLSMIIKEEKLCLAQLYSGDETDLFWKSMPENSQASRKDICLPGKKINTERLSAFLC ANADGTHKLKSIIIGKSKLPKSVKEDTSTLPVIYKPSKDVWFTRELFSEWFFQNFVPEVRHFQLNVLRFHDE DVRALLLLDSCPAHPSSESLTSEDGRIKCMFFPHNSSTLIQPMNQGVILSCKRLYRWKQLEESLVIFEESDD EQEKGDKGVSKIKIYNIKSAIFNWAKSWEEVKQITIANAWENLLYKKEPEYDFQGLEHGDYREILEKCGELE TKLDDDRVWLNGDEEKGCLLKTKGGITKEVVQKGGEAEKQTAEFKLSAVRESLDYLLDFVDATPEFQRFHFT LCEFSDDS" thanks, Aaron On Jul 23, 2004, at 3:35 PM, Jeffrey Chang wrote: > Hi Aaron, > > NCBIDictionary requires parameters telling it what database to > retrieve from, and what format it uses. I believe these changes were > made when we switched over to using NCBI EUtils API to retrieve > sequences. Try doing: > >>> ncbi_dict = GenBank.NCBIDictionary("nucleotide", "genbank", > parser=record_parser) > >>> gb_record = ncbi_dict["6273291"] > >>> print gb_record.seq > > I'm not sure why you are getting a timeout. Is there a web proxy or > firewall blocking HTTP connections on your network? > > Jeff > > > > On Jul 23, 2004, at 3:23 PM, Aaron Zschau wrote: > >> Thanks for the help, though I am still having some trouble getting >> things working. I am now getting a different timeout error: >> >> [error] [client 10.0.0.22] (20507)The timeout specified has expired: >> ap_content_length_filter: apr_bucket_read() failed, referer: >> http://serval.atroxen.com:8080/interface.html >> >> I tried updating to version 1.3 of biopython (I was running the >> previous version) and now I get a type error: >> >> >> Traceback (most recent call last): >> File "cluster-debug.py", line 88, in ? >> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser) >> TypeError: __init__() takes at least 3 non-keyword arguments (1 given) >> >> relating to this piece of code: >> >> record_parser = GenBank.FeatureParser() >> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser) >> gb_record = ncbi_dict[gi_list[0]] >> >> this part worked just fine before the update to 1.3 and looking >> through the posted API I haven't been able to figure out what >> arguments are missing from the GenBank.NCBIDictionary creation. >> >> thanks >> >> Aaron >> >> On Jul 22, 2004, at 8:35 PM, Jeffrey Chang wrote: >> >>> On Jul 22, 2004, at 7:30 PM, Aaron Zschau wrote: >>> >>>> I recently started having my program hang during the part that does >>>> BLAST queries. >>> >>> Yes, NCBI has recently changed their BLAST server, and broke the >>> Biopython code. It has been fixed now in the CVS version, which you >>> can retrieve at: >>> http://cvs.biopython.org/ >>> >>> Please grab the latest NCBIWWW.py file from there, and save it over >>> the older version. >>> >>> The major change in this version is that this blast code has been >>> deprecated in favor of the NCBI QBlast API, which should be more >>> stable. Thus, after you install the new file, change the >>> NCBIWWW.blast call to NCBIWWW.qblast in your code. >>> >>> Jeff >> From sameet at nccs.res.in Sat Jul 24 13:10:31 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Sat Jul 24 13:18:25 2004 Subject: [BioPython] Help regarding multiple alignment Message-ID: <20040724170451.M4145@linux.nccs.res.in> Hi, I had downloaded a set of sequences at different points after querying the NCBI database the old fashioned way. I had stored the files individually and then i copy-pasted the sequences such that all the sequences are not in a single file. It seems that during this excercise there has been a lot of repetition in the sequences. I want to curate these sequences such that i take only single occurence of each sequence. I wrote a code for this whcih i am giving here from __future__ import division import string from Bio import Fasta def curate(infile, outfile): ## inf = raw_input('Path to Fasta file: ') ## outfile = raw_input('Path to output file: ') outf = open(outfile, 'w') file = open(infile, 'r') parser = Fasta.RecordParser() iterator = Fasta.Iterator(file, parser) titleList = [] t_d = {} s = ' ' while 1: cur_record = iterator.next() if cur_record is None: break # Get the title set and validate to dict title_atoms = string.split(cur_record.title) title = title_atoms[0] titleList.append(title) titleList = find_same(titleList) file = open(inf, 'r') parser = Fasta.RecordParser() iterator = Fasta.Iterator(file, parser) while 1: cur_record = iterator.next() if cur_record is None: break title_atoms = string.split(cur_record.title) title = title_atoms[0] if title in titleList: writestring = title+'\n'+cur_record.sequence+'\n\n' outf.writelines(writestring) outf.close() print 'file written to ',outfile,'\n' def find_same(title_list): list = title_list curated = [] repeated = [] for a in list: if str(list).count(a) == 1: curated.append(a) else: repeated.append(a) return curated print """Description of the program""" inf = raw_input('Path to Fasta file: ') outfile = raw_input('Path to output file: ') curate(inf, outfile) Now i understand that there would be a lot of redundunt code. However, the output file i get doesnt seem to be an 'authentic' fasta file, because no multiple alignment programs are recognizing it. I could have done something really wrong, but i am not able to figure that out! All the heelp is highly solicitated. regards Thaking you in anticipation Sameet -- National Centre for Cell Science, Pune From su-lin at t-online.de Sat Jul 24 16:42:28 2004 From: su-lin at t-online.de (jakov) Date: Sat Jul 24 16:51:07 2004 Subject: [BioPython] =?windows-1251?b?4eXr/OU=?= Message-ID: <200407242051.i6OKp0Kr000975@portal.open-bio.org> ???????? ? ???????? ??????????? ????? ?? www.mypresent.ru ??? ????? ?????? ?????. From dawn at alh.com Sun Jul 25 03:37:11 2004 From: dawn at alh.com (=?Windows-1251?B?3ezo6+j/IMDh8ODs7uLt4A==?=) Date: Sun Jul 25 03:50:44 2004 Subject: [BioPython] Re: Message-ID: <200407250750.i6P7oKKr006491@portal.open-bio.org> ???????? INFOCOM ??????????: ? ??????? ??????? TRS, ?????????????? ??? ?????? ?????????? ?????????? ?? ????????? ? ??????? ??????? ??? ?????? ? ?????? ?????????? ???????? ? ???????? ? ??????? ????????????? ??? ?????? ? ?????????????? ?????????? ? ????????? ????????? ???????? ????? ? ???????. ??????????? ?? ????? http://bazezs.p9.org.uk/ From sameet at nccs.res.in Tue Jul 27 00:56:00 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Tue Jul 27 01:04:05 2004 Subject: [BioPython] Help for BLAST Message-ID: <20040727044835.M75069@linux.nccs.res.in> Hi, I want to do a NCBIWWW BLAST, from a set of files that i havve. The sequences are in FASTA format. The Blast Runs perfectly, however, i have problems parsing the output. I am doing the following : >>> from Bio import Fasta >>> from Bio.Blast import NCBIWWW >>> file_to_blast = open('C:\Sameet\Data\H9.txt', 'r') >>> f_iterator = Fasta.Iterator(file_to_blast) >>> f_record = f_iterator.next() >>> b_result = NCBIWWW.qblast('blastn', 'nr', f_record, descriptions=20, alignments=20) >>> b_parser = NCBIWWW.BlastParser() >>> b_record = b_parser.parse(b_result) I am getting the follwing error Traceback (most recent call last): File "", line 1, in -toplevel- b_record = b_parser.parse(b_result) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 47, in parse self._scanner.feed(handle, self._consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 101, in feed self._scan_rounds(uhandle, consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 244, in _scan_rounds self._scan_alignments(uhandle, consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 327, in _scan_alignments self._scan_pairwise_alignments(uhandle, consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 350, in _scan_pairwise_alignments self._scan_one_pairwise_alignment(uhandle, consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 381, in _scan_one_pairwise_alignment self._scan_alignment_header(uhandle, consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 419, in _scan_alignment_header raise SyntaxError, "I missed the Length in an alignment header" SyntaxError: I missed the Length in an alignment header Am i missing something or doing something wrong. I need this information urgently. Regards sameet -- National Centre for Cell Science, Pune From nores at e-ticket-marketing.com Mon Jul 26 13:50:04 2004 From: nores at e-ticket-marketing.com (eTicket) Date: Tue Jul 27 07:26:49 2004 Subject: [BioPython] free 4 room digital satellite TV system Message-ID: <20040726135003.uqbsekatcj@redmanbroadcasting.com> FREE Digital Satellite TV System with FREE Installation in up to FOUR ROOMS from DishNetwork! Plus, FREE Digital Video Recorders in every room! No equipment to buy! Hurry - offer expires soon! http://redmanbroadcasting.com/dbm83/l.php?1103&31327204&phlp=0&chnl=194357&ofr=1070014 -------------------------------------------- We hope you enjoyed receiving this email, but if you no longer wish to receive our emails please respond here: http://redmanbroadcasting.com/dbm83/un.php?781&31327204 To Remove by Mail Removal Department PO Box 9 Irvine Ca 92650 xfrylmp From jeffrey_chang at stanfordalumni.org Tue Jul 27 11:13:00 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Tue Jul 27 11:14:40 2004 Subject: [BioPython] Help for BLAST In-Reply-To: <20040727044835.M75069@linux.nccs.res.in> References: <20040727044835.M75069@linux.nccs.res.in> Message-ID: <72A78A5C-DFDF-11D8-8307-000A956845CE@stanfordalumni.org> Hi Sameet, There are two things going on here. First, the output from qblast is slightly different from the standard blast output. Therefore, I have updated the parser to handle the new output. Second, please use the Text format out, as the HTML is much messier and harder to parse. So in your qblast call, you need to add format_type="Text" and change the NCBIWWW.BlastParser to NCBIStandalone.BlastParser, making sure to import the NCBIStandalone module before you use it. Jeff On Jul 27, 2004, at 12:56 AM, Sameet Mehta wrote: > Hi, > I want to do a NCBIWWW BLAST, from a set of files that i havve. The > sequences are in FASTA format. The Blast Runs perfectly, however, i > have > problems parsing the output. I am doing the following : > >>>> from Bio import Fasta >>>> from Bio.Blast import NCBIWWW >>>> file_to_blast = open('C:\Sameet\Data\H9.txt', 'r') >>>> f_iterator = Fasta.Iterator(file_to_blast) >>>> f_record = f_iterator.next() >>>> b_result = NCBIWWW.qblast('blastn', 'nr', f_record, descriptions=20, > alignments=20) >>>> b_parser = NCBIWWW.BlastParser() >>>> b_record = b_parser.parse(b_result) > > I am getting the follwing error > Traceback (most recent call last): > File "", line 1, in -toplevel- > b_record = b_parser.parse(b_result) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 47, > in > parse > self._scanner.feed(handle, self._consumer) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 101, > in > feed > self._scan_rounds(uhandle, consumer) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 244, > in > _scan_rounds > self._scan_alignments(uhandle, consumer) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 327, > in > _scan_alignments > self._scan_pairwise_alignments(uhandle, consumer) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 350, > in > _scan_pairwise_alignments > self._scan_one_pairwise_alignment(uhandle, consumer) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 381, > in > _scan_one_pairwise_alignment > self._scan_alignment_header(uhandle, consumer) > File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 419, > in > _scan_alignment_header > raise SyntaxError, "I missed the Length in an alignment header" > SyntaxError: I missed the Length in an alignment header > > Am i missing something or doing something wrong. I need this > information > urgently. > > Regards > sameet > > -- > National Centre for Cell Science, Pune > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From crocha at dc.uba.ar Tue Jul 27 15:18:50 2004 From: crocha at dc.uba.ar (Cristian Sebastian Rocha) Date: Tue Jul 27 15:24:37 2004 Subject: [BioPython] bug in DatabaseRemover class. Message-ID: <32942.157.92.27.121.1090955930.squirrel@webmail.dc.uba.ar> Hi, I just find a little bug in DatabaseRemover class, defined in BioSQL.Loader module. The remove() function call the adaptor.execute function as: self.adaptor.execute(sql, (self.dbid)) Python understand it as an element and not as a tuple of one element. You must call these function in the following way: self.adaptor.execute(sql, (self.dbid,)) bye, Cristian. -- Lic. Cristian S. Rocha Universidad de Buenos Aires, FCEyN, Departamento de Computaci?n. From chi-shun at nethomebiz.net Wed Jul 28 22:25:40 2004 From: chi-shun at nethomebiz.net (info) Date: Wed Jul 28 22:34:36 2004 Subject: [BioPython] Re: Message-ID: <200407290234.i6T2YNKr013761@portal.open-bio.org> ?????? - ???????????, ?????? - ?????????, ???? ?????? ?? http://progz.p7.org.uk From sameet at nccs.res.in Thu Jul 29 01:33:10 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Thu Jul 29 01:41:07 2004 Subject: [BioPython] Feature Request Message-ID: <20040729052837.M57791@linux.nccs.res.in> Hi all, I have a slight problem. I canot figure out the say to blast a given set of sequences only gainst a particular genome only. I have a set of files that i need to blast agains the human genome only and against the mouse genome only. Is there a way to do this? regards Sameet -- National Centre for Cell Science, Pune From lou at hotmail.com Thu Jul 29 02:46:54 2004 From: lou at hotmail.com (=?Windows-1251?B?y+7t4+jtIMzl6+Xt8vzl4uj3?=) Date: Thu Jul 29 03:00:00 2004 Subject: [BioPython] =?windows-1251?b?xO7x8uDr6CDx7uHg6ug/?= Message-ID: <129591976.20040729065154@> ??? ???? ??? ?? ???? ?????????? ????????????. http://www.dazer2.ru From idoerg at burnham.org Thu Jul 29 12:02:41 2004 From: idoerg at burnham.org (Iddo) Date: Thu Jul 29 12:04:23 2004 Subject: [BioPython] Feature Request In-Reply-To: <20040729052837.M57791@linux.nccs.res.in> References: <20040729052837.M57791@linux.nccs.res.in> Message-ID: <41091FA1.60809@burnham.org> The best way would be to download your favorite version of the human genome, formatdb it, and run BLAST locally. Best, Iddo Sameet Mehta wrote: >Hi all, > >I have a slight problem. I canot figure out the say to blast a given set of >sequences only gainst a particular genome only. I have a set of files that >i need to blast agains the human genome only and against the mouse genome >only. Is there a way to do this? > >regards >Sameet > >-- >National Centre for Cell Science, Pune > >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython > > > > -- 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) 713 9930 http://ffas.ljcrf.edu/~iddo From lewis at t-online.de Fri Jul 30 00:13:24 2004 From: lewis at t-online.de (julia) Date: Fri Jul 30 00:20:30 2004 Subject: [BioPython] =?windows-1251?b?4eXr/OU=?= Message-ID: <200407300420.i6U4KHKr002929@portal.open-bio.org> ???????? ? ???????? ??????????? ????? ?? www.mypresent.ru ??? ????? ?????? ?????. 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Our site http://greatservus.biz/?y=biopython@biopython.org&add=s&item=pavsoft From aaron at ocelot-atroxen.dyndns.org Fri Jul 30 14:41:14 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Fri Jul 30 14:42:39 2004 Subject: [BioPython] BLAST/Tutorial more problems Message-ID: <0936DD49-E258-11D8-A2DC-003065706E3A@atroxen.com> I'm still having some trouble making a section of my code copied from the tutorial work properly with the latest version of biopython. From this piece of code, I get the following error when executing the f_record = f_iterator.next() line Traceback (most recent call last): File "cluster-debug.py", line 111, in ? f_record = f_iterator.next() File "/root/biopython-1.30/build/lib.linux-i586-2.2/Bio/Fasta/__init__.py", line 72, in next result = self._iterator.next() File "/root/biopython-1.30/build/lib.linux-i586-2.2/Martel/IterParser.py", line 152, in iterateFile self.header_parser.parseString(rec) File "/root/biopython-1.30/build/lib.linux-i586-2.2/Martel/Parser.py", line 361, in parseString self._err_handler.fatalError(ParserIncompleteException(pos)) File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserIncompleteException: error parsing at or beyond character 0 (unparsed text remains) #----------------------------------------------------------------------- gi_list = GenBank.search_for("vhl") ncbi_dict = GenBank.NCBIDictionary("nucleotide", "genbank") gb_record = ncbi_dict["6273291"] record_parser = GenBank.FeatureParser() ncbi_dict = GenBank.NCBIDictionary("nucleotide", "genbank", parser = record_parser) gb_seqrecord = ncbi_dict["6273291"] genbank_file = open(data_path_prefix + file_unique_id + 'fasta', 'w') genbank_file.write(gb_record) genbank_file.close() sys.stdout.flush() file_for_blast = open('/var/www/html/data/a12345.fasta','r') f_iterator = Fasta.Iterator(file_for_blast) print "iterator created" sys.stdout.flush() f_record = f_iterator.next() print "f_record created" sys.stdout.flush() file_for_blast.close() #----------------------------------------------------------------------- There seems to be a problem somewhere in the parsing of the FASTA file generated by the genbank lookup, however when I look at the contents of the fasta file, it looks fine and the formatting is the same as what I used in version 1.24 does anyone know what might be going on here? thanks Aaron Zschau From sbassi at asalup.org Fri Jul 30 15:26:21 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Fri Jul 30 15:28:25 2004 Subject: [BioPython] BLAST: No hit? Message-ID: <410AA0DD.4050903@asalup.org> Hello, How do I parse using BLAST parser that there is no hit? May I use description.title=""? From heath.h_kaplan_ym at arcetri.astro.it Sat Jul 31 16:41:38 2004 From: heath.h_kaplan_ym at arcetri.astro.it (Heath H. Kaplan) Date: Sat Jul 31 17:30:55 2004 Subject: [BioPython] 189547 dol-lars Message-ID: <588601c4773e$3e7ec7d9$07038d08@etfis> Hello, Did you recieve my email from last week? I'm happy to tell you that you could be approved for a Re~fi~nance with a 3.70% rate. Your tracking site 1 is: http://justthisday.net/prime/dWorld/index.htm Site 2 is: http://lostmasquerade.biz/prime/Munsuwest/index.htm You must visit the site in 24 hrs to confirm your eligibility. Best Regards, Carrie Griffin, Account Manager Montgomery Holdings Co.