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From biopython-dev-bounces at portal.open-bio.org Mon Aug 2 10:33:26 2004 From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org) Date: Mon Aug 2 10:33:32 2004 Subject: [BioPython] Your message to Biopython-dev awaits moderator approval Message-ID: Your mail to 'Biopython-dev' with the subject :) Is being held until the list moderator can review it for approval. The reason it is being held: Message has a suspicious header Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://biopython.org/mailman/confirm/biopython-dev/0fd5a984534f633ab4fe94a5441e8b1a73329aeb From Gelato at xmltwig.com Mon Aug 2 12:51:27 2004 From: Gelato at xmltwig.com (Gelato@xmltwig.com) Date: Mon Aug 2 12:52:46 2004 Subject: [BioPython] new O E M site In-Reply-To: <3E7C86K3K1L4DI1E@biopython.org> References: <3E7C86K3K1L4DI1E@biopython.org> Message-ID: <9B47D27L3KE6F7FJ@xmltwig.com> Huge of O E M Software! You will find everything you need on our site 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://lookoo.biz/ From chapmanb at uga.edu Mon Aug 2 16:41:09 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Aug 2 16:43:04 2004 Subject: [BioPython] Some Biopython news, plans, and grants Message-ID: <20040802204109.GD15421@lebowski.bos.east.verizon.net> Hello everyone; As some of you may have noticed, I've been relatively absent from the Biopython lists over the last couple of months. This was due to the unfortunate arrival of dissertation and defense time for me; thankfully all of my painful finishing work is, well, finished and I am happily in PhD land as of this upcoming Saturday. What that means is that I'm going to make a concerted effort to go through the mailing list and try and sort out problems and bugs that have been posted that no one has been able to get to. I'd like this to lead up to a semi-soonish release, and then we'll worry about what goes from there. For the upcoming release, I'll stay simple. The main things I'd like to do before release are: -> Cleaning up bugs, problems from the mailing lists. This will take a bit; there are a lot of things that need attention. -> Move from using Numeric (Numpy, Numerical Python) to Numarray (http://www.stsci.edu/resources/software_hardware/numarray). Since development on this package is now entirely focused on Numarray, I think it makes the most sense for us to migrate over. That's it. Pretty simple. Besides a new release, another idea I'd like to toss out there is trying to write a grant for the Python Software Foundation to get money to "hire" someone to help with Biopython documentation. The PSF is accepting proposals up until October 1st: http://www.python.org/psf/call-2004.html Jeff pointed this out to me, and I think it is the perfect chance to try and find some individuals who might be motivated by supplemental financial gain to work on improving Biopython documentation. If there is anyone who has any interest in this, let me know, and I can start trying to imagine specifics for writing the proposal. Hope everyone is doing well. Boo dissertations. Yay Biopython. Brad From thamelry at binf.ku.dk Tue Aug 3 09:22:44 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Tue Aug 3 09:35:13 2004 Subject: [BioPython] Problem superimposing structures In-Reply-To: References: Message-ID: <200408031522.44704.thamelry@binf.ku.dk> Hi Sergio, Sorry about the delay in replying. > 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) You haven't sent in all the code. What is the sup variable? I suspect you erroneously assigned sup to the Superimposer class itself, and not to an instance of this class - hence the complaint about an unbound method. The correct code should be something like: from Bio.PDB import * sup=Superimposer() sup.set_atoms( ebg_res1, ebh_res1) Let me know if your problem is solved. Best regards, -- Dr. Thomas Hamelryck Bioinformatics center University of Copenhagen Universitetsparken 15 Bygning 10 2100 Copenhagen, Denmark --- http://www.binf.ku.dk/users/thamelry/ From pwilkinson at videotron.ca Tue Aug 3 10:59:08 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 3 11:00:46 2004 Subject: [BioPython] Entrez module In-Reply-To: <200408031522.44704.thamelry@binf.ku.dk> References: <200408031522.44704.thamelry@binf.ku.dk> Message-ID: <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> I suddenly had an urge to query entrez with python .... I have looked through the latest release ... but did not find an entrez module is there an interface to Entrez hidden somewhere? Peter From pwilkinson at videotron.ca Tue Aug 3 11:06:17 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 3 11:07:46 2004 Subject: [BioPython] Entrez module In-Reply-To: <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> References: <200408031522.44704.thamelry@binf.ku.dk> <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> Message-ID: <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> I just found the interface in Bio.WWW Peter At 10:59 AM 8/3/2004, Peter Wilkinson wrote: >I suddenly had an urge to query entrez with python .... > >I have looked through the latest release ... but did not find an entrez module > >is there an interface to Entrez hidden somewhere? > >Peter > >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython From chapmanb at uga.edu Tue Aug 3 12:24:35 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Aug 3 12:26:32 2004 Subject: [BioPython] Entrez module In-Reply-To: <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> References: <200408031522.44704.thamelry@binf.ku.dk> <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> Message-ID: <20040803162435.GA93656@lebowski.bos.east.verizon.net> Hi Peter; > >I suddenly had an urge to query entrez with python .... > > > >I have looked through the latest release ... but did not find an entrez > >module [...] > I just found the interface in Bio.WWW The best way to query Entrez from programs is using the EUtils interfaces at NCBI: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Biopython has a interface to EUtils in Bio.EUtils. There is a lot of source code documentation within there. For instance, for an example of retrieving PubMed information, Bio.EUtils.HistoryClient provides some good code examples: http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html The only thing you have to do is adjust the imports to be from Biopython, like from Bio.EUtils import HistoryClient (sorry, older documentation from when EUtils was not within Biopython -- I updated this). If you have specific questions feel free to ask, but the EUtils interfaces should definitely be more stable than the older stuff in Bio.WWW. Hope this helps! Brad From pwilkinson at videotron.ca Tue Aug 3 12:44:17 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 3 12:45:47 2004 Subject: [BioPython] Entrez module In-Reply-To: <20040803162435.GA93656@lebowski.bos.east.verizon.net> References: <200408031522.44704.thamelry@binf.ku.dk> <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> <20040803162435.GA93656@lebowski.bos.east.verizon.net> Message-ID: <6.0.3.0.0.20040803124313.01b11c50@pop.videotron.ca> That is good to know. I will have a loot at the EUtils first. Peter At 12:24 PM 8/3/2004, Brad Chapman wrote: >Hi Peter; > > > >I suddenly had an urge to query entrez with python .... > > > > > >I have looked through the latest release ... but did not find an entrez > > >module >[...] > > I just found the interface in Bio.WWW > >The best way to query Entrez from programs is using the EUtils >interfaces at NCBI: > >http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html > >Biopython has a interface to EUtils in Bio.EUtils. There is a lot of >source code documentation within there. For instance, for an example >of retrieving PubMed information, Bio.EUtils.HistoryClient provides >some good code examples: > >http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html > >The only thing you have to do is adjust the imports to be from >Biopython, like from Bio.EUtils import HistoryClient (sorry, older >documentation from when EUtils was not within Biopython -- I updated >this). > >If you have specific questions feel free to ask, but the EUtils >interfaces should definitely be more stable than the older stuff in >Bio.WWW. > >Hope this helps! >Brad >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython From pwilkinson at videotron.ca Tue Aug 3 13:16:38 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 3 13:18:15 2004 Subject: [BioPython] Some Biopython news, plans, and grants In-Reply-To: <20040802204109.GD15421@lebowski.bos.east.verizon.net> References: <20040802204109.GD15421@lebowski.bos.east.verizon.net> Message-ID: <6.0.3.0.0.20040803130727.01b9d488@pop.videotron.ca> I certainly would be interested in the documentation project, if you can find funding. I do like working on tutorials and documentation 'solutions'... my own personal war on bad and thin documentation. Please add me to a list, and let me know what the time commitments would be. With regards to numarray, i will be exploring this module for the use in microarray analysis as I need some structures (I think) that would be useful in vectorising calculations. I am working on some code that is structured after the RGlist and MAlist objects you find in Bioconductor's limma package. I am doing some large scale micrarra analysis (in the hundreds of arrays per project), and I find that R is not the tool for batch work, but it is a good tool for statistical analysis. Python + rpy or RSpython might = batch work. I am still exploring. It might turn out better to implement some new normalization algorithms directly in Python or in C++. R has memory management problems, and it is built for you to load all the data you want to work with at once ... this is limits batch processing. I am hoping numarray can help. Peter At 04:41 PM 8/2/2004, Brad Chapman wrote: >Hello everyone; >As some of you may have noticed, I've been relatively absent from >the Biopython lists over the last couple of months. This was due to >the unfortunate arrival of dissertation and defense time for me; >thankfully all of my painful finishing work is, well, finished and I >am happily in PhD land as of this upcoming Saturday. > >What that means is that I'm going to make a concerted effort to go >through the mailing list and try and sort out problems and bugs that >have been posted that no one has been able to get to. I'd like this >to lead up to a semi-soonish release, and then we'll worry about >what goes from there. > >For the upcoming release, I'll stay simple. The main things I'd >like to do before release are: > >-> Cleaning up bugs, problems from the mailing lists. This will take >a bit; there are a lot of things that need attention. > >-> Move from using Numeric (Numpy, Numerical Python) to Numarray >(http://www.stsci.edu/resources/software_hardware/numarray). Since >development on this package is now entirely focused on Numarray, I >think it makes the most sense for us to migrate over. > >That's it. Pretty simple. Besides a new release, another idea I'd >like to toss out there is trying to write a grant for the Python >Software Foundation to get money to "hire" someone to help with >Biopython documentation. The PSF is accepting proposals up until >October 1st: > >http://www.python.org/psf/call-2004.html > >Jeff pointed this out to me, and I think it is the perfect chance to >try and find some individuals who might be motivated by supplemental >financial gain to work on improving Biopython documentation. If >there is anyone who has any interest in this, let me know, and I can >start trying to imagine specifics for writing the proposal. > >Hope everyone is doing well. Boo dissertations. Yay Biopython. > >Brad >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython From pwilkinson at videotron.ca Tue Aug 3 13:30:50 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 3 13:32:20 2004 Subject: [BioPython] BioEutils In-Reply-To: <6.0.3.0.0.20040803124313.01b11c50@pop.videotron.ca> References: <200408031522.44704.thamelry@binf.ku.dk> <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> <20040803162435.GA93656@lebowski.bos.east.verizon.net> <6.0.3.0.0.20040803124313.01b11c50@pop.videotron.ca> Message-ID: <6.0.3.0.0.20040803130152.01b89c50@pop.videotron.ca> This is my first attempt with this package ... on win32 with what I think is the latest Biopython. I would like to look up records for image clones like: clone = client.search("IMAGE:624360",db="nucleotide") This would be the way I look for a clone in the nucleotide set using the search field on the root of the ncbi homepage. I know that this clone is in nucleotide, but this query does not work here, I get a result of length = 0. or by accession number if the clone has one: clone = client.search("AA759046",db="nucleotide") however I get the following error Traceback (most recent call last): File "", line 1, in -toplevel- clone = client.search("AA759046",db="nucleotide") File "C:\Python23\lib\site-packages\Bio\EUtils\HistoryClient.py", line 354, in search searchinfo = parse.parse_search(infile, self.webenv_ref) File "C:\Python23\lib\site-packages\Bio\EUtils\parse.py", line 201, in parse_search for ele in pom["TranslationStack"]: File "C:\Python23\lib\site-packages\Bio\EUtils\POM.py", line 355, in __getitem__ raise IndexError, "no item matches" IndexError: no item matches. I might be doing something wrong here, but I am just following the help manual. Peter W. At 12:44 PM 8/3/2004, Peter Wilkinson wrote: >That is good to know. I will have a loot at the EUtils first. > >Peter > >At 12:24 PM 8/3/2004, Brad Chapman wrote: >>Hi Peter; >> >> > >I suddenly had an urge to query entrez with python .... >> > > >> > >I have looked through the latest release ... but did not find an entrez >> > >module >>[...] >> > I just found the interface in Bio.WWW >> >>The best way to query Entrez from programs is using the EUtils >>interfaces at NCBI: >> >>http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html >> >>Biopython has a interface to EUtils in Bio.EUtils. There is a lot of >>source code documentation within there. For instance, for an example >>of retrieving PubMed information, Bio.EUtils.HistoryClient provides >>some good code examples: >> >>http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html >> >>The only thing you have to do is adjust the imports to be from >>Biopython, like from Bio.EUtils import HistoryClient (sorry, older >>documentation from when EUtils was not within Biopython -- I updated >>this). >> >>If you have specific questions feel free to ask, but the EUtils >>interfaces should definitely be more stable than the older stuff in >>Bio.WWW. >> >>Hope this helps! >>Brad >>_______________________________________________ >>BioPython mailing list - BioPython@biopython.org >>http://biopython.org/mailman/listinfo/biopython > >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython From idoerg at yahoo.com Tue Aug 3 13:33:15 2004 From: idoerg at yahoo.com (Iddo Friedberg) Date: Tue Aug 3 13:34:29 2004 Subject: [BioPython] Some Biopython news, plans, and grants In-Reply-To: <20040802204109.GD15421@lebowski.bos.east.verizon.net> Message-ID: <20040803173315.12526.qmail@web41609.mail.yahoo.com> DR. CHAPMAN!! DR. CHAPMAN!! DR. CHAPMAN!! DR. CHAPMAN!! You will never be bumped off a flight again. Iddo ===== -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA, 92037 USA T: (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From pwilkinson at videotron.ca Tue Aug 3 13:40:26 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Tue Aug 3 13:41:58 2004 Subject: [BioPython] Entrez module In-Reply-To: <20040803162435.GA93656@lebowski.bos.east.verizon.net> References: <200408031522.44704.thamelry@binf.ku.dk> <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> <20040803162435.GA93656@lebowski.bos.east.verizon.net> Message-ID: <6.0.3.0.0.20040803133807.01b10e18@pop.videotron.ca> I dont seem to be getting any of the EUtils to work. I have tried the dbIds client sample code: >>> result = client.search("dalke", retmax = 100) Traceback (most recent call last): File "", line 1, in -toplevel- result = client.search("dalke", retmax = 100) File "C:\Python23\lib\site-packages\Bio\EUtils\DBIdsClient.py", line 294, in search searchinfo = parse.parse_search(infile, [None]) File "C:\Python23\lib\site-packages\Bio\EUtils\parse.py", line 219, in parse_search raise TypeError("Unknown OP code: %r" % (s,)) TypeError: Unknown OP code: u'GROUP' NCBI changing things around so the EUtils packages breaks? Peter At 12:24 PM 8/3/2004, Brad Chapman wrote: >Hi Peter; > > > >I suddenly had an urge to query entrez with python .... > > > > > >I have looked through the latest release ... but did not find an entrez > > >module >[...] > > I just found the interface in Bio.WWW > >The best way to query Entrez from programs is using the EUtils >interfaces at NCBI: > >http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html > >Biopython has a interface to EUtils in Bio.EUtils. There is a lot of >source code documentation within there. For instance, for an example >of retrieving PubMed information, Bio.EUtils.HistoryClient provides >some good code examples: > >http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html > >The only thing you have to do is adjust the imports to be from >Biopython, like from Bio.EUtils import HistoryClient (sorry, older >documentation from when EUtils was not within Biopython -- I updated >this). > >If you have specific questions feel free to ask, but the EUtils >interfaces should definitely be more stable than the older stuff in >Bio.WWW. > >Hope this helps! >Brad >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython From aaron at ocelot-atroxen.dyndns.org Tue Aug 3 15:42:57 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Tue Aug 3 15:44:15 2004 Subject: [BioPython] FASTA parsing errors Message-ID: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> I've sent a couple messages to the list about this but I'm not sure if they're going through as I haven't seen any replies. I am trying to get a section of my code that worked before the 1.30 revision of biopython, based on the cookbook tutorials. My code looks up a gene by name in genbank and saves the FASTA version of that data so that the protein string can be fed into a BLAST search. The lookup works fine and I get a FASTA file saved just fine, however I then get an error at the parse stage at character 0 of the file. Any help would be greatly appreciated thanks Aaron Zschau #file_for_blast = open(data_path_prefix + file_unique_id + 'fasta', 'r') 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() ----------------------- iterator created Traceback (most recent call last): File "cluster-debug.py", line 119, 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) From jeffrey_chang at stanfordalumni.org Tue Aug 3 16:23:33 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Tue Aug 3 16:24:50 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> Message-ID: Hi Aaron, Can you send the file that is generating the error? I believe it is called /var/www/html/data/a12345.fasta. In general, the fasta parser should be well-tested. It works on a test file in fasta format that I have here. It would help most if someone could look at your file to see what's going on. Thanks, Jeff On Aug 3, 2004, at 3:42 PM, Aaron Zschau wrote: > I've sent a couple messages to the list about this but I'm not sure if > they're going through as I haven't seen any replies. I am trying to > get a section of my code that worked before the 1.30 revision of > biopython, based on the cookbook tutorials. My code looks up a gene by > name in genbank and saves the FASTA version of that data so that the > protein string can be fed into a BLAST search. The lookup works fine > and I get a FASTA file saved just fine, however I then get an error at > the parse stage at character 0 of the file. > > Any help would be greatly appreciated > > thanks > > Aaron Zschau > > > > > > > #file_for_blast = open(data_path_prefix + file_unique_id + 'fasta', > 'r') > 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() > > ----------------------- > > iterator created > Traceback (most recent call last): > File "cluster-debug.py", line 119, 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) > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From aaron at ocelot-atroxen.dyndns.org Tue Aug 3 16:48:36 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Tue Aug 3 16:49:51 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> Message-ID: <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> This is the file that is being read. I know it worked in 1.24 just fine but maybe something changed in the versions that make it not like this format thanks, Aaron Zschau ------a12345.fasta---------- LOCUS XM_414447 2107 bp mRNA linear VRT 28-JUL-2004 DEFINITION PREDICTED: Gallus gallus similar to von Hippel-Lindau protein (LOC416117), mRNA. ACCESSION XM_414447 VERSION XM_414447.1 GI:50754623 KEYWORDS . SOURCE Gallus gallus (red jungle fowl) ORGANISM Gallus gallus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus. COMMENT MODEL REFSEQ: This record is predicted by automated computational analysis. This record is derived from an annotated genomic sequence (NW_060494) using gene prediction method: GNOMON, supported by EST evidence. Also see: Documentation of NCBI's Annotation Process FEATURES Location/Qualifiers source 1..2107 /organism="Gallus gallus" /mol_type="mRNA" /strain="inbred line UCD001" /isolate="#256" /db_xref="taxon:9031" /chromosome="12" /sex="female" /note="inbred line derived from a wild population of red jungle fowl in Malaysia in the late 1930s, with the possible introgression of a limited amount of White Leghorn genome during its captive breeding history common: red jungle fowl" gene 1..2107 /gene="LOC416117" /note="Derived by automated computational analysis using gene prediction method: GNOMON." /db_xref="GeneID:416117" /db_xref="InterimID:416117" CDS 1..486 /gene="LOC416117" /codon_start=1 /product="similar to von Hippel-Lindau protein" /protein_id="XP_414447.1" /db_xref="GI:50754624" /db_xref="GeneID:416117" /db_xref="InterimID:416117" /translation="MAPPGPGPAGPCLRSANTRELSEVVFNNRSPRAVLPIWVDFEGR PRYYPVLRPRTGRIMHSYRGHLWLFRDAGTHDGLLVNRQELFVAAPDVNKADITLPVF TLKERCLQVVRSLVRPGDYRKLDIVRSLYEELEDHPDVKKDLQRLSMERSKTLQEEIL H" misc_feature 37..453 /gene="LOC416117" /note="VHL; Region: von Hippel-Lindau disease tumour suppressor protein. VHL forms a ternary complex with the elonginB and elonginC proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor mRNA" /db_xref="CDD:pfam01847" ORIGIN 1 atggcgccgc cgggtccggg tcccgccggg ccgtgcctgc gctccgccaa cacgcgcgaa 61 ctctccgagg tcgtcttcaa caaccgcagc ccgcgcgccg tgctccccat ctgggtggac 121 ttcgagggcc ggccgcgcta ctaccccgtg ctgcggccgc gcaccgggcg gatcatgcac 181 agctaccgcg ggcacctgtg gctgttccgc gacgcgggca cgcacgacgg gctgctcgtc 241 aaccggcagg agctgttcgt ggccgcgccg gacgtcaaca aggccgacat cacgctgcca 301 gtgttcacgc tgaaggagcg gtgcctgcag gtggtgcgca gcctggtccg gccgggggac 361 taccggaagc tggacatcgt gcgctcgctg tacgaggagc tggaggacca ccccgacgtc 421 aagaaggacc tgcagcggct ctccatggag aggagcaaaa cgttacagga ggaaatcctc 481 cactaacagg gctgtgcgtc ccgagccgtg tagatagcaa agcaccgagc ttaggagggg 541 cagctgccgt gcagcgtgcc gggagctaac gtctgcatcg acgttctgga acgaactcag 601 tcatgctgta gaacatttgc tatgctggta ggtcagattc caaagagcaa acagtgtgca 661 ggaacgtact gctttgtgag ggctctgctc ccggtctcat gcactggtga gcagtgaccc 721 cagtggcctg gcacagacgg ggctcagaga agcttgcttc cgactgtttc agaacattcc 781 atagtaacac aagatttatc cgtctggagg aaatacatgc agctcagctt cctctgagtt 841 agaaagaaaa ctacatcaag ggttcactta atccagacta taaaatcagt ggcagagcag 901 caccaggttt gcttgaatga tttggttttg gcagaaattc gctctcacat gctaaattta 961 cttttgaatc acaaagcgtg gagcgtgttc atgtgagagc ttccacggtt gccttctgag 1021 ggctcggccc aaaacttctg tgctggcgga aagatgtccg taagcatttc tgtgttagcc 1081 tctgtctgtg cgttcataaa ccctcattgt agcaactctg aagctgacaa attcttacac 1141 agaacatgcc ttgaatgcct taatttgtct ttcattcctg aattcctgct tagtttatct 1201 ctagatgatg gaaccttgtc agccatatgg actgcatctt ggttttagga cccctttctg 1261 ctttgcacct ctgtgcccac accctcagct cccatagtgg tataccaagg gagcgttccc 1321 agaaggtggg tgctctgagc ctcatctttc ccttgtccca gggattggcc ttggggagca 1381 cagtccgccc aggccgctgg tgccccctga ggcacagaag ctgccccagc tgcaggcgtg 1441 gctcccccaa gcagagctgt gcttttcagc aggccagctg cacagagaga aatcatagaa 1501 tcacagaatc atacaatggc ctgggctgaa aaggaccaca atgcccatcc agttccaacc 1561 ccctgctatg tgcagggtca ccaaccagca gaccaggctg cccagagcca catccagcct 1621 ggccttgaat gcctccaggg atggggcctc cttgggcgac ctgttccaat gcatcaacac 1681 cctccaagtg aaaaacttcc tcctgatata cctgaacatc ccctgtctta tttaagatca 1741 ttcccccttg tcctgtcact atccaccctc gtgaacagct gttccccttc ctgtttatat 1801 gcttcctaaa atcaagaaag gttctaggcc tatatgttct cttcccccat acatcaaata 1861 cacaggtgtg tgtctgtatg tctctgtgca taactcaaag cagcgttgtt tttagcagat 1921 aggtgaattg ttccccaagt tgcaggcagg cgcagtgctg ctcagcatgc agagcagcag 1981 gttgctaaca gatagcagca ggctgttctg tggtgtaagg ttcttaagta tgcaatgtgt 2041 gcccttctcg tggacttttt ttttcttaaa tgtttgtgta tgaactgatc tttgtttctc 2101 ataaaaa // ------end file---------- On Aug 3, 2004, at 4:23 PM, Jeffrey Chang wrote: > Hi Aaron, > > Can you send the file that is generating the error? I believe it is > called /var/www/html/data/a12345.fasta. In general, the fasta parser > should be well-tested. It works on a test file in fasta format that I > have here. It would help most if someone could look at your file to > see what's going on. > > Thanks, > Jeff > > > On Aug 3, 2004, at 3:42 PM, Aaron Zschau wrote: > >> I've sent a couple messages to the list about this but I'm not sure >> if they're going through as I haven't seen any replies. I am trying >> to get a section of my code that worked before the 1.30 revision of >> biopython, based on the cookbook tutorials. My code looks up a gene >> by name in genbank and saves the FASTA version of that data so that >> the protein string can be fed into a BLAST search. The lookup works >> fine and I get a FASTA file saved just fine, however I then get an >> error at the parse stage at character 0 of the file. >> >> Any help would be greatly appreciated >> >> thanks >> >> Aaron Zschau >> >> >> >> >> >> >> #file_for_blast = open(data_path_prefix + file_unique_id + 'fasta', >> 'r') >> 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() >> >> ----------------------- >> >> iterator created >> Traceback (most recent call last): >> File "cluster-debug.py", line 119, 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) >> >> _______________________________________________ >> BioPython mailing list - BioPython@biopython.org >> http://biopython.org/mailman/listinfo/biopython > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From jonathan.taylor at utoronto.ca Tue Aug 3 17:01:50 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Tue Aug 3 17:03:13 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> Message-ID: <1091566910.20811.4.camel@nostromo> Hi, I don't think that file conforms to the fasta format: see http://ngfnblast.gbf.de/docs/fasta.html I could be wrong though. Jon Taylor. On Tue, 2004-08-03 at 16:48, Aaron Zschau wrote: > This is the file that is being read. I know it worked in 1.24 just fine > but maybe something changed in the versions that make it not like this > format > > > thanks, > > Aaron Zschau > > ------a12345.fasta---------- > > > LOCUS XM_414447 2107 bp mRNA linear VRT > 28-JUL-2004 > DEFINITION PREDICTED: Gallus gallus similar to von Hippel-Lindau > protein > (LOC416117), mRNA. > ACCESSION XM_414447 > VERSION XM_414447.1 GI:50754623 > KEYWORDS . > SOURCE Gallus gallus (red jungle fowl) > ORGANISM Gallus gallus > Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; > Euteleostomi; > Archosauria; Aves; Neognathae; Galliformes; Phasianidae; > Phasianinae; Gallus. > COMMENT MODEL REFSEQ: This record is predicted by automated > computational > analysis. This record is derived from an annotated genomic > sequence > (NW_060494) using gene prediction method: GNOMON, supported > by EST > evidence. > Also see: > Documentation of NCBI's Annotation Process > > FEATURES Location/Qualifiers > source 1..2107 > /organism="Gallus gallus" > /mol_type="mRNA" > /strain="inbred line UCD001" > /isolate="#256" > /db_xref="taxon:9031" > /chromosome="12" > /sex="female" > /note="inbred line derived from a wild population > of red > jungle fowl in Malaysia in the late 1930s, with the > possible introgression of a limited amount of White > Leghorn genome during its captive breeding history > common: red jungle fowl" > gene 1..2107 > /gene="LOC416117" > /note="Derived by automated computational analysis > using > gene prediction method: GNOMON." > /db_xref="GeneID:416117" > /db_xref="InterimID:416117" > CDS 1..486 > /gene="LOC416117" > /codon_start=1 > /product="similar to von Hippel-Lindau protein" > /protein_id="XP_414447.1" > /db_xref="GI:50754624" > /db_xref="GeneID:416117" > /db_xref="InterimID:416117" > > /translation="MAPPGPGPAGPCLRSANTRELSEVVFNNRSPRAVLPIWVDFEGR > > PRYYPVLRPRTGRIMHSYRGHLWLFRDAGTHDGLLVNRQELFVAAPDVNKADITLPVF > > TLKERCLQVVRSLVRPGDYRKLDIVRSLYEELEDHPDVKKDLQRLSMERSKTLQEEIL > H" > misc_feature 37..453 > /gene="LOC416117" > /note="VHL; Region: von Hippel-Lindau disease > tumour > suppressor protein. VHL forms a ternary complex > with the > elonginB and elonginC proteins. This complex binds > Cul2, > which then is involved in regulation of vascular > endothelial growth factor mRNA" > /db_xref="CDD:pfam01847" > ORIGIN > 1 atggcgccgc cgggtccggg tcccgccggg ccgtgcctgc gctccgccaa > cacgcgcgaa > 61 ctctccgagg tcgtcttcaa caaccgcagc ccgcgcgccg tgctccccat > ctgggtggac > 121 ttcgagggcc ggccgcgcta ctaccccgtg ctgcggccgc gcaccgggcg > gatcatgcac > 181 agctaccgcg ggcacctgtg gctgttccgc gacgcgggca cgcacgacgg > gctgctcgtc > 241 aaccggcagg agctgttcgt ggccgcgccg gacgtcaaca aggccgacat > cacgctgcca > 301 gtgttcacgc tgaaggagcg gtgcctgcag gtggtgcgca gcctggtccg > gccgggggac > 361 taccggaagc tggacatcgt gcgctcgctg tacgaggagc tggaggacca > ccccgacgtc > 421 aagaaggacc tgcagcggct ctccatggag aggagcaaaa cgttacagga > ggaaatcctc > 481 cactaacagg gctgtgcgtc ccgagccgtg tagatagcaa agcaccgagc > ttaggagggg > 541 cagctgccgt gcagcgtgcc gggagctaac gtctgcatcg acgttctgga > acgaactcag > 601 tcatgctgta gaacatttgc tatgctggta ggtcagattc caaagagcaa > acagtgtgca > 661 ggaacgtact gctttgtgag ggctctgctc ccggtctcat gcactggtga > gcagtgaccc > 721 cagtggcctg gcacagacgg ggctcagaga agcttgcttc cgactgtttc > agaacattcc > 781 atagtaacac aagatttatc cgtctggagg aaatacatgc agctcagctt > cctctgagtt > 841 agaaagaaaa ctacatcaag ggttcactta atccagacta taaaatcagt > ggcagagcag > 901 caccaggttt gcttgaatga tttggttttg gcagaaattc gctctcacat > gctaaattta > 961 cttttgaatc acaaagcgtg gagcgtgttc atgtgagagc ttccacggtt > gccttctgag > 1021 ggctcggccc aaaacttctg tgctggcgga aagatgtccg taagcatttc > tgtgttagcc > 1081 tctgtctgtg cgttcataaa ccctcattgt agcaactctg aagctgacaa > attcttacac > 1141 agaacatgcc ttgaatgcct taatttgtct ttcattcctg aattcctgct > tagtttatct > 1201 ctagatgatg gaaccttgtc agccatatgg actgcatctt ggttttagga > cccctttctg > 1261 ctttgcacct ctgtgcccac accctcagct cccatagtgg tataccaagg > gagcgttccc > 1321 agaaggtggg tgctctgagc ctcatctttc ccttgtccca gggattggcc > ttggggagca > 1381 cagtccgccc aggccgctgg tgccccctga ggcacagaag ctgccccagc > tgcaggcgtg > 1441 gctcccccaa gcagagctgt gcttttcagc aggccagctg cacagagaga > aatcatagaa > 1501 tcacagaatc atacaatggc ctgggctgaa aaggaccaca atgcccatcc > agttccaacc > 1561 ccctgctatg tgcagggtca ccaaccagca gaccaggctg cccagagcca > catccagcct > 1621 ggccttgaat gcctccaggg atggggcctc cttgggcgac ctgttccaat > gcatcaacac > 1681 cctccaagtg aaaaacttcc tcctgatata cctgaacatc ccctgtctta > tttaagatca > 1741 ttcccccttg tcctgtcact atccaccctc gtgaacagct gttccccttc > ctgtttatat > 1801 gcttcctaaa atcaagaaag gttctaggcc tatatgttct cttcccccat > acatcaaata > 1861 cacaggtgtg tgtctgtatg tctctgtgca taactcaaag cagcgttgtt > tttagcagat > 1921 aggtgaattg ttccccaagt tgcaggcagg cgcagtgctg ctcagcatgc > agagcagcag > 1981 gttgctaaca gatagcagca ggctgttctg tggtgtaagg ttcttaagta > tgcaatgtgt > 2041 gcccttctcg tggacttttt ttttcttaaa tgtttgtgta tgaactgatc > tttgtttctc > 2101 ataaaaa > // > > > ------end file---------- > On Aug 3, 2004, at 4:23 PM, Jeffrey Chang wrote: > > > Hi Aaron, > > > > Can you send the file that is generating the error? I believe it is > > called /var/www/html/data/a12345.fasta. In general, the fasta parser > > should be well-tested. It works on a test file in fasta format that I > > have here. It would help most if someone could look at your file to > > see what's going on. > > > > Thanks, > > Jeff > > > > > > On Aug 3, 2004, at 3:42 PM, Aaron Zschau wrote: > > > >> I've sent a couple messages to the list about this but I'm not sure > >> if they're going through as I haven't seen any replies. I am trying > >> to get a section of my code that worked before the 1.30 revision of > >> biopython, based on the cookbook tutorials. My code looks up a gene > >> by name in genbank and saves the FASTA version of that data so that > >> the protein string can be fed into a BLAST search. The lookup works > >> fine and I get a FASTA file saved just fine, however I then get an > >> error at the parse stage at character 0 of the file. > >> > >> Any help would be greatly appreciated > >> > >> thanks > >> > >> Aaron Zschau > >> > >> > >> > >> > >> > >> > >> #file_for_blast = open(data_path_prefix + file_unique_id + 'fasta', > >> 'r') > >> 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() > >> > >> ----------------------- > >> > >> iterator created > >> Traceback (most recent call last): > >> File "cluster-debug.py", line 119, 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) > >> > >> _______________________________________________ > >> BioPython mailing list - BioPython@biopython.org > >> http://biopython.org/mailman/listinfo/biopython > > > > _______________________________________________ > > BioPython mailing list - BioPython@biopython.org > > http://biopython.org/mailman/listinfo/biopython > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From aaron at ocelot-atroxen.dyndns.org Tue Aug 3 17:50:57 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Tue Aug 3 17:52:14 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: <0ACD89E3-E591-11D8-BA05-000A956845CE@stanfordalumni.org> References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> <0ACD89E3-E591-11D8-BA05-000A956845CE@stanfordalumni.org> Message-ID: <33C1FB74-E597-11D8-BC35-003065706E3A@atroxen.com> That parsed just fine and I'm getting output now, however I'm now having trouble figuring out how to extract the protein sequence from this record. Looking at the API for the Record class, there isn't a nice clear 'protein' attribute the way that 'sequence' is. Do you have any recommendations on how I would access that part of the Record? thanks for your help so far, Aaron On Aug 3, 2004, at 5:06 PM, Jeffrey Chang wrote: > Hi Aaron, > > This looks like a Genbank format file, so try using the Genbank parser > by doing something like (untested code): > from Bio import GenBank > parser = GenBank.RecordParser() > rec = parser.parse(open('/var/www/html/data/a12345.fasta','r')) > print rec.sequence > > Also, for future reference, please send samples of files as an > attachment rather than as part of the email. Many email clients > change the text (for example, wrapping long lines) so that it is no > longer parseable by Biopython. Thus, I was not able to check to make > sure that the Genbank parser can handle this file correctly. :) > > Jeff > > > On Aug 3, 2004, at 4:48 PM, Aaron Zschau wrote: > >> This is the file that is being read. I know it worked in 1.24 just >> fine but maybe something changed in the versions that make it not >> like this format >> >> >> thanks, >> >> Aaron Zschau >> >> ------a12345.fasta---------- >> >> >> LOCUS XM_414447 2107 bp mRNA linear VRT >> 28-JUL-2004 >> DEFINITION PREDICTED: Gallus gallus similar to von Hippel-Lindau >> protein >> (LOC416117), mRNA. >> ACCESSION XM_414447 >> VERSION XM_414447.1 GI:50754623 >> KEYWORDS . >> SOURCE Gallus gallus (red jungle fowl) >> ORGANISM Gallus gallus >> Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; >> Euteleostomi; >> Archosauria; Aves; Neognathae; Galliformes; Phasianidae; >> Phasianinae; Gallus. >> COMMENT MODEL REFSEQ: This record is predicted by automated >> computational >> analysis. This record is derived from an annotated >> genomic sequence >> (NW_060494) using gene prediction method: GNOMON, >> supported by EST >> evidence. >> Also see: >> Documentation of NCBI's Annotation Process >> >> FEATURES Location/Qualifiers >> source 1..2107 >> /organism="Gallus gallus" >> /mol_type="mRNA" >> /strain="inbred line UCD001" >> /isolate="#256" >> /db_xref="taxon:9031" >> /chromosome="12" >> /sex="female" >> /note="inbred line derived from a wild >> population of red >> jungle fowl in Malaysia in the late 1930s, with >> the >> possible introgression of a limited amount of >> White >> Leghorn genome during its captive breeding >> history >> common: red jungle fowl" >> gene 1..2107 >> /gene="LOC416117" >> /note="Derived by automated computational >> analysis using >> gene prediction method: GNOMON." >> /db_xref="GeneID:416117" >> /db_xref="InterimID:416117" >> CDS 1..486 >> /gene="LOC416117" >> /codon_start=1 >> /product="similar to von Hippel-Lindau protein" >> /protein_id="XP_414447.1" >> /db_xref="GI:50754624" >> /db_xref="GeneID:416117" >> /db_xref="InterimID:416117" >> >> /translation="MAPPGPGPAGPCLRSANTRELSEVVFNNRSPRAVLPIWVDFEGR >> >> PRYYPVLRPRTGRIMHSYRGHLWLFRDAGTHDGLLVNRQELFVAAPDVNKADITLPVF >> >> TLKERCLQVVRSLVRPGDYRKLDIVRSLYEELEDHPDVKKDLQRLSMERSKTLQEEIL >> H" >> misc_feature 37..453 >> /gene="LOC416117" >> /note="VHL; Region: von Hippel-Lindau disease >> tumour >> suppressor protein. VHL forms a ternary complex >> with the >> elonginB and elonginC proteins. This complex >> binds Cul2, >> which then is involved in regulation of vascular >> endothelial growth factor mRNA" >> /db_xref="CDD:pfam01847" >> ORIGIN >> 1 atggcgccgc cgggtccggg tcccgccggg ccgtgcctgc gctccgccaa >> cacgcgcgaa >> 61 ctctccgagg tcgtcttcaa caaccgcagc ccgcgcgccg tgctccccat >> ctgggtggac >> 121 ttcgagggcc ggccgcgcta ctaccccgtg ctgcggccgc gcaccgggcg >> gatcatgcac >> 181 agctaccgcg ggcacctgtg gctgttccgc gacgcgggca cgcacgacgg >> gctgctcgtc >> 241 aaccggcagg agctgttcgt ggccgcgccg gacgtcaaca aggccgacat >> cacgctgcca >> 301 gtgttcacgc tgaaggagcg gtgcctgcag gtggtgcgca gcctggtccg >> gccgggggac >> 361 taccggaagc tggacatcgt gcgctcgctg tacgaggagc tggaggacca >> ccccgacgtc >> 421 aagaaggacc tgcagcggct ctccatggag aggagcaaaa cgttacagga >> ggaaatcctc >> 481 cactaacagg gctgtgcgtc ccgagccgtg tagatagcaa agcaccgagc >> ttaggagggg >> 541 cagctgccgt gcagcgtgcc gggagctaac gtctgcatcg acgttctgga >> acgaactcag >> 601 tcatgctgta gaacatttgc tatgctggta ggtcagattc caaagagcaa >> acagtgtgca >> 661 ggaacgtact gctttgtgag ggctctgctc ccggtctcat gcactggtga >> gcagtgaccc >> 721 cagtggcctg gcacagacgg ggctcagaga agcttgcttc cgactgtttc >> agaacattcc >> 781 atagtaacac aagatttatc cgtctggagg aaatacatgc agctcagctt >> cctctgagtt >> 841 agaaagaaaa ctacatcaag ggttcactta atccagacta taaaatcagt >> ggcagagcag >> 901 caccaggttt gcttgaatga tttggttttg gcagaaattc gctctcacat >> gctaaattta >> 961 cttttgaatc acaaagcgtg gagcgtgttc atgtgagagc ttccacggtt >> gccttctgag >> 1021 ggctcggccc aaaacttctg tgctggcgga aagatgtccg taagcatttc >> tgtgttagcc >> 1081 tctgtctgtg cgttcataaa ccctcattgt agcaactctg aagctgacaa >> attcttacac >> 1141 agaacatgcc ttgaatgcct taatttgtct ttcattcctg aattcctgct >> tagtttatct >> 1201 ctagatgatg gaaccttgtc agccatatgg actgcatctt ggttttagga >> cccctttctg >> 1261 ctttgcacct ctgtgcccac accctcagct cccatagtgg tataccaagg >> gagcgttccc >> 1321 agaaggtggg tgctctgagc ctcatctttc ccttgtccca gggattggcc >> ttggggagca >> 1381 cagtccgccc aggccgctgg tgccccctga ggcacagaag ctgccccagc >> tgcaggcgtg >> 1441 gctcccccaa gcagagctgt gcttttcagc aggccagctg cacagagaga >> aatcatagaa >> 1501 tcacagaatc atacaatggc ctgggctgaa aaggaccaca atgcccatcc >> agttccaacc >> 1561 ccctgctatg tgcagggtca ccaaccagca gaccaggctg cccagagcca >> catccagcct >> 1621 ggccttgaat gcctccaggg atggggcctc cttgggcgac ctgttccaat >> gcatcaacac >> 1681 cctccaagtg aaaaacttcc tcctgatata cctgaacatc ccctgtctta >> tttaagatca >> 1741 ttcccccttg tcctgtcact atccaccctc gtgaacagct gttccccttc >> ctgtttatat >> 1801 gcttcctaaa atcaagaaag gttctaggcc tatatgttct cttcccccat >> acatcaaata >> 1861 cacaggtgtg tgtctgtatg tctctgtgca taactcaaag cagcgttgtt >> tttagcagat >> 1921 aggtgaattg ttccccaagt tgcaggcagg cgcagtgctg ctcagcatgc >> agagcagcag >> 1981 gttgctaaca gatagcagca ggctgttctg tggtgtaagg ttcttaagta >> tgcaatgtgt >> 2041 gcccttctcg tggacttttt ttttcttaaa tgtttgtgta tgaactgatc >> tttgtttctc >> 2101 ataaaaa >> // >> >> >> ------end file---------- >> On Aug 3, 2004, at 4:23 PM, Jeffrey Chang wrote: >> >>> Hi Aaron, >>> >>> Can you send the file that is generating the error? I believe it is >>> called /var/www/html/data/a12345.fasta. In general, the fasta >>> parser should be well-tested. It works on a test file in fasta >>> format that I have here. It would help most if someone could look >>> at your file to see what's going on. >>> >>> Thanks, >>> Jeff >>> >>> >>> On Aug 3, 2004, at 3:42 PM, Aaron Zschau wrote: >>> >>>> I've sent a couple messages to the list about this but I'm not sure >>>> if they're going through as I haven't seen any replies. I am >>>> trying to get a section of my code that worked before the 1.30 >>>> revision of biopython, based on the cookbook tutorials. My code >>>> looks up a gene by name in genbank and saves the FASTA version of >>>> that data so that the protein string can be fed into a BLAST >>>> search. The lookup works fine and I get a FASTA file saved just >>>> fine, however I then get an error at the parse stage at character 0 >>>> of the file. >>>> >>>> Any help would be greatly appreciated >>>> >>>> thanks >>>> >>>> Aaron Zschau >>>> >>>> >>>> >>>> >>>> >>>> >>>> #file_for_blast = open(data_path_prefix + file_unique_id + 'fasta', >>>> 'r') >>>> 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() >>>> >>>> ----------------------- >>>> >>>> iterator created >>>> Traceback (most recent call last): >>>> File "cluster-debug.py", line 119, 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) >>>> >>>> _______________________________________________ >>>> BioPython mailing list - BioPython@biopython.org >>>> http://biopython.org/mailman/listinfo/biopython >>> >>> _______________________________________________ >>> BioPython mailing list - BioPython@biopython.org >>> http://biopython.org/mailman/listinfo/biopython >> From chapmanb at uga.edu Tue Aug 3 18:26:28 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Aug 3 18:28:29 2004 Subject: [BioPython] BioEutils In-Reply-To: <6.0.3.0.0.20040803130152.01b89c50@pop.videotron.ca> References: <200408031522.44704.thamelry@binf.ku.dk> <6.0.3.0.0.20040803105648.01af57d0@pop.videotron.ca> <6.0.3.0.0.20040803110558.01b1c4d0@pop.videotron.ca> <20040803162435.GA93656@lebowski.bos.east.verizon.net> <6.0.3.0.0.20040803124313.01b11c50@pop.videotron.ca> <6.0.3.0.0.20040803130152.01b89c50@pop.videotron.ca> Message-ID: <20040803222628.GN93656@lebowski.bos.east.verizon.net> Hi Peter; [Using EUtils] > I dont seem to be getting any of the EUtils to work. [...] > NCBI changing things around so the EUtils packages breaks? Yes, that looks to be the case. Thanks for providing the examples of things that weren't working. I went through and updated EUtils with some testing code, and think I have all your problems fixed. If you could update EUtils from CVS and test that would be very helpful. The major changes are in Bio/EUtils/ThinClient.py and Bio/EUtils/parse.py. > I would like to look up records for image clones like: > > clone = client.search("IMAGE:624360",db="nucleotide") > > This would be the way I look for a clone in the nucleotide set using the > search field on the root of the ncbi homepage. I know that this clone is > in nucleotide, but this query does not work here, I get a result of length > = 0. The problem here is that you can't use colons within queries, because Entrez treats them as a range operation. There might be a way to escape them, but I don't know of it. The easiest way, which seems to work fine, is to leave out the colon in your search: >>> from Bio.EUtils import HistoryClient >>> client = HistoryClient.HistoryClient() >>> clone = client.search("IMAGE 624360",db="nucleotide") >>> len(clone) 2 > clone = client.search("AA759046",db="nucleotide") > > however I get the following error > > Traceback (most recent call last): > raise IndexError, "no item matches" > IndexError: no item matches. This search is fine, but this was an internal error which is now fixed in the changes in CVS. > >>> result = client.search("dalke", retmax = 100) > > Traceback (most recent call last): > raise TypeError("Unknown OP code: %r" % (s,)) > TypeError: Unknown OP code: u'GROUP' This was a change in what NCBI was returning. It should now handle this just fine. I also fixed a few other bugs I came across in the process. Sorry about the problems. I appreciate you testing this, and hope the new code works better for you. Brad From chapmanb at uga.edu Tue Aug 3 18:26:36 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Aug 3 18:28:39 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: <1091566910.20811.4.camel@nostromo> References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> <1091566910.20811.4.camel@nostromo> Message-ID: <20040803222636.GO93656@lebowski.bos.east.verizon.net> Hi Aaron; Aaron: > > This is the file that is being read. I know it worked in 1.24 just fine > > but maybe something changed in the versions that make it not like this > > format > > > > LOCUS XM_414447 2107 bp mRNA linear VRT [....] Jon: > I don't think that file conforms to the fasta format: > see http://ngfnblast.gbf.de/docs/fasta.html > I could be wrong though. Right. That's a GenBank file, which is why the Fasta parser is choking on it (the error message should be a lot nicer, for sure). You have two options: 1. Use a GenBank parser. 2. Retrieve Fasta sequences. Going from the code you posted previously, you could retrieve your search in FASTA format with the following: from Bio import GenBank from Bio import Fasta ncbi_dict = GenBank.NCBIDictionary("nucleotide", "fasta", Fasta.RecordParser()) seqrecord = ncbi_dict["6273291"] genbank_file = open(data_path_prefix + file_unique_id + 'fasta', 'w') genbank_file.write(seqrecord + "\n") genbank_file.close() This may have changed with the most recent release because the default for GenBank retrieval used to be fasta. Because of changes at NCBI this had to be updated, and I believe now defaults to GenBank. So, if you didn't specify "fasta" as the second argument, that's probably now why you are getting GenBank data. Hopefully this small change in your code will fix everything. Hope this helps. Brad From aaron at ocelot-atroxen.dyndns.org Tue Aug 3 18:50:28 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Tue Aug 3 18:51:43 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: <20040803222636.GO93656@lebowski.bos.east.verizon.net> References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> <1091566910.20811.4.camel@nostromo> <20040803222636.GO93656@lebowski.bos.east.verizon.net> Message-ID: <83CC67AB-E59F-11D8-BC35-003065706E3A@atroxen.com> That was the answer I was looking for, I figured something small had changed with the new version and the defaulting to FASTA no longer being the case was what was throwing things off. I have to sort out some new errors now but this definitely got me going along on my way. thanks much for the detailed reply. Aaron Zschau On Aug 3, 2004, at 6:26 PM, Brad Chapman wrote: > Hi Aaron; > > Aaron: >>> This is the file that is being read. I know it worked in 1.24 just >>> fine >>> but maybe something changed in the versions that make it not like >>> this >>> format >>> >>> LOCUS XM_414447 2107 bp mRNA linear VRT > [....] > > Jon: >> I don't think that file conforms to the fasta format: >> see http://ngfnblast.gbf.de/docs/fasta.html >> I could be wrong though. > > Right. That's a GenBank file, which is why the Fasta parser is > choking on it (the error message should be a lot nicer, for sure). > > You have two options: > > 1. Use a GenBank parser. > > 2. Retrieve Fasta sequences. Going from the code you posted > previously, you could retrieve your search in FASTA format with the > following: > > from Bio import GenBank > from Bio import Fasta > > ncbi_dict = GenBank.NCBIDictionary("nucleotide", "fasta", > Fasta.RecordParser()) > > seqrecord = ncbi_dict["6273291"] > > genbank_file = open(data_path_prefix + file_unique_id + 'fasta', > 'w') > genbank_file.write(seqrecord + "\n") > genbank_file.close() > > This may have changed with the most recent release because the > default for GenBank retrieval used to be fasta. Because of changes > at NCBI this had to be updated, and I believe now defaults to > GenBank. So, if you didn't specify "fasta" as the second argument, > that's probably now why you are getting GenBank data. Hopefully this > small change in your code will fix everything. > > Hope this helps. > Brad > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From aaron at ocelot-atroxen.dyndns.org Tue Aug 3 19:15:19 2004 From: aaron at ocelot-atroxen.dyndns.org (Aaron Zschau) Date: Tue Aug 3 19:16:38 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: <20040803222636.GO93656@lebowski.bos.east.verizon.net> References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> <1091566910.20811.4.camel@nostromo> <20040803222636.GO93656@lebowski.bos.east.verizon.net> Message-ID: I seem to still have a problem with the results I'm getting, I need a protein sequence in order to do a BLAST search with the data from my genbank lookup, however the FASTA file created now just contains the nucleotide. I tried the following line: ncbi_dict = GenBank.NCBIDictionary("protein", "fasta", Fasta.RecordParser()) thinking that possibly changing "nucleotide" to "protein" in your original recommendation would help things but I still get the following results which are not in protein sequence form: >gi|6273291|gb|AF191665.1|AF191665 Opuntia marenae rpl16 gene; chloroplast gene for chloroplast product, partial intron sequence TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAAAAAAATGAAT CTAAATGATATAGGATTCCACTATGTAAGGTCTTTGAATCATATCATAAAAGACAATGTA ATAAAGCATGAATACAGATTCACACATAATTATCTGATATGAATCTATTCATAGAAAAAA GAAAAAAGTAAGAGCCTCCGGCCAATAAAGACTAAGAGGGTTGGCTCAAGAACAAAGTTC ATTAAGAGCTCCATTGTAGAATTCAGACCTAATCATTAATCAAGAAGCGATGGGAACGAT GTAATCCATGAATACAGAAGATTCAATTGAAAAAGATCCTATGNTCATTGGAAGGATGGC GGAACGAACCAGAGACCAATTCATCTATTCTGAAAAGTGATAAACTAATCCTATAAAACT AAAATAGATATTGAAAGAGTAAATATTCGCCCGCGAAAATTCCTTTTTTATTAAATTGCT CATATTTTCTTTTAGCAATGCAATCTAATAAAATATATCTATACAAAAAAACATAGACAA ACTATATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAA TATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTATTATTAAATGTAT ATATTAATTCAATATTATTATTCTATTCATTTTTATTCATTTTCAAATTTATAATATATT AATCTATATATTAATTTAGAATTCTATTCTAATTCGAATTCAATTTTTAAATATTCATAT TCAATTAAAATTGAAATTTTTTCATTCGCGAGGAGCCGGATGAGAAGAAACTCTCATGTC CGGTTCTGTAGTAGAGATGGAATTAAGAAAAAACCATCAACTATAACCCCAAAAGAACCA GA thanks, Aaron Zschau On Aug 3, 2004, at 6:26 PM, Brad Chapman wrote: > Hi Aaron; > > Aaron: >>> This is the file that is being read. I know it worked in 1.24 just >>> fine >>> but maybe something changed in the versions that make it not like >>> this >>> format >>> >>> LOCUS XM_414447 2107 bp mRNA linear VRT > [....] > > Jon: >> I don't think that file conforms to the fasta format: >> see http://ngfnblast.gbf.de/docs/fasta.html >> I could be wrong though. > > Right. That's a GenBank file, which is why the Fasta parser is > choking on it (the error message should be a lot nicer, for sure). > > You have two options: > > 1. Use a GenBank parser. > > 2. Retrieve Fasta sequences. Going from the code you posted > previously, you could retrieve your search in FASTA format with the > following: > > from Bio import GenBank > from Bio import Fasta > > ncbi_dict = GenBank.NCBIDictionary("nucleotide", "fasta", > Fasta.RecordParser()) > > seqrecord = ncbi_dict["6273291"] > > genbank_file = open(data_path_prefix + file_unique_id + 'fasta', > 'w') > genbank_file.write(seqrecord + "\n") > genbank_file.close() > > This may have changed with the most recent release because the > default for GenBank retrieval used to be fasta. Because of changes > at NCBI this had to be updated, and I believe now defaults to > GenBank. So, if you didn't specify "fasta" as the second argument, > that's probably now why you are getting GenBank data. Hopefully this > small change in your code will fix everything. > > Hope this helps. > Brad > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From chapmanb at uga.edu Wed Aug 4 09:26:26 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Aug 4 09:28:42 2004 Subject: [BioPython] FASTA parsing errors In-Reply-To: References: <51C20F6A-E585-11D8-BC35-003065706E3A@atroxen.com> <7DF823E6-E58E-11D8-BC35-003065706E3A@atroxen.com> <1091566910.20811.4.camel@nostromo> <20040803222636.GO93656@lebowski.bos.east.verizon.net> Message-ID: <20040804132626.GP93656@lebowski.bos.east.verizon.net> Hi Aaron; [Retrieval from NCBI] > I seem to still have a problem with the results I'm getting, I need a > protein sequence in order to do a BLAST search with the data from my > genbank lookup, however the FASTA file created now just contains the > nucleotide. I tried the following line: > > ncbi_dict = GenBank.NCBIDictionary("protein", "fasta", > Fasta.RecordParser()) > > thinking that possibly changing "nucleotide" to "protein" in your > original recommendation would help things but I still get the following > results which are not in protein sequence form: > > >gi|6273291|gb|AF191665.1|AF191665 Opuntia marenae rpl16 gene; > chloroplast gene for chloroplast product, partial intron sequence > TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAAAAAAATGAAT [...] You are are still retrieving with a nucleotide GenBank ID. If you want protein sequence, you need to use a protein GI number. This is just a handy interface to what NCBI provides, so no magic is going on at all -- you just get what you ask for. If there is available protein sequence for the specific similarity searches you are trying to do, retrieving with their protein GI numbers will work. If protein is not available, your best bet is to use one of the translated BLAST search programs (blastx, tblastx). [Parsing GenBank records] > That parsed just fine and I'm getting output now, however I'm now > having trouble figuring out how to extract the protein sequence from > this record. Looking at the API for the Record class, there isn't a > nice clear 'protein' attribute the way that 'sequence' is. Do you have > any recommendations on how I would access that part of the Record? 'sequence' is the protein sequence, provided that you are dealing with a GenBank protein record. If you are talking about doing translations, then this is something that isn't done automatically. Biopython can't know whether this is coding sequence, if it is in the right frame, and so on. If you know all this, then you can translate the DNA sequence yourself: >>> from Bio import Translate >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> dna = Seq("GACTAGCCC", IUPAC.unambiguous_dna) >>> translator = Translate.unambiguous_dna_by_name["Standard"] >>> prot = translator.translate(dna) >>> prot Seq('D*P', HasStopCodon(IUPACProtein(), '*')) Hope this helps. Brad From chapmanb at uga.edu Wed Aug 4 09:32:15 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Aug 4 09:34:22 2004 Subject: [BioPython] bug in DatabaseRemover class. In-Reply-To: <32942.157.92.27.121.1090955930.squirrel@webmail.dc.uba.ar> References: <32942.157.92.27.121.1090955930.squirrel@webmail.dc.uba.ar> Message-ID: <20040804133215.GR93656@lebowski.bos.east.verizon.net> Hi Cristian; > 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,)) Thanks for the bug report. This is fixed in CVS. Much appreciated! Brad From pwilkinson at videotron.ca Wed Aug 4 13:35:26 2004 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Wed Aug 4 13:36:58 2004 Subject: [BioPython] BioEutils Message-ID: <6.0.3.0.0.20040804133444.01b923d8@pop.videotron.ca> This apparently did not get to the list, I did not reply-all. Hi Brad, I really appreciate your efforts. And by the way I can never be disappointed with biopython modules that have problems, especially the ones you write, you are always supporting them well. I will load the module from the public CVS and try again. If I come across how to escape the ":" I will let you know. I have looked through the code and it looks like a massive work. I would like to know your approach to planning a module like this and what is the way in which you cycle through coding and testing? I try to plan with one or two diagrams (and I mean a few, as one can get wrapped up in making pretty pictures), then try to use more of an extreme programming approach (not strictly as some might want), except I am coding as 1. I am interesting in knowing how you plan your project before coding. Peter At 06:26 PM 8/3/2004, you wrote: >Hi Peter; > >[Using EUtils] > > I dont seem to be getting any of the EUtils to work. >[...] > > NCBI changing things around so the EUtils packages breaks? > >Yes, that looks to be the case. Thanks for providing the examples of >things that weren't working. I went through and updated EUtils with >some testing code, and think I have all your problems fixed. If you >could update EUtils from CVS and test that would be very helpful. >The major changes are in Bio/EUtils/ThinClient.py and >Bio/EUtils/parse.py. > > > I would like to look up records for image clones like: > > > > clone = client.search("IMAGE:624360",db="nucleotide") > > > > This would be the way I look for a clone in the nucleotide set using the > > search field on the root of the ncbi homepage. I know that this clone is > > in nucleotide, but this query does not work here, I get a result of length > > = 0. > >The problem here is that you can't use colons within queries, >because Entrez treats them as a range operation. There might be a >way to escape them, but I don't know of it. The easiest way, which >seems to work fine, is to leave out the colon in your search: > > >>> from Bio.EUtils import HistoryClient > >>> client = HistoryClient.HistoryClient() > >>> clone = client.search("IMAGE 624360",db="nucleotide") > >>> len(clone) >2 > > > clone = client.search("AA759046",db="nucleotide") > > > > however I get the following error > > > > Traceback (most recent call last): > > raise IndexError, "no item matches" > > IndexError: no item matches. > >This search is fine, but this was an internal error which is now >fixed in the changes in CVS. > > > >>> result = client.search("dalke", retmax = 100) > > > > Traceback (most recent call last): > > raise TypeError("Unknown OP code: %r" % (s,)) > > TypeError: Unknown OP code: u'GROUP' > >This was a change in what NCBI was returning. It should now handle >this just fine. > >I also fixed a few other bugs I came across in the process. Sorry >about the problems. I appreciate you testing this, and hope the new >code works better for you. > >Brad >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython From dionnepinnock at myfolsom.com Wed Aug 4 14:52:44 2004 From: dionnepinnock at myfolsom.com (alan eiser) Date: Wed Aug 4 14:20:42 2004 Subject: [BioPython] :)) fw: moisture therapy for your skin Message-ID: <179A593F.55EAD2C@myfolsom.com> alkoholisasie`zacherl-mtrmordellidae'smwk_ehinger start feeling better today. overn_itedelivery! aans? jrcyrus ziehen http://lwmmg.vxk.feminine2966biz.us/f74/ -----Original Message----- From: Angelena Carpenter [mailto:cxjer@evhxho.com] To: diego heyward; angelo mcmahan; thurman aiello Sent: Friday, July, 2004 5:02 PM Subject: fw: moisture therapy for your skin Fatality was not significantly different Failures were significantly more common with combination therapy Among all trials we found no evidence for any potential prevention of infection by resistant isolates with combination therapy vestuario11susoaya`15jerez,acates tascador. 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Although O E M software does not come with a box or a manual, it is the typical and actual software, no trial or demo versions. http://www.lookoo.biz/ RedHat Linux 9.0 Retail price: $79.99 Our low Price: $60.00 You Save: $19.99 Adobe Photoshop CS V 8.0 PC Retail price: $609.99 Our low Price: $80.00 You Save: $529.99 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 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 Symantec Norton Antivirus 2004 Professional Retail price: $69.95 Our low Price: $15.00 You Save: $54.95 or site is http://www.lookoo.biz/ From kai-yuen at bkkmail.com Wed Aug 11 15:30:46 2004 From: kai-yuen at bkkmail.com (annette) Date: Wed Aug 11 15:44:22 2004 Subject: [BioPython] =?windows-1251?b?0eDs4P8g5OX45eLg/yDw5err4OzgIOIg?= =?windows-1251?b?0eXy6A==?= Message-ID: <200408111944.i7BJi5Kr001823@portal.open-bio.org> ???????????????? ???????? ????? ?????????? ?? ??????????? ????? ? ??? ????????????? ??????. ???????????? ?????? ?????????. ???????? ????????. ??????, ???????, ??????? ?? ???????? (095) 995-1865 From sameet at nccs.res.in Thu Aug 12 02:32:43 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Thu Aug 12 02:40:40 2004 Subject: [BioPython] Regarding GenBank Message-ID: <20040812060815.M70982@linux.nccs.res.in> Hi all, I am getting strange problems with the indexing of the GenBank file. Is there any upper limit on the size of GenBank file that can be indexed. I am sending the commands i typed on the IDLE and the trace that i got back. I know that the Genbank files are fine because i downloaded it directly from the net >>> from Bio import GenBank >>> dict_file = r'C:\Sameet\correspondence\genbank.gb' >>> index_file = r'C:\Sameet\correspondence\genbank.idx' >>> GenBank.index_file(dict_file, index_file) This is the trace that i get. Am i doing something wrong Traceback (most recent call last): File "", line 1, in -toplevel- GenBank.index_file(dict_file, index_file) File "C:\Python23\Lib\site-packages\Bio\GenBank\__init__.py", line 1283, in index_file SimpleSeqRecord.create_flatdb([filename], indexname, indexer) File "C:\Python23\Lib\site-packages\Bio\Mindy\SimpleSeqRecord.py", line 152, in create_flatdb creator.load(filename, builder = builder, fileid_info = {}) File "C:\Python23\Lib\site-packages\Bio\Mindy\BaseDB.py", line 52, in load for record in iterator.iterate(source, cont_handler = builder): File "C:\Python23\Lib\site-packages\Martel\IterParser.py", line 76, in iterateFile self.record_parser.parseString(rec) File "C:\Python23\Lib\site-packages\Martel\Parser.py", line 356, in parseString self._err_handler.fatalError(result) File "C:\Python23\lib\xml\sax\handler.py", line 38, in fatalError raise exception ParserPositionException: error parsing at or beyond character 1843 Is there any bug? regards Sameet -- National Centre for Cell Science, Pune From anand at hut.nl Thu Aug 12 13:03:54 2004 From: anand at hut.nl (anand@hut.nl) Date: Thu Aug 12 13:05:04 2004 Subject: [BioPython] software In-Reply-To: <879L3E2G0A0DAE34@biopython.org> References: <879L3E2G0A0DAE34@biopython.org> Message-ID: Adobe Illustrator 10 - 80 Macromedia Studio MX 2004 - 180 Adobe Photoshop cs - 80 Corel Draw Graphics Suite 11 - 120 Adobe Photoshop 7.0 - 60 Microsoft Office XP Professional - 100 Adobe Photoshop 7.0 - 60 Adobe Illustrator 10 - 80 Microsoft Windows 2000 Professional - 50 Windows 2000 Server - 50 and a lot more http://www.bestsoftconvert.info/ From chapmanb at 50mail.com Thu Aug 12 17:02:45 2004 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu Aug 12 17:06:59 2004 Subject: [BioPython] Regarding GenBank In-Reply-To: <20040812060815.M70982@linux.nccs.res.in> References: <20040812060815.M70982@linux.nccs.res.in> Message-ID: <20040812210245.GD65525@lebowski.bos.east.verizon.net> Hi Sameet; > I am getting strange problems with the indexing of the GenBank file. Is > there any upper limit on the size of GenBank file that can be indexed. I am > sending the commands i typed on the IDLE and the trace that i got back. I > know that the Genbank files are fine because i downloaded it directly from > the net > > >>> from Bio import GenBank > >>> dict_file = r'C:\Sameet\correspondence\genbank.gb' > >>> index_file = r'C:\Sameet\correspondence\genbank.idx' > >>> GenBank.index_file(dict_file, index_file) > > This is the trace that i get. Am i doing something wrong > > Traceback (most recent call last): [...] > ParserPositionException: error parsing at or beyond character 1843 This error just indicates that the parser is unable to parse the GenBank file. To find out the problem we're really going to need to see the genbank.gb file that you are trying to index. The parsing error indicates that it has a problem very early in the file -- can you reproduce the error with just the first record of the file? Or at the very least get it down to one or two records that show the problem? The key is to provide a minimal GenBank file that demonstrates the problem. Give this, if you could either post a bug with the file as an attachment (http://bugzilla.open-bio.org/), or send the file as an attachment to the biopython-dev list, we can take a look at see why it is failing. GenBank parsing is tricky since new records can come out all the time which break the parser, so we do need to have a look. Thanks! Brad From chapmanb at 50mail.com Thu Aug 12 18:35:29 2004 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu Aug 12 18:39:13 2004 Subject: [BioPython] BioEutils In-Reply-To: <6.0.3.0.0.20040804133444.01b923d8@pop.videotron.ca> References: <6.0.3.0.0.20040804133444.01b923d8@pop.videotron.ca> Message-ID: <20040812223529.GB82849@lebowski.bos.east.verizon.net> Hi Peter; > I really appreciate your efforts. And by the way I can never be > disappointed with biopython modules that have problems, especially the ones > you write, you are always supporting them well. I will load the module > from the public CVS and try again. If I come across how to escape the ":" I > will let you know. Thanks for the kind words. Glad it worked for you. > I have looked through the code and it looks like a massive work. I would > like to know your approach to planning a module like this and what is the > way in which you cycle through coding and testing? > > I try to plan with one or two diagrams (and I mean a few, as one can get > wrapped up in making pretty pictures), then try to use more of an extreme > programming approach (not strictly as some might want), except I am coding > as 1. I am interesting in knowing how you plan your project before coding. Actually, the EUtils module was written by Andrew Dalke -- I'm only providing the fixes -- so he could probably give you more information about his programming philosophies. As for me, I normally take the approach that you suggest. First I try to come up with the requirements and goals, as I can figure them, for a module. In this regard, I tend to be much less thorough then they teach you in programming classes (since I find too much modeling kind of boring and prefer to get to programming). In general, I just try to do the best I can to get a scope of the project and design decent objects to start with. >From there, I just program, and see what problems come up. So yeah, extreme programming. In my experience no matter how hard I try to come up with all of the requirement for my module, I'll run into bits I never thought of as I program. Or similarly, requirements change once you get into things. This will eventually require re-programming of objects to make them more flexible. In this regard, designing objects using well known design patterns often helps ease the painfulness of the rewrites and updates. Sometimes, however, you just need to scrap parts and re-code them when you find out you haven't been general enough in your design to adapt objects. Optimizing the planning and re-programming parts is the hardest part of the work, and is not something I can claim to have any kind of firm grasp on. Python is really nice in making the re-writing parts less painful, at least in my experience. As far as the testing, it ideally should be done throughout the whole process. I find it easier to get a skeleton bit working and tested and build on it from there, rather than try to code it all and then debug it with tests. Balancing the scope of the tests with the need to get the module done in some reasonable time is another bit that is tricky. Not much of a programming philosopher, but I hope this helps a bit in your designs. Brad From kael at sonic.net Thu Aug 12 18:55:25 2004 From: kael at sonic.net (Kael Fischer) Date: Thu Aug 12 18:56:25 2004 Subject: [BioPython] Regarding GenBank In-Reply-To: <20040812060815.M70982@linux.nccs.res.in> References: <20040812060815.M70982@linux.nccs.res.in> Message-ID: <6.1.1.1.2.20040812154136.03917150@pop.sonic.net> Sameet, et al: In my experience, there definitely is an upper limit on the size of the genbank file you can index, and when you go over that limit you get exactly that error. Furthermore, apropos of Brads reply, files that fail for this reason can be split and indexed fine - hence the minimal file that creates the problem is the enormous beast that crashed the parser, not any particular record or pair of records. (I have not gone back and checked this in 1.30) I believe this has been discussed on the list before. I recall that it was attributed to underlying text handling libraries, and not the GenBank module per se. You might try a smaller file or iterating though the large one, if you can get away without random access to the records. Regards, Kael At 11:32 PM 8/11/2004, Sameet Mehta wrote: >Hi all, >I am getting strange problems with the indexing of the GenBank file. Is >there any upper limit on the size of GenBank file that can be indexed. [snip] >Is there any bug? > >regards >Sameet > >-- >National Centre for Cell Science, Pune > >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython -- Kael Fischer, Ph.D. DeRisi Lab, University of California San Francisco From chapmanb at 50mail.com Thu Aug 12 22:40:30 2004 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu Aug 12 22:45:15 2004 Subject: [BioPython] Regarding GenBank In-Reply-To: <6.1.1.1.2.20040812154136.03917150@pop.sonic.net> References: <20040812060815.M70982@linux.nccs.res.in> <6.1.1.1.2.20040812154136.03917150@pop.sonic.net> Message-ID: <20040813024030.GC82849@lebowski.bos.east.verizon.net> Hi Kael; > In my experience, there definitely is an upper limit on the size of the > genbank file you can index, and when you go over that limit you get exactly > that error. > > Furthermore, apropos of Brads reply, files that fail for this reason can be > split and indexed fine - hence the minimal file that creates the problem is > the enormous beast that crashed the parser, not any particular record or > pair of records. (I have not gone back and checked this in 1.30) > > I believe this has been discussed on the list before. I recall that it was > attributed to underlying text handling libraries, and not the GenBank > module per se. This did used to be true, but should be fixed with the 1.30 release, since the file indexing uses a different underlying indexing system. If you have files with failed with the old system (which did have those limitations) please do check them to be sure they work on 1.30. However (fingers crossed) I do think this has been ironed out. Brad From sameet at nccs.res.in Thu Aug 12 23:32:00 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Thu Aug 12 23:40:08 2004 Subject: [BioPython] Regarding GenBank In-Reply-To: <6.1.1.1.2.20040812154136.03917150@pop.sonic.net> References: <20040812060815.M70982@linux.nccs.res.in> <6.1.1.1.2.20040812154136.03917150@pop.sonic.net> Message-ID: <20040813033005.M30210@linux.nccs.res.in> Hi, The file that i was trying to index here has only 3 records!! And the file per se is not a huge file. Irrespective of the number of records it gives the same error! Is there a way around this! regards Sameet -- National Centre for Cell Science, Pune ---------- Original Message ----------- From: Kael Fischer To: "Sameet Mehta" , biopython@biopython.org Sent: Thu, 12 Aug 2004 15:55:25 -0700 Subject: Re: [BioPython] Regarding GenBank > Sameet, et al: > > In my experience, there definitely is an upper limit on the size of > the genbank file you can index, and when you go over that limit you > get exactly that error. > > Furthermore, apropos of Brads reply, files that fail for this reason > can be split and indexed fine - hence the minimal file that creates > the problem is the enormous beast that crashed the parser, not any > particular record or pair of records. (I have not gone back and > checked this in 1.30) > > I believe this has been discussed on the list before. I recall that > it was attributed to underlying text handling libraries, and not the > GenBank module per se. > > You might try a smaller file or iterating though the large one, if > you can get away without random access to the records. > > Regards, > Kael > > At 11:32 PM 8/11/2004, Sameet Mehta wrote: > >Hi all, > >I am getting strange problems with the indexing of the GenBank file. Is > >there any upper limit on the size of GenBank file that can be indexed. > > [snip] > > >Is there any bug? > > > >regards > >Sameet > > > >-- > >National Centre for Cell Science, Pune > > > >_______________________________________________ > >BioPython mailing list - BioPython@biopython.org > >http://biopython.org/mailman/listinfo/biopython > > -- > Kael Fischer, Ph.D. > DeRisi Lab, University of California San Francisco ------- End of Original Message ------- From dalke at xebte.pair.com Fri Aug 13 01:10:14 2004 From: dalke at xebte.pair.com (Andrew Dalke) Date: Fri Aug 13 01:11:13 2004 Subject: [BioPython] EUtils Message-ID: <20040813051014.86463.qmail@xebte.pair.com> Hi all, I'm on vacation -- in between a tropical depression and a hurricane here in Florida - and was busy at BOSC/ISMB before that and with other work and travel before that so I haven't been following the mailings. I'm working on an update of EUtils. The code that's there is fragile in the face of changes so I'm using another approach, along with better docs. But it's not going to happen within the next couple of weeks. Andrew From anupam at ubi.com Fri Aug 13 01:05:55 2004 From: anupam at ubi.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Fri Aug 13 01:18:22 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogyu7s7/z+8uXw7fvpIPHl?= =?windows-1251?b?8OLo8SDoIOzg8Orl8ujt4yEgIM/w7uTg5uAg7e7z8uHz6u7iIQ==?= Message-ID: <1627163146.20040813051055@> ???????????? ?????? ? ?????????! ??????? ?????????! ????????? ???????????? ??????? Windows'98/2000/NT/XP - ?? 30 ?.?. ?????, ????????? ? ????????? ?????? ???????????? ??????????? - ?? 520 ???. ?? ?????????. ??????????? ????????????? ????? - ?? 15 ?.?. (?? 1 ????). ????????? ????? - 650 ??? ? ???. ?????????????? ?????? - ?? 200 ?.?. ????? ? ??????????? ??????? - 960 ???. ? ???. ??????????? ? ???????? "??? ????" - ?? 940 ???. ??????????? ???????????? 1-3 ?????? ? ???. - ?? 50 ?.?. (????? ? ??????? 2-3 ?????!) ???????? ????????? ???? ? ????? ? ???????????? ????????? ??? ??????????? ???????. ?????? ? ????????? - ?? 150 ?.?. (4 ?????). ???????????????? ?? ?????? ???????-?????????? (???????? ???? ??????????? ? ?????????) - ?? 20 ?.?. ???????????????? ?? web - ??????? - ?? 15 ?.?.
??????????? ???????? ???? ? ????????? ????? ????????? (.ru, .su, .com, net, .org, .biz, .info, .edu, .tv, .cc, .ws, .bz, .name, .tm, .aero, coop, .museum, .pro, ? ? ???? .??, .???, .???, .???) - ?? 20 ?.?. ? ???. WEB - ?????? (???????? ??????, ???????? ?? ?????, web - ???????????? ?? ?????, ????????? ???????? ? ???????? ?? ????) - ?? 50 ?.?. ???????????????? ?? ???????? ???????????? ???????????? - ?? 25 ?.?. ???????????? ? ???????? ?? ??????, ?????????, ?????????? - ?? 15 ?.?. ????????-?????????, ?????? ???????????? ?????, ???????????????? ?? ????? (??????????? ????????????) - ?? 500 ?.?. ? ?????. ??????? ? ????????, ?????????, ???????????, ?????????? ?????? ?? ??? ???? ? ????????? ? ??????????? - ?? 300 ?.?. ?????? ?? ??????????? ?????? ????? - ?? 200 ?.?. ??????? ???????? ????? ????????????! ????? ??????? ? ??????? 1 ???! ???????? ? ????????? ? ???????? ???! ???.: (095) 976-9092 From fsms at users.sourceforge.net Fri Aug 13 07:19:59 2004 From: fsms at users.sourceforge.net (fsms@users.sourceforge.net) Date: Fri Aug 13 07:10:29 2004 Subject: [BioPython] Restriction analysis package. In-Reply-To: <20040516182321.GA53985@misterbd.agtec.uga.edu> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> Message-ID: <411CA3DF.5040001@users.sourceforge.net> Hi, I would like to know where do we stand for the Restriction analysis package. I posted a message on the biopython-dev list but got no response. As previously said, I am ready to maintain the package in Biopython. Just tell me if you still are interested. best regards Fred. From play at ujsa.com Fri Aug 13 09:49:46 2004 From: play at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Fri Aug 13 10:02:24 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4DogzeDy/+bt++Ug7+7y7uvq?= =?windows-1251?b?6CDn4CAkMjMg6uIu7C4sIO7q7eAgz8LVLCDr5e/t6O3gIQ==?= Message-ID: <183978473.20040813135446@> ???????? ??????? ?? $23 ??.?., ???? ???, ???????! ??????????????? ?????????? ????????? ????????? ? 1997 ????! ???? ??????????? ?????? ???????????? ?? ???????! ??????? ????! ???? ????????? ??????????? ?????! ??? ?????????????, ????? ???????????? ???????????? ????????? ??????????! ????????? ??????? ??????, ?? ??? ????????? ????????!!! Economic (?? $23 ?? ??. ????, ??????? ??????) Middle (?? 25 Euro ?? ??. ????, ??????? ??????) Prestige (?? 33 Euro ?? ??. ????, ??????? ??????) ??????? ?? ??? ???? ? ???????? ???? ??????? ?? ??? ????: http://raxon.narod.ru ????? ????????????? ??? ??? ? ?????? ????: ??????????? ???? VEKA, ??????????? ??????????? ??? ???? ? ?????, ???????? ??????? ???????????? ? ??????????????? ???????????? (?? $10 ?? ???????? ???? ? ??????????). ?????????? ????? ???????-?????????! "???????? ??????" ???????: (095) 778 - 18 - 62 (??????????????) ??? ??????????? ?????: (501) 439 - 77 - 52 (? 7-00 ?? 22-00) ??????????, ?? ????????? ????? ?? ???????? ?????! ??????????? ?????? ?? ?????????! From jonathan.taylor at utoronto.ca Fri Aug 13 11:06:30 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Fri Aug 13 11:07:28 2004 Subject: [BioPython] Restriction analysis package. In-Reply-To: <411CA3DF.5040001@users.sourceforge.net> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> <411CA3DF.5040001@users.sourceforge.net> Message-ID: <1092409590.18213.1.camel@coder> I definately think it should be included. Currently I am having to manually add the beta's you maintain to my Bio python tree for my project. Seems like it fits nicely and that would save me that headache. Thanks for the work there. Cheers. Jon. On Fri, 2004-08-13 at 07:19, fsms@users.sourceforge.net wrote: > Hi, > > I would like to know where do we stand for the Restriction analysis package. > I posted a message on the biopython-dev list but got no response. > As previously said, I am ready to maintain the package in Biopython. > Just tell me if you still are interested. > > best regards > > Fred. > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From chapmanb at 50mail.com Fri Aug 13 14:19:16 2004 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri Aug 13 14:20:11 2004 Subject: [BioPython] Re: [Biopython-dev] Restriction analysis package. In-Reply-To: <411CA3DF.5040001@users.sourceforge.net> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> <411CA3DF.5040001@users.sourceforge.net> Message-ID: <20040813181916.GC727@lebowski.bos.east.verizon.net> Hi Fred; > I would like to know where do we stand for the Restriction analysis package. > I posted a message on the biopython-dev list but got no response. > As previously said, I am ready to maintain the package in Biopython. > Just tell me if you still are interested. Sorry for the delay in getting back with you. We are definitely still interested in the code, and I've went and integrated into Biopython CVS. Please let me know if I didn't get anything into CVS correctly. For those who are interested in checking it out, here is what is included: Bio/Restriction -- very nice set of modules for dealing with Restriction Enzymes, including searching for enzymes within sequences and performing cuts with them Doc/cookbook/Restriction -- documentation on using the modules (also included on the website) Scripts/Restriction -- scripts for updating the enzyme classes from Rebase The only modification I made was to add a catalyze function (which just calls the catalyse function). I was having a bit of trouble getting used to the British spelling :-). I also added some basic tests in Tests/test_Restriction.py -- please do feel free to add to these, they are pretty basic right now. Thanks much for this contribution -- everything looks very well designed and useful. And with documentation. Woo. Brad From ban at t-online.de Fri Aug 13 17:36:24 2004 From: ban at t-online.de (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Fri Aug 13 17:49:35 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogzurt4CDPwtUhIMrg9+Xx?= =?windows-1251?b?8uLl7e376SDw5ezu7fIhIMru7eTo9uju7eXw+yE=?= Message-ID: <1587015037.20040813214124@> ???? ???! ???????????? ??????! ????????????! ????? ????! ????? ????????! ??????, ??????????? ????????? ? ???????? ???? ??? ?? ???????? ????????!!! ???? ?? ????: ?????? ???? ?? $50 ?? ??. ?.! ???? ? ????????? ?? $120 ?? ??. ?.! ???? ? ????????? ? ?????????-???????? ?? $150 ?? ??. ?.! ?????? ?? $25 ?? ??. ?.! ????????! ??????? ???????? ? ???????????? ?????????! ????? ??????? ? ?????? ????????????!!! ? ??? ???????? ????? ? ????????? ?????!!! ??????? ????! ??????????? (?? 1 ???? ?? 3 ???!) ? ???????????????? ????????????! ??????? ???? ??????! ?????? ???? ??????? - ?? ???????? ?? ???????????! ????????? ????? ?????? ? ??????? ???? ????! ???.: (095) 508-7591, 504-8630, 976-90-74. ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ?????: Delete/??????? ?? ??????: nevajno2003@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From supportsmartness at servicemagic.com Sat Aug 14 08:04:40 2004 From: supportsmartness at servicemagic.com (Berlin) Date: Sat Aug 14 07:04:58 2004 Subject: [BioPython] Update your software Message-ID: visit us http://www.goodsoft4u.info/ Microsoft Windows XP Professional - 50 Adobe Photoshop 7.0 - 60 Microsoft Office XP Professional - 100 Microsoft Windows 2000 Professional - 50 Adobe PageMaker 7.0 - 60 Adobe Illustrator 10 - 80 Corel Draw Graphics Suite 11 - 120 Norton Antivirus 2004 Professional - 15 Borland Delphi 7 Professional - 70 Adobe Acrobat 6.0 Professional - 100 Adobe Acrobat 6.0 Proffessional - 100 Adobe Photoshop cs - 80 System Works 2004 Professional - 40 Microsoft SQL Server 2000 Enterprise Edition - 200 Windows 2000 Server - 50 Linux Redhat 7.3 - 200 Office 2003 Professional - 110 Quark Express 6.0 - 60 Macromedia Studio MX 2004 - 180.00 Adobe InDesign CS - 100.00 Adobe Illustrator CS - 90.00 Easy CD & DVD Creator 6 - 29.99 Ahead Nero v6.3 Powerpack - 40.00 Symantec WinFax PRO v10.03 - 40.00 .. and more ! visit us http://www.goodsoft4u.info/ fittingly workhorse aflame screws shampoo involve recesses randomize tantrums humidly Buchanan dactylic tinniness chords imprints household beechen forlorn irreverent Ithacan Goldstine fattens callers raindrop tampering sellers Nilsen Montgomery villainy aloud statuette exempting refute toils From crocha at dc.uba.ar Sat Aug 14 12:34:00 2004 From: crocha at dc.uba.ar (Cristian S. Rocha) Date: Sat Aug 14 12:35:00 2004 Subject: [BioPython] Genbank parser. Message-ID: <1092501239.3442.20.camel@felix> hi, Trying to parse genbank files with Martel parser I found with the following problems: 1) The parser can't read files with white lines at the begin/end of the file. 2) The parser can't read files with more than one record. I'm using an updated source from the CVS. To solve that problems I was change the file Bio/expressions/genbank.py in the following way: append before the format parser definition: header_lines = Martel.Rep( Martel.ToEol() + \ Martel.AssertNot(Martel.Str("LOCUS ")) ) and change the format definition to: format = Martel.HeaderFooter("genbank", {"format" : "genbank"}, header_lines, RecordReader.Until, ("LOCUS ",), record, RecordReader.StartsWith, ("LOCUS ",), header_lines, RecordReader.Everything, ()) bye, Cristian. -- Lic. Cristian S. Rocha Departamento de Computaci?n, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. From theresa at seznam.cz Sat Aug 14 14:52:19 2004 From: theresa at seznam.cz (beppe) Date: Sat Aug 14 15:03:54 2004 Subject: [BioPython] =?windows-1251?b?4eXr/OU=?= Message-ID: <200408141903.i7EJ3hKr020500@portal.open-bio.org> ???????? ? ???????? ??????????? ????? ?? www.mypresent.ru ??? ????? ?????? ?????. From joaquim at allsaintsfan.com Mon Aug 16 00:58:22 2004 From: joaquim at allsaintsfan.com (lydia) Date: Mon Aug 16 01:12:20 2004 Subject: [BioPython] =?windows-1251?b?0ODn7vjr5ewg4uD48yDw5err4OzzIO/u?= =?windows-1251?b?INHl8ugu?= Message-ID: <200408160512.i7G5CAKr011928@portal.open-bio.org> ???????? ???? ?????????? ?? ??????????? ???????. ????? ?????? ???? ??????, ??????, ???. ????? ?????? ???? ? ???????? ????????! ???????: (095) 518-7313 From carlo_bif at yahoo.com Mon Aug 16 21:33:03 2004 From: carlo_bif at yahoo.com (carlo bifulco) Date: Mon Aug 16 21:33:53 2004 Subject: [BioPython] ExPASy.py Message-ID: <20040816213303.6b787bda@gentooBox> The Expasy module, or at least it's get_sprot_raw function, ceased to function a few days ago (I imagine for a change of address of the server). I had to change the function's cgi argument from 'http://www.expasy.ch/cgi-bin/get-sprot-raw.pl' to 'http://ca.expasy.org/cgi-bin/get-sprot-raw.pl' to get it back in shape. Regards, Carlo From f.sohm at whsmithnet.co.uk Tue Aug 17 05:35:37 2004 From: f.sohm at whsmithnet.co.uk (f.sohm@whsmithnet.co.uk) Date: Tue Aug 17 05:36:31 2004 Subject: [BioPython] Re: Restriction analysis package. In-Reply-To: <20040813181916.GC727@lebowski.bos.east.verizon.net> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> <411CA3DF.5040001@users.sourceforge.net> <20040813181916.GC727@lebowski.bos.east.verizon.net> Message-ID: Hi Brad Felicitation for your PhD and thank you for uploading the code into the CVS. For the catalyse method, you are right and I should have made the change earlier. There is a simpler way to add a catalyze method though : in the classes : Unknown, Blunt, Ov5 and Ov3 at the end of the definition of the catalyse method, you need to replace : catalyse = classmethod(catalyse) by catalyze = catalyse = classmethod(catalyse) This suppress the need for a new class and avoid to add a function call. I have made the modif but how do you want me to send them ? a bug report against Restriction and the module as an attachement ? Bye Fred From idoerg at yahoo.com Tue Aug 17 05:58:16 2004 From: idoerg at yahoo.com (Iddo Friedberg) Date: Tue Aug 17 05:59:06 2004 Subject: [BioPython] Obsolete import in MMCIF2Dict? Message-ID: <20040817095816.2839.qmail@web41605.mail.yahoo.com> Hi all (and Michiel :), I recently tried to read in and old pickled dictionary I have. I got the following traceback: Traceback (most recent call last): File "", line 1, in ? File "/home/idoerg/soft/NN/NN.py", line 919, in ? from PDBUtil import PDBUtil File "/home/idoerg/soft/PDBUtil/PDBUtil.py", line 7, in ? from Bio.PDB.PDBParser import PDBParser File "/home/idoerg/biopy_cvs/biopython/Bio/PDB/__init__.py", line 13, in ? from MMCIFParser import MMCIFParser File "/home/idoerg/biopy_cvs/biopython/Bio/PDB/MMCIFParser.py", line 6, in ? from MMCIF2Dict import MMCIF2Dict File "/home/idoerg/biopy_cvs/biopython/Bio/PDB/MMCIF2Dict.py", line 2, in ? import Bio.PDB.mmCIF.MMCIFlex ImportError: No module named mmCIF.MMCIFlex Old leftover? Comment this out? Iddo __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - Send 10MB messages! http://promotions.yahoo.com/new_mail From j.frazieryp at advocate.com Tue Aug 17 08:55:06 2004 From: j.frazieryp at advocate.com (Jay Frazier) Date: Tue Aug 17 10:10:40 2004 Subject: [BioPython] Hey you totally forgot!! Message-ID: Hello, Ra[t]es dropped last week ... Jump on it! 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I want to iterate over the results, Now i am doing the following >>> from Bio.Blast import NCBIStandalone >>> infile = open(r'C:\Sameet\only2blast.txt', 'r') >>> parser = NCBIStandalone.BlastParser() >>> iterator = NCBIStandalone.Iterator(infile, parser) >>> while 1: record = iterator.next() if record is None: break for alignment in record.alignments: for hsp in alignments.hsps: if hsp.expect < 0.000000001: print alignment.title, hsp.sbjct_start The code taken as is from the tutorial I am getting the following trace Traceback (most recent call last): File "", line 2, in -toplevel- record = iterator.next() File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 1378, in next return self._parser.parse(File.StringHandle(data)) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 603, in parse self._scanner.feed(handle, self._consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 93, in feed read_and_call_until(uhandle, consumer.noevent, contains='BLAST') File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 335, in read_and_call_until line = safe_readline(uhandle) File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 411, in safe_readline raise SyntaxError, "Unexpected end of stream." SyntaxError: Unexpected end of stream. Now i have downloaded the latest version of the NCBIStandalone as advised by Jeff. The module is working fine. I can get the individual blast results one by one using the 'iterator.next()' command. But when i have a big file, with 4 reports one after the other. I get this error. Now I see that there is no problem with the NCBIStandalone, however, i dont know if i am diong anything wrong. As far as the tutorial is concerned, i am following it to the line. regards Sameet -- National Centre for Cell Science, Pune From sameet at nccs.res.in Thu Aug 19 11:07:55 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Thu Aug 19 11:15:52 2004 Subject: [BioPython] Iterating over Blast file update Message-ID: <20040819150031.M12926@linux.nccs.res.in> HI, i looked more closely at the file, and the trace, tried out a few things on the idle interpreter, and i realized that the error was being reported only with the first record in the blast file. The other are working fine. I guess i will have to do some error handling. Can anybody tell me how do i do that, because i dont understand what is do be doneusing the tutorial. I think i also had the same problem (first record not being parsed properly) with another file, but i am not sure. I will get back on this issue soon regards Sameet -- National Centre for Cell Science, Pune From clyde_benson at charterinternet.com Fri Aug 20 04:26:01 2004 From: clyde_benson at charterinternet.com (Clyde Benson) Date: Fri Aug 20 04:26:47 2004 Subject: [BioPython] Seeking Auto Accident Personal Injury attorney; for Landmark Case Message-ID: <200408200826.i7K8QhKs031012@portal.open-bio.org> Hello biopython@biopython.org, I have a landmark auto accident case where some very unusual things happened. A female ran a red light in her big rotor rooter van and broadsided me going around 50 miles per hour. I had the right of way, two green left turn arrows, and she admitted in the police report that she was looking down into her purse and didn't notice the light was red. The accident happened on October 12 of 1999. My five year statute of limitations expires around the middle of October. I'm turning in the lawsuit paperwork next week. I can be reached by email, if you are interested in helping me with this case. You can also reach me by phone at 1-573-837-4092 Sincerely, Clyde L. Benson Cape Girardeau, Missouri 63701 From sameet at nccs.res.in Sat Aug 21 05:57:57 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Sat Aug 21 06:05:45 2004 Subject: [BioPython] parsing Blast Output Message-ID: <20040821093638.M19852@linux.nccs.res.in> Hi, I have two earlier posts regarding this. The problem is much peculiar than I thought earlier. I did the following >>> from Bio.Blast import NCBIStandalone >>> infh = file(r'C:\Sameet\only2blast.txt', 'r') >>> b_parser = NCBIStandalone.BlastParser() >>> b_iterator = NCBIStandalone.Iterator(infh, b_parser) then when i did this: >>> x = b_iterator.next() i got the following trace Traceback (most recent call last): File "", line 1, in -toplevel- x = b_iterator.next() File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 1378, in next return self._parser.parse(File.StringHandle(data)) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 603, in parse self._scanner.feed(handle, self._consumer) File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 93, in feed read_and_call_until(uhandle, consumer.noevent, contains='BLAST') File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 335, in read_and_call_until line = safe_readline(uhandle) File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 411, in safe_readline raise SyntaxError, "Unexpected end of stream." SyntaxError: Unexpected end of stream. However, when i did this (without starting from the beginging): >>> while 1: rec = b_iterator.next() if rec is None: break for a in rec.alignments: for h in a.hsps: if h.expect == 0: print a.title print h.sbjct_start, (h.sbjct_start + len (h.match)) I got the expected result. So the first call to iterator.next() is giving error, however later it is working just fine. There is no loss of data. After the second call all the 6 records were retrived and printed properly. Can this is fixed, or is there a work around regards Sameet -- National Centre for Cell Science, Pune From adminstringers at carmax.com Sun Aug 22 15:27:35 2004 From: adminstringers at carmax.com (Berlin) Date: Sun Aug 22 14:26:32 2004 Subject: [BioPython] your health Message-ID: roster Portland underling unjust Carruthers Generlc pharmacy for you http://abates.jmnemei.info/?DT9LFM7GgbK.P7Dfanfare Men's health: Vlagra - 0.95 Clalis - 2.00 Weight loss: Xenical - 1.31 Generic Meridia- 82.50 Hair loss: Generic Propecia - 19.51 Diabebetes threat: Generic Glucophage - 0.49 Pain relief: Generic Vioxx - 1.45 Generic Celebrex - 0.80 Anti depressants: Generic Paxil - 1.16 Generic Zoloft - 0.64 Muscul relaxers: Generic Soma - 1.33 Stop smoking: Generic Zyban - 1.17 Lower cholesterol: Lipitor - 0.48 and a lot more http://depressed.jmnemei.info/?DT9LFM7GgbK.P7Ddowngrade entertain Ukrainians longhand Kernighan sediments Salton inductions abasement talented Lemke odiously gumption blacks reverted From cheryl at t-online.de Mon Aug 23 10:43:59 2004 From: cheryl at t-online.de (tatsuo) Date: Mon Aug 23 10:56:42 2004 Subject: [BioPython] =?windows-1251?b?4eXr/OU=?= Message-ID: <200408231456.i7NEuZKr026597@portal.open-bio.org> ???????? ? ???????? ??????????? ????? ?? www.mypresent.ru ??? ????? ?????? ?????. From crashes at cts.com Mon Aug 23 23:09:11 2004 From: crashes at cts.com (crashes@cts.com) Date: Mon Aug 23 23:14:38 2004 Subject: [BioPython] updates In-Reply-To: References: Message-ID: <2IE7BCH6BAI6KJ6A@cts.com> New Q E M software QuickBooks Premier 2004 - 110 Maya 6.0 Unlimited - 150 Corel Photobook - 25 3D Home Architect V 6 Deluxe - 15 Adobe Atmosphere 1.0 - 60 Roxio Easy Media Creator 7 - 30 QuarkXPress 6 - 110 SuSe Linux 9.1 Professional Edition - 50 Delphi 8 Architect - 130 Goldmine Business Contact Manager 6.5 - 59 Linux, Apple software and a lot more http://www.bolguarou.biz/ From jadamkew at exelixis.com Tue Aug 24 00:27:42 2004 From: jadamkew at exelixis.com (Joanne Adamkewicz) Date: Tue Aug 24 00:28:28 2004 Subject: [BioPython] public Smith-Waterman implementation? Message-ID: Hi all, A non-python related question, but very much in biocomputing: Can someone point me to a publicly available implementation of the Smith-Waterman algorithm? I'm aware of wise2 (http://www.ebi.ac.uk/Wise2/doc_wise2.html), but it implements swp (protein-protein) only. I'm looking for something that also includes tswn and the others. Thanks in advance for any help, Joanne From JBonis at imim.es Tue Aug 24 13:00:03 2004 From: JBonis at imim.es (Bonis Sanz, Julio) Date: Tue Aug 24 13:00:42 2004 Subject: [BioPython] Getting SNPs from a given gene Message-ID: Hi, I am writing a script with biopython. The aim is that given a gi, the scripts returns a list of the SNPs (variations) in that given gene. (I work with mRNA). I did it some months ago and seems to work, but now, I have found that for the gi-s I try (mRNA for Homo sapiens and using only refseq as source database) there are no "variation" features in the record!. Any idea? I attach an example of code. def populateByGI(self,gi): from Bio import GenBank rParser = GenBank.FeatureParser() rDict = GenBank.NCBIDictionary(parser = rParser) sq = rDict[gi] self.gi = gi sequence = '' for a in sq.seq: sequence = sequence + a self.seq = sequence for feature in sq.features: if (feature.type == 'gene'): self.names.append(feature.qualifiers['gene'][0]) dbrefs = feature.qualifiers['db_xref'] for dbref in dbrefs: if (dbref[:3] == 'MIM'): self.mim = dbref[4:] if (dbref[:7] == 'LocusID'): self.locusID = dbref[8:] if (feature.type == 'variation'): newVar = GBvariation() newVar.gi = gi newVar.position = feature.location._end.position newVar.dbsnp = feature.qualifiers['db_xref'][0][6:] newVar.allele1 = feature.qualifiers['replace'][0] newVar.allele2 = feature.qualifiers['replace'][1] self.variations.append(newVar) From april at ubi.com Wed Aug 25 01:19:45 2004 From: april at ubi.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Wed Aug 25 01:38:31 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4DogyNLAy8jfISEh7vLk+/Ug?= =?windows-1251?b?7eAg7O7w5SDoIO/u5+3g4uDy5ev87fvlIPLz8PshISE=?= Message-ID: <1005315678.20040825052445@> ??????!!! ????? ?? ???? ? ?????????????? ????!!! ???????????? ????? ?? ????!!! ??????????? ????????? - ????????? ???????!!! ???????? ?????, ????????!!! Ambasador 4* 19-26/06:7????- 840 ????, 14 ????-1480 ???? 03-31/07:7????- 940 ????, 14 ????-1650 ???? 07-14/08:7????-1100 ????, 14 ????-1850 ???? 21-28/08:7????- 950 ????, 14 ????-1620 ???? Europa Concordia 4* 19-26/06:7????- ????, 14 ????-1480 ???? 03-31/07:7????- 940 ????, 14 ????-1650 ???? 07-14/08:7????-1100 ????, 14 ????-1850 ???? 21-28/08:7????- 950 ????, 14 ????-1620 ???? -??????????? -?????? ???????????????? ???? -?????????? -?????????? -??????? -??????????? ????????? ????????????? ???????????? -???? -??????? "???????????? ??????" 8 ????/7?????!!! ??????-???????-?????_????-?????????-?????-???-???????-???????/??????-??????-???-?????? ????? ????????? ?? ????????. ? ????? ????? ?? ?????? ???????????? ? ????????????? ?????? ?? ??????! ?????????? ???????????? ????? ?? ????, ? ????? 4-5 *, ??????????????? ?????! ??????? ???????? ????????????? ? ??????? ??? ??? ?????! ?????????? ????????? "??????? ? ??????!" ??????, ??. ?????????, ?. 12, ???. 6 ???????/????: (095) 7-888-769, 101-35-27 ??????? ??? ??????????? ?????: 8-926-230-68-68 ??????????, ?? ?????????? ????? ?? ???????? ?????! ?????? ?????????? ?? ?????????! ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ?????: Delete/??????? ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From idoerg at yahoo.com Wed Aug 25 01:55:42 2004 From: idoerg at yahoo.com (Iddo Friedberg) Date: Wed Aug 25 01:56:20 2004 Subject: [BioPython] public Smith-Waterman implementation? In-Reply-To: Message-ID: <20040825055542.50946.qmail@web41610.mail.yahoo.com> Hi, In Wise2 there is a protein Smith-Waterman implementation: http://www.ebi.ac.uk/Wise2/doc_wise2.html#SECTION00082000000000000000 Also, you can try "water" from EMBOSS. Biopython also has a Smith-Waterman code. Bio.pairwise2 Best, Iddo --- Joanne Adamkewicz wrote: > Hi all, > > A non-python related question, but very much in biocomputing: > > Can someone point me to a publicly available implementation of the > Smith-Waterman algorithm? I'm aware of wise2 > (http://www.ebi.ac.uk/Wise2/doc_wise2.html), but it implements swp > (protein-protein) only. I'm looking for something that also > includes tswn > and the others. > > Thanks in advance for any help, > Joanne > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > ===== -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA, 92037 USA T: (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo _______________________________ Do you Yahoo!? Win 1 of 4,000 free domain names from Yahoo! Enter now. http://promotions.yahoo.com/goldrush From chungen at hideakifan.com Wed Aug 25 17:11:50 2004 From: chungen at hideakifan.com (chan-hon) Date: Wed Aug 25 17:18:54 2004 Subject: [BioPython] =?windows-1251?b?z+7q8+/q6A==?= Message-ID: <200408252118.i7PLIWKr011001@portal.open-bio.org> ???????? ? ?????? ??????? ???? ? ??????? ?????! http://pokupki.net From sameet at nccs.res.in Sat Aug 28 12:59:24 2004 From: sameet at nccs.res.in (Sameet Mehta) Date: Sat Aug 28 13:07:09 2004 Subject: [BioPython] BioSQL problems Message-ID: <20040828164251.M66218@linux.nccs.res.in> Hi, I had the following problems when trying to populate a MySQL database with information from a GenBank file. I am giving what i have done, and the trace that i got below >>> from BioSQL import BioSeqDatabase >>> server = BioSeqDatabase.open_database(driver="MySQLdb", user='root', ... passwd='mysql1', host='localhost', db='bioseqdb') >>> db = server.new_database("promoter") >>> from Bio import GenBank >>> parser = GenBank.FeatureParser() >>> iterator = GenBank.Iterator(open("/home/sameet/Desktop/GenBankData/promotergb.gb"), parser) >>> db.load(iterator) I had already prepared the database with all the tables from the biosql.sql for MySQL. The file contains about 1800 entries but i am getting this error, where the program just exits! Traceback (most recent call last): File "", line 1, in ? File "/root/Desktop/biopython-1.30/build/lib.linux-i686-2.2/BioSQL/BioSeqDatabase.py", line 414, in load File "/root/Desktop/biopython-1.30/build/lib.linux-i686-2.2/BioSQL/Loader.py", line 43, in load_seqrecord File "/root/Desktop/biopython-1.30/build/lib.linux-i686-2.2/BioSQL/Loader.py", line 322, in _load_reference File "/root/Desktop/biopython-1.30/build/lib.linux-i686-2.2/BioSQL/BioSeqDatabase.py", line 287, in execute_and_fetch_col0 File "/usr/lib/python2.2/site-packages/MySQLdb/cursors.py", line 95, in execute return self._execute(query, args) File "/usr/lib/python2.2/site-packages/MySQLdb/cursors.py", line 114, in _execute self.errorhandler(self, exc, value) File "/usr/lib/python2.2/site-packages/MySQLdb/connections.py", line 33, in defaulterrorhandler raise errorclass, errorvalue _mysql_exceptions.ProgrammingError: (1064, "You have an error in your SQL syntax near 'USING (dbxref_id) WHERE dbname = 'PUBMED' AND accession = '10570245'' at line 1") am i doing something wrong, using something i am not supposed to use I am using python2.2 and the MySQLdb module is working fine. I am using RHL9.0, and MySQL version 3.23.54 thanks for the help in advance, regards Sameet -- National Centre for Cell Science, Pune From delivery at hosyou-b01.mine.nu Sat Aug 28 17:27:53 2004 From: delivery at hosyou-b01.mine.nu (=?iso-2022-jp?Q?=1B=24B7P=3AQJ88K=25a=25k=25=5E=25=2CC4Ev=1B=28B?=) Date: Sat Aug 28 17:30:28 2004 Subject: [BioPython] =?iso-2022-jp?b?GyRCIXZMJD41QnokSD41QnohSktcP00bKEI=?= =?iso-2022-jp?b?GyRCRVBPPyFLOS05cCIjGyhCNhskQkBpS3wxXyRHOiMkTkc6JF8bKEI=?= =?iso-2022-jp?b?GyRCMnI3aCIjRy82YiRPOXEwTUI4JEdIYTdgISY8KzhKQFVHJCRHGyhC?= =?iso-2022-jp?b?OBskQkBpS3wxXyIjN0o1JDJzSXwzKztPJE47fiQzJD0lQSVjJXMbKEI=?= =?iso-2022-jp?b?GyRCJTkhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= Message-ID: <9913470.1093728473681.JavaMail.nobody@hosyou-b.mine.nu> biopython@biopython.org$BMM(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!7P:QJ88K%a%k%^%,C4Ev!';v6Hl9g$O$=$N;]$r(Bhttp://gogoway.orgdns.org/melmaga/teishi.html$B$^$G(B $B!!!!!!!!!!!!!!!!!!%a!<%k%^%,%8%s9XFI$N?=$79~$N>l9g$O!"$=$N;]$r!!(Bhttp://gogoway.orgdns.org/melmaga/$B!!$^$G(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!J0-5:$GB>?M$N9XFI$N?=$79~$r$5$l$?$N$,L$>5Bz9-9p!&K\?M?=$79~$_$O>5Bz9-9p!K!!(B $B!!!!!!!!!!!!!!%a!<%k%^%,%8%s9-9p?=$79~$_$O!"$=$N;]$r(Bhttp://gogoway.orgdns.org/doc/honmousikomi.htm$B!!$^$G(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!$=$NB>$NI=<(;v9`$O!"FC>&K!$K$h$j!"3F9-9p$N%j%s%/@h$KI=<((B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!(B----$B#6@iK|1_$GG/6bIT0B$O2r7h(B----$BJ}K!$O$"$j$^$9!*(B------$B#6@iK|1_0J2e$NCK=w$J$i=PMh$k![(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!:#$NG:$_$O!&!&!@iK|1_$G2r7h=PMh$k!*L\E*$K$b;HMQ=PMh$k!*@83h8~>e=PMh$k(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!>-Mh$NIT0B$O!&!&!@iK|1_Cy6b$G0B?4=PMh$k!*0B?48~>e$N:`NA$O;q6b$G=PMh$k!*(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=PMh$k$NJ}K!$OM-$j$^$9!Z5rM-<}F~%S%8%M%9!U7P1DeCK=w?=$79~$_=PMh$^$9!#(B $B!!!!!!I{6H!&7s6H!&EZF|7P1D2K3hMQ7P1D$NJ}!9$KBg9%I>!*(B $B!!!!!!!!(B $B!!!!!!!!#3#8G/$N\$7$/$O(B http://newjapan.orgdns.org/$B!!(B $B!!(B $B!!(B $B2?;v$bO@$h$j>Z5r!&1=$h$j>Z5r!&>u67>Z5r$h$jJ*E*>Z5r!&:[H=41$HF1$8J*E*>Z5r$N$_$G;ve$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o(^$B"&(B^)o$B=i$a$F$NI{<}F~$OMb7n$K$b$i$($?$o(B(*^-$B!,(B)v $B!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B *-----$B#P#R(B------------------------------------------------------------------------------------------------* $B#87n%W%l%*!<%W%sFCJL1o8NJg=8$N30;q7O%M%C%H%o!<%/4k6H$N0lHL8xJgOH(B $B!!!!!!!!!!(B $B!!(B http://askmebiz.net/click/2/ad5.cgi $B!z!y(B $B!2#P#R!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z(B $B!!(B $B1?L?$rJQ$($k%o%s%/%j%C%/$bM-$j$^$9!#!!FCJL5.IP@J!!;D$j$o$:$+(B *-------------------------------------------------------* $B!z(Bo(^$B"`(B^o) $BKhF|$,%a%C%A%c3Z$7$$$s$G$9$%$%!7W;;5!!"9bB.%3%$%s%+%&%s%?!l!W!"!VBgGW:V!W$,$"$J$?$N7HBS$GM7$Y$^$9!*(B $B!!!!!!!!!!!J(BBREW$B!"(BVodafone$BBP1~!K(B $B#1%"%W%j!o#1#5#7!A$G$9$N$G!"$*;E;v$N9g4V$N$A$g$C$H$7$?B)H4$-$K(B $B!!$*5$7Z$K@'Hs$4MxMQ2<$5$$"v(B http://www.metro-japan.com/mobile/index.html $B!z(B--$B!~(B-$B!N(BPR]-$B!z(B--$B"!(B--$B!z(B--$B!~(B--$B!z!z(B-$B!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B-$B!~(B--$B!z(B--$B"!(B--$B!z=i$a$F$NI{<}F~$OMb7n(B--$B!~(B-$B!z(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B $B!!(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! $B$7$+$b!V40A4:_Bp!W"v$@$C$Fe$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o $B!!!!!!!!!!!!!!!!!!!!!!!!!!!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B $B!!!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B *:$B!z(B $B!!!!!}!!K\F|$bEj9F!*$"$j$,$H$&$4$6$$$^$7$?"v!}%a%k%^%,H/9TpJspJs$K4X$7$FH/9T5$/$@$5$$!#7G:\5-;v$K4X$9$k$*Ld$$9g$o$;$OD>@\Ej9Fl9g$O5$/$@$5$$!#(B $B!!!!!!!!!!!!$^$?9-9pFbMF$K$h$C$F$O!!7G:\$r95$($5$;$F$$$?$@$/>l9g$b$4$6$$$^$9!#(B $B!!!!!!!!!!!!9-9p$r?=$79~$s$G$$$?$@$$$?J}$K$O!"%a!<%k%^%,%8%s$rG[?.$5$;$F$$$?$@$-$^$9!#(B $B!!!!!!!!!!!!$4N;>5$N>e!!$*?=$79~$_$/$@$5$$!#(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(Bhttp://gogoway.orgdns.org/doc/honmousikomi.htm ---------------------------------------------------------- $B!!!!!!!!!!!!!!!!!!!!!!(B $B%a!<%k%^%,%8%s!!9-9pC4EvLpBt!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!(B ------------------------------------------- 8$B7n(B28$BF|(B17$B;~H/I=(B $B8E20(B $BF^$j(B $BF^$j$N$A0l;~1+(B $B?73c(B $B@2$l(B $B@2$l$N$A;~!9F^$j(B $B6bBt(B $BF^$j(B $BF^$j(B $BBg:e(B $BF^$j;~!9@2$l(B $BF^$j(B $B2,;3(B $B@2$l;~!9F^$j(B $BF^$j;~!9@2$l(B $B9-Eg(B $BF^$j;~!9@2$l(B $B@2$l;~!9F^$j(B $B9b>>(B $BF^$j(B $BF^$j$N$A0l;~1+(B $BJ!2,(B $B@2$l(B $B@2$l$N$A0l;~1+(B $B Hello, I'm trying to install Biopython on a new Opteron AMD 64 computer. It has Mandrake 10 for AMD64. Python 2.3.3 is installed. First thing I tried was to install mxTextTools. Here is what I got: [root@reslinux egenix-mx-base-2.0.5]# python setup.py install running install error: invalid Python installation: unable to open /usr/lib64/python2.3/config/Makefile (No such file or directory) There is no such a Config directory under python2.3 directory. Any hint? From idoerg at yahoo.com Mon Aug 30 13:36:07 2004 From: idoerg at yahoo.com (Iddo Friedberg) Date: Mon Aug 30 13:36:36 2004 Subject: [BioPython] Installing BioPython on AMD64 In-Reply-To: <38546.208.254.167.5.1093886715.webmail@panel.powered-hosting.com> Message-ID: <20040830173608.37817.qmail@web41604.mail.yahoo.com> Hey Sebastian, This has to do with Mandrake. You should install the libpython2.3-devel package using urpmi. Cheers, Iddo --- Sebastian Bassi wrote: > Hello, > > I'm trying to install Biopython on a new Opteron AMD 64 computer. > It has > Mandrake 10 for AMD64. Python 2.3.3 is installed. First thing I > tried was > to install mxTextTools. > > Here is what I got: > > [root@reslinux egenix-mx-base-2.0.5]# python setup.py install > running install > error: invalid Python installation: unable to open > /usr/lib64/python2.3/config/Makefile (No such file or directory) > > There is no such a Config directory under python2.3 directory. > Any hint? > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > _______________________________ Do you Yahoo!? Win 1 of 4,000 free domain names from Yahoo! Enter now. http://promotions.yahoo.com/goldrush From sbassi at asalup.org Mon Aug 30 16:14:19 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Mon Aug 30 16:14:06 2004 Subject: [BioPython] Installing BioPython on AMD64 In-Reply-To: <20040830173608.37817.qmail@web41604.mail.yahoo.com> References: <38546.208.254.167.5.1093886715.webmail@panel.powered-hosting.com> <20040830173608.37817.qmail@web41604.mail.yahoo.com> Message-ID: <41115.208.254.167.5.1093896859.webmail@panel.powered-hosting.com> > Hey Sebastian, > This has to do with Mandrake. > You should install the libpython2.3-devel package using urpmi. OK, I've just found it. It took me a while because Mandrake call it lib64python2.3-devel, it adds 64 after lib on all its 64 bits libraries. So I will try installation again. Thank you! From sbassi at asalup.org Mon Aug 30 19:10:10 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Mon Aug 30 19:10:23 2004 Subject: [BioPython] More problems with Biopython on AMD64 Message-ID: <14554.208.254.167.5.1093907410.webmail@panel.powered-hosting.com> Hello all, I keep on trying to install biopython on AMD64. I already installed mxtexttools. Now I want to install Numpy. Numpy requires lapack a Linear Algebra package. I don't find this package on Mandrakes CDs, but I found online the lapack-3.0-9mdk.src.rpm. So I try to rebuild lapack with: rpm --rebuild lapack-3.0-9mdk.src.rpm and I get this: (lot of output cuted...) gcc -shared -Wl,-soname,liblapack.so.3 -o liblapack.so.3.0 *.o -L../BLAS/SRC -lblas -lm -lc /usr/bin/ld: ../BLAS/SRC/libblas.a(cgbmv.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC ../BLAS/SRC/libblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [shared] Error 1 + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.7622 + umask 022 + cd /usr/src/RPM/BUILD + cd LAPACK + /bin/mkdir -p /var/tmp/lapack-buildroot/usr/bin + /bin/mkdir -p /var/tmp/lapack-buildroot/usr/lib64 + /bin/mkdir -p /var/tmp/lapack-buildroot/usr/share/man/manl + /bin/cp equivalence /var/tmp/lapack-buildroot/usr/bin + /bin/cp SRC/liblapack.so.3.0 /var/tmp/lapack-buildroot/usr/lib64 /bin/cp: cannot stat `SRC/liblapack.so.3.0': No such file or directory error: Bad exit status from /var/tmp/rpm-tmp.7622 (%install) RPM build errors: user lenny does not exist - using root user lenny does not exist - using root user lenny does not exist - using root user lenny does not exist - using root user lenny does not exist - using root user lenny does not exist - using root user lenny does not exist - using root Bad exit status from /var/tmp/rpm-tmp.7622 (%install) (BTW, I don't know how is lenny, I use another unixname and this was tried as root). I found one liblapack.so.3.0 on a Red Hat linux disk that works on 32 bits (Red Hat 8 under Xeon), so I am not sure if I could use it. If so, where should I put it? Anyone else here with AMD64? From sbassi at asalup.org Tue Aug 31 09:52:10 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Tue Aug 31 09:51:48 2004 Subject: [BioPython] Another problem with Biopython compilation on AMD64 Message-ID: <9422.208.254.167.5.1093960330.webmail@panel.powered-hosting.com> Hello, When I tried to compile Biopython with python setup.py build I got this: (cuted some output...) building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-x86_64-2.3/Bio/KDTree g++ -pthread -I/usr/include/python2.3 -c Bio/KDTree/KDTree.cpp -o build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o g++ -pthread -I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.swig.o g++ -pthread -shared build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.swig.o -lstdc++ -o build/lib.linux-x86_64-2.3/Bio/KDTree/_CKDTree.so /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols: Bad value collect2: ld returned 1 exit status error: command 'g++' failed with exit status 1 I googled and I found this post that seems related: http://www.mail-archive.com/debian-ocaml-maint@lists.debian.org/msg05778.html But I am not sure about wwhat to do :( From d.lapointe at comcast.net Tue Aug 31 10:54:39 2004 From: d.lapointe at comcast.net (d.lapointe@comcast.net) Date: Tue Aug 31 10:55:03 2004 Subject: [BioPython] Another problem with Biopython compilation on AMD64 Message-ID: <083120041454.1403.4134912E000D2D670000057B22007589420A9B0207019F0E04D20B@comcast.net> Sebastian, I encountered the exact same problem using SUSE 9.1 with X86_64. There are a few customizations that need to be made to makefiles for some packages when moving to x86_64, The NCBI toolbox is one. I will just mention that there are some math libraries optimized for AMD64 that can be used to advantage. AMD supplies one, and there are several BLAS based ones also for AMD64. I compiled R with the GOTO BLAS library for X86_64. A 3000x3000 matrix multiply ( m %*% m) went from 320 sec w/o to 9 sec with the library. solve(m) went from about 300 sec to 28 seconds. Of course only operations using BLAS benefit from this. David > Hello, > > When I tried to compile Biopython with python setup.py build I got this: > > (cuted some output...) > building 'Bio.KDTree._CKDTree' extension > creating build/temp.linux-x86_64-2.3/Bio/KDTree > g++ -pthread -I/usr/include/python2.3 -c Bio/KDTree/KDTree.cpp -o > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o > g++ -pthread -I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.swig.o > g++ -pthread -shared build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.swig.o -lstdc++ -o > build/lib.linux-x86_64-2.3/Bio/KDTree/_CKDTree.so > /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation > R_X86_64_32 can not be used when making a shared object; recompile with > -fPIC > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols: > Bad value > collect2: ld returned 1 exit status > error: command 'g++' failed with exit status 1 > > I googled and I found this post that seems related: > http://www.mail-archive.com/debian-ocaml-maint@lists.debian.org/msg05778.html > But I am not sure about wwhat to do :( > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From ariella at myfunnymail.com Tue Aug 31 12:16:11 2004 From: ariella at myfunnymail.com (shariyn) Date: Tue Aug 31 12:32:44 2004 Subject: [BioPython] - Message-ID: <200408311632.i7VGWZKr025669@portal.open-bio.org> From biopython-dev-bounces at portal.open-bio.org Tue Aug 31 13:59:03 2004 From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org) Date: Tue Aug 31 13:59:07 2004 Subject: [BioPython] Your message to Biopython-dev awaits moderator approval Message-ID: Your mail to 'Biopython-dev' with the subject foto Is being held until the list moderator can review it for approval. The reason it is being held: Message has a suspicious header Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://biopython.org/mailman/confirm/biopython-dev/211fd374199ebaad0c6e4585f23aece93f4abe0b