From dalke at xebte.pair.com Tue May 4 03:31:25 2004 From: dalke at xebte.pair.com (Andrew Dalke) Date: Tue May 4 03:35:30 2004 Subject: [BioPython] 1 day to BOSC abstracts deadline! Message-ID: <20040504073125.96208.qmail@xebte.pair.com> Working on a cool project? Want to talk about it at BOSC? Only 1 day left before the abstract submission deadline. That's for the full (10 to 30 minute) talks. If you only want to talk for 5 minutes or give a demo, there's still time left, but please do let us know so we can schedule things. Andrew dalke@dalkescientific.com From chapmanb at uga.edu Tue May 4 12:44:21 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue May 4 16:53:32 2004 Subject: [BioPython] RecordFile.py In-Reply-To: <4088A3A5.8010901@uth.tmc.edu> References: <4088A3A5.8010901@uth.tmc.edu> Message-ID: <20040504164421.GC602@misterbd.agtec.uga.edu> Hi Chunlei; > I just tried "RecordFile.py", but it failed for both fasta > file and genbank file I tested. > > >>> rec_h=RecordFile.RecordFile(open(r"gb_test.txt" ),'LOCUS','\\') > or > >>> rec_h=RecordFile.RecordFile(open(r"gb_test.txt" ),'>','') > > both returned the same error: Thanks for the report -- it does look like RecordFile is really code that is not completely finished. I think the best course of action is to deprecate this module, which is not really used inside of Biopython. Mostly it might be useful for building up parsers, but we are currently encouraging the use of Martel for this. > Actually, I wrote a simply script before using Bio.File's UndoHandle for > the same purpose. It looks much simpler, maybe not as powerful as > RecordFile.py, but it does works for me. I post it here and hope it is > worth sharing with you. Thanks for the code. In many ways, I think both RecordFile and this kind of duplicate the functionality that already exists in Biopython. You can get a text record iterator of Fasta and GenBank files using: from Bio import Fasta handle = open("your_file.fasta") iterator = Fasta.Iterator(handle) for rec in iterator: # do something with your text record That is -- if you don't pass a parser then you get back the text. Thanks for the report! Hope this helps Brad From chapmanb at uga.edu Tue May 4 12:55:38 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue May 4 17:03:35 2004 Subject: [BioPython] Solved BioPython & Zope problem and a Bug? In-Reply-To: <1082736999.23447.67.camel@numero2> References: <1082736999.23447.67.camel@numero2> Message-ID: <20040504165538.GD602@misterbd.agtec.uga.edu> Hi Cristian; > I could solve my problem with BioPython in Zope. Thanks for your work on this. I suspect there are not many people out there (myself included) working with Zope and Biopython, so I appreciate your work treading into unknown territory. > The main problem was > Zope can't import some functions defined in some modules. These modules > have other modules with relative imports and Zope can't import them. Okay, I guess the problem is that both Zope and Biopython are probably playing around with import hooks. I don't know enough about all of what Zope does to fix all of the problems, but I guess the best way is trial and error. > Bio.config.FormatRegistry.py have the following relative import: > > import _support > > I change it to: > > from Bio.config import _support Fixed. > I do the same with FormatIO.py with ReseekFile import. Where specifically are these problems and I can add the relevant full import? Do all relative imports need to be removed? > The second problem IS """Bio.MultiProc.copen""". I really don't know > why, but Zope begin an infinity loop when I ask for the symbol table of > the module. To solve these problem I commented the import on the > Bio.config._support module. Okay, I moved this import into the __call__ function where it is used. Hopefully that'll fix the import loops. Both of those changes are in CVS -- please let me know if that fixes things or if other changes are needed. Thanks again for the work! Brad From sbassi at asalup.org Tue May 4 22:02:14 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Tue May 4 22:09:13 2004 Subject: [BioPython] New version of Tm Message-ID: <40984B26.4000808@asalup.org> I did send this to Brad the 4-18, but still is not into the CVS. So I send it here, maybe the original mail fell into a spam filter :) Here is a code update (1.4 version). It has some correction that Olivier Friard point me at my code. This should go here: [biopython]/biopython/Bio/SeqUtils/MeltingTemp.py I send it as an attach. -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info -------------- next part -------------- A non-text attachment was scrubbed... Name: tmstalucJSF2_modified.zip Type: application/zip Size: 1833 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040504/5bf14bc2/tmstalucJSF2_modified.zip From chapmanb at uga.edu Wed May 5 05:39:28 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 09:47:20 2004 Subject: [BioPython] PSIBlastParser behavior In-Reply-To: <200404220100.i3M107fI026284@itsa.ucsf.edu> References: <200404220100.i3M107fI026284@itsa.ucsf.edu> Message-ID: <20040505093928.GB4372@misterbd.agtec.uga.edu> Hi John; Sorry for the delay in getting back with you about this. > I am observing an unexpected behavior using the PSIBlastParser. I am > doing a simple PSI-Blast run: [...] > SyntaxError: Line does not start with ' Database': > Results from round 1 Hmmm, I can not seem to repeat this. I tried both Blast 2.2.6 and the most recent 2.2.8 version and both seem to parse fine, using the following code: from Bio import db input_file = "channel.fasta" fasta_fetch = db["fasta"] fasta_info = fasta_fetch["CNG4_BOVIN"] input_handle = open(input_file, "w") input_handle.write(fasta_info.read()) input_handle.close() from Bio.Blast import NCBIStandalone result_handle, error_handle = NCBIStandalone.blastpgp( "/usr/local/bin/blastpgp", "swissprot", input_file, expectation = 1e-5, npasses = 2) parser = NCBIStandalone.PSIBlastParser() rec = parser.parse(result_handle) print rec Would you be able to give me more information so I can try to fix the parser? Either sending an output file that demonstrates the problem to me directly, or letting me know what version of BLAST and databases and everything that you are using, would work great. Thanks for the report. Brad From chapmanb at uga.edu Wed May 5 07:58:58 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 12:06:50 2004 Subject: [BioPython] Looking for functions In-Reply-To: <408E58F6.5010604@loria.fr> References: <1082986523.31151.5.camel@numero2> <408E587A.5060209@loria.fr> <408E58F6.5010604@loria.fr> Message-ID: <20040505115858.GA610@misterbd.agtec.uga.edu> Hi Myriam; > >- convert a swissprot file to a fasta file, > >I try this one : > > > >from Bio.SeqIO import FASTA > >from Bio.SwissProt import SProt > >from sys import * > > > >def convert_sp_fasta(infile,outfile): > > """ > > convert a SwissProt file into a Fasta formatted file > > """ > > in_h = open(infile) > > sp = SProt.Iterator(in_h, SProt.SequenceParser()) > > out_h = FASTA.FastaWriter(outfile) > > sequence = sp.next() > > out_h.write(sequence) > > in_h.close() > > out_h.close() The code is fine, as far as the use of the Biopython goes. The only problem is that you are supposed to pass an open file handle to the FastaWriter, hence the error: AttributeError: 'str' object has no attribute 'write' when the code tries to write to the name of the file (outfile) instead of an open handle. You can fix this by changing: out_h = FASTA.FastaWriter(outfile) to: out_h = FASTA.FastaWriter(open(outfile, "w")) Converting files is also covered in documentation on the Biopython website: http://www.biopython.org/docs/cookbook/genbank_to_fasta.html Here is some equivalent code that would do your job using the system described there: from Bio import formats from Bio.FormatIO import FormatIO import sys def convert_sp_fasta(infile, outfile): """ convert a SwissProt file into a Fasta formatted file """ in_h = open(infile) out_h = open(outfile, "w") formatter = FormatIO("SeqRecord", formats["swissprot"], formats["fasta"]) formatter.convert(in_h, out_h) in_h.close() out_h.close() if __name__ == "__main__": convert_sp_fasta(sys.argv[1], sys.argv[2]) > >- find EcoRI restriction sites in a fasta sequence. In the simplest case, you can just use python's string.find find occurrences of "GAATTC" in the sequence: >>> cur_pos = -1 >>> all_sites = [] >>> while 1: ... pos = seq.find("GAATTC", cur_pos + 1) ... if pos == -1: ... break ... cur_pos = pos ... all_sites.append(pos) Hope this helps! Brad From chapmanb at uga.edu Wed May 5 13:54:52 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 14:03:57 2004 Subject: [BioPython] Robustness of parsing In-Reply-To: References: Message-ID: <20040505175452.GA65164@evostick.agtec.uga.edu> Hi Stephan; > I have a question about the robustness of parsing in my case the UniGene > at NCBI. > I have been assigned to write a parser to put the UniGene flat files > into an existing database structure, before starting writing code I thought > I'd better search the web to find some existing solutions. This is when I > opened your site and found a parser for the UniGene. The Biopython parser is designed to parse the UniGene cluster HMTL pages which list the EST sequences making up a cluster. Honestly, I'm not sure if it is well maintained currently and will work with the current UniGene pages. I'm not sure exactly what kind of UniGene information you want to be parsing. If by flatfiles you are talking about the downloads available from: ftp://ftp.ncbi.nih.gov/repository/UniGene/ then you can parse this with the standard Fasta parser in Biopython, but would then need to build up some code to parse the UniGene specific information out of of the Fasta headers. > At my work we already have a parser for these flat files written in C, > the only problem with this parser is, is that it will not run anymore > if the structure of the UniGene changes. For instance if a new field is > added or if relations change from a 1-to-1 to 1-to-many. > My question about biopython; has it the same problems? If that is the case; > in what timespan are updates available? To answer in general terms (due to my lack of understanding about exactly what you are parsing), most parsers will suffer from this same problem -- it is really not possible to anticipate all of the various changes which will happen to flat file formats. The benefit of writing code in a Biopython-ish (or BioPerl-ish, BioJava-ish -- it applies to them all) are two fold: 1. There are already existing utilities and structures for parsing flat files which make writing the parsers easier. In Biopython these include the Martel regular expression and the Scanner/Consumer frameworks. 2. Since your code is publicly available and others are using it, the inevitable job of updating parsers is distributed over multiple people who can offer suggestions and fixes. > If biopython is also lacking these problems I want to write a > more generetic solution, perhaps in python. We certainly would welcome a robust solution for parsing UniGene in Biopython. Please feel free to ask more questions here; sorry if I don't have a full grasp on exactly what you are parsing but I hope this helps some. Brad From chapmanb at uga.edu Wed May 5 13:57:55 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 14:06:59 2004 Subject: [BioPython] GenBank parser In-Reply-To: <40910B22.6040705@scri.sari.ac.uk> References: <40910B22.6040705@scri.sari.ac.uk> Message-ID: <20040505175755.GB65164@evostick.agtec.uga.edu> Hi Leighton; > I've noticed an oddity in the GenBank FeatureParser (CVS installation > 19/4). While parsing the Salmonella typhi file NC_003198.gbk, my way of > dealing with 'gene' tags fell over. This turned out to be because the > GenBank file contains entries with valueless tags such as /partial and > /pseudo. The current parser concatenates these tags with the following > tag. Ah, good catch. Yes, I was dealing with these incorrectly in the parsing. The problem, briefly, was that Martel generates two feature_qualifier_name XML tags in a row (pseudo and gene) without an intervening XML tag. In these cases, the parsing framework assumes that the two tags are the same set of information, but split up over multiple tags. Since XML can split long reems of information over multiple tags, this is a safe assumption in most places but falls apart here. A fix for this was just checked in CVS, in which the feature_qualifier_name tags are handled correctly. Thanks for the bug report! Brad From chapmanb at uga.edu Wed May 5 14:08:42 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 14:17:47 2004 Subject: [BioPython] FormatIO + Fasta parser + BioDB. In-Reply-To: <1083273079.14904.37.camel@numero2> References: <1083273079.14904.37.camel@numero2> Message-ID: <20040505180842.GE65164@evostick.agtec.uga.edu> Hi Christian; > I'm writing a procedure to store files in a BioDB but I have the > following error: > """ > ... > File "/usr/lib/python2.2/site-packages/BioSQL/Loader.py", line 209, in > _load_bioentry_table > if record.id.find('.') >= 0: # try to get a version from the id > AttributeError: 'NoneType' object has no attribute 'find' > """ > I feel that is because I don't define the title2ids function for the > Fasta parser. If I'm right, how can I tell to the FormatIO module to use > a title2ids function? Yes, you have the problem figured exactly. The solution is actually to not use the FormatIO module. That's more appropriate for automated format conversions and you will probably need a finer scale of work here to specifically parse out ids and descriptions from the Fasta title headers. To do this, use the standard Fasta.SequenceParser and Fasta.Iterator classes, along with a title2ids function. The adjusted code which should work is: from Bio import Fasta def your_title_to_ids(title): # write this for your specific FASTA titles # to return name, id and description def SequenceStoreFile(SeqFile, database, format='genbank'): server = BioSeqDatabase.open_database(driver='MySQLdb', user='bio', passwd='bio', host='localhost', db='bio') if server[database]: db = server[database] else: db = server.new_database(database) parser = Fasta.SequenceParser(title2ids = your_title_to_ids) itr = Fasta.Iterator(SeqFile, parser) db.load(itr) return if __name__ == "__main__": SequenceStoreFile(open('example.fasta'), 'estC', 'fasta') Sorry about the confusion and I hope this helps. Brad From chapmanb at uga.edu Wed May 5 14:56:19 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 15:05:26 2004 Subject: [BioPython] HSPs in Blast parser In-Reply-To: <20040430042600.6570.qmail@web90001.mail.scd.yahoo.com> References: <20040430042600.6570.qmail@web90001.mail.scd.yahoo.com> Message-ID: <20040505185619.GF65164@evostick.agtec.uga.edu> Hi Jawad; Sorry for the delay in getting back with you. > I am stuck on parsing a BlastN output and would appreciate some help. > I am working on multiple HSPs for a single hit . For example if there > are two hsps found for one hit, I need to find where query and subject > ends for one hsp and then compare it with the query and subject start > for the next hsp > > I have noticed that in the blast parser one can iterate through each > hsp for every single hit, but am not too sure how to treat two hsps of > a single hit as related and iterate through the two hsps of a single hit > in order to find the query (and subject) end of one and query (and subject) > start of the other. You just need to iterate through each alignment and then through the HSPs in each alignment. Then you can collect up the start and end coordinates of each HSP and associate them with the overall alignment. So, step by step: 1. Iterate through each alignment. 2. Create lists of HSP information for queries and subjects 2a. Iterate through each HSP 2b. Get the start and end coordinates from the hsp.query_start and hsp.sbjct_start attributes of the hsps 2c. Calculate the HSP ends using the query and subject information, removing gaps added by BLAST 2d. Add each start, end to the lists 3. You have the HSP lists, associated with the alignment title. Here is some code which demonstrates this: from Bio.Blast import NCBIStandalone parser = NCBIStandalone.BlastParser() rec = parser.parse(open("blast.out")) for align in rec.alignments: query_hsps = [] sbjct_hsps = [] for hsp in align.hsps: # adjust query starts to python (0-based) coordinates query_start = hsp.query_start - 1 # get the end from the length minus gaps query_end = query_start + len(hsp.query.replace("-", "")) sbjct_start = hsp.sbjct_start - 1 sbjct_end = sbjct_start + len(hsp.sbjct.replace("-", "")) query_hsps.append((query_start, query_end)) sbjct_hsps.append((sbjct_start, sbjct_end)) print "Hit", align.title print "Query HSPs", query_hsps print "Subject HSPs", sbjct_hsps Hope this helps! Brad From chapmanb at uga.edu Wed May 5 15:07:23 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 15:16:27 2004 Subject: [BioPython] Lowess function for nonparametric regression In-Reply-To: <4091F915.2060101@ims.u-tokyo.ac.jp> References: <4091F915.2060101@ims.u-tokyo.ac.jp> Message-ID: <20040505190723.GG65164@evostick.agtec.uga.edu> Hi Michiel; > Recently I wrote a pure Python implementation of the Lowess function for > nonparametric regression. Great. I see no reason why it shouldn't go into Biopython -- if it is a computational bit useful to you, then I'm sure it's useful to others doing gene expression work. > If this function is useful for other computational biologists, I can submit > it to Biopython. In that case, which module would this fall under? Or can I > just make a Lowess.py under Bio? The code is very short, about 25 lines of > Python for the actual function. The Lowess.py under Bio makes the most sense under the current scheme, but I guess I'm not sure if that is the overall best thing. Do you think it would be more useful to have a "Stats" module or something which would collect some of these various useful statistics bits into an easier to find place then scattered throughout Bio? I don't really think we need a deep directory structure, but maybe something analogous to Bio/SeqUtils. On the other hand, I guess I'm not sure if this would lead to moving a lot of modules under Bio to there, which might be too much of a mess. Since you're using these, what's your opinion? Thinking about it now, adding a Lowess.py is the "easiest" solution now, so I may lean towards that. But-yeah-we-definitely-want-it-even-if-I-am-quite-confused-ly yr's, Brad From chapmanb at uga.edu Wed May 5 15:12:11 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 5 15:21:15 2004 Subject: [BioPython] New version of Tm In-Reply-To: <40984B26.4000808@asalup.org> References: <40984B26.4000808@asalup.org> Message-ID: <20040505191211.GH65164@evostick.agtec.uga.edu> Hi Sebastian; > I did send this to Brad the 4-18, but still is not into the CVS. So I > send it here, maybe the original mail fell into a spam filter :) > Here is a code update (1.4 version). It has some correction that Olivier > Friard point me at my code. > This should go here: [biopython]/biopython/Bio/SeqUtils/MeltingTemp.py > I send it as an attach. Thanks. Yes, I didn't get the other mail from you -- I think .zip attachments do actually get a lot of attention from spam filters these days, so it's possible it ended up in my junk folder without noticing. But, either way -- I've got it now and just committed it to CVS. Let me know if I messed anything up -- thanks for the update! Brad From JBonis at imim.es Thu May 6 05:12:19 2004 From: JBonis at imim.es (Bonis Sanz, Julio) Date: Thu May 6 05:16:26 2004 Subject: [BioPython] Problems parsing proteins Message-ID: <492487A64F98A94EBAC5AE2CBA7D1A18B5A16F@fornells.imim.es> Hi all!, I am trying to get some info about proteins from NCBI. This is a very simple example: ####################### from Bio import GenBank rParser = GenBank.FeatureParser() rDict = GenBank.NCBIDictionary(database='proteins'),parser = rParser) rDict[4503383] ####################### but it returns this error: Traceback (most recent call last): File "", line 1, in ? File "c:\apache2\python\Lib\site-packages\Bio\GenBank\__init__.py", line 1574, in __getitem__ raise KeyError, "I unexpectedly got back html-formatted data." KeyError: I unexpectedly got back html-formatted data. I can not find a solution, maybe NCBI has change its formats?... If somebody can help!!!!! Julio Bonis Sanz MD http://www.juliobonis.com/portal/ Biomedical Informatics Laboratory Group of Research in Biomedical Informatics (GRIB) http://www.imim.es/grib/ Municipal Institute of Medical Research (IMIM) http://www.imim.es/ Barcelona - Spain From JBonis at imim.es Thu May 6 05:47:14 2004 From: JBonis at imim.es (Bonis Sanz, Julio) Date: Thu May 6 05:51:14 2004 Subject: [BioPython] Problems parsing proteins Message-ID: <492487A64F98A94EBAC5AE2CBA7D1A18B5A170@fornells.imim.es> I have reviewed and get an error: The code is now: ####################### from Bio import GenBank rParser = GenBank.FeatureParser() rDict = GenBank.NCBIDictionary(database='protein'),parser = rParser) rDict[33990955] ####################### (the error was in the definition of database, protein is correct instead of proteins) but it gives me an error also: Traceback (most recent call last): File "", line 1, in ? File "c:\apache2\python\Lib\site-packages\Bio\GenBank\__init__.py", line 1554, in __getitem__ raise KeyError, x KeyError: ERROR, possibly because id not available? If you try in a browser: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=33990955 It works (so the id 33990955 is available). In my computer, I have no problems to retrieve genes (nucleotide database)... I have found errors with proteins only. Waiting for comments. Julio Bonis Sanz MD http://www.juliobonis.com/portal/ Biomedical Informatics Laboratory Group of Research in Biomedical Informatics (GRIB) http://www.imim.es/grib/ Municipal Institute of Medical Research (IMIM) http://www.imim.es/ Barcelona - Spain -----Mensaje original----- De: Bonis Sanz, Julio Enviado el: jueves, 06 de mayo de 2004 11:12 Para: biopython@biopython.org Asunto: [BioPython] Problems parsing proteins Hi all!, I am trying to get some info about proteins from NCBI. This is a very simple example: ####################### from Bio import GenBank rParser = GenBank.FeatureParser() rDict = GenBank.NCBIDictionary(database='proteins'),parser = rParser) rDict[4503383] ####################### but it returns this error: Traceback (most recent call last): File "", line 1, in ? File "c:\apache2\python\Lib\site-packages\Bio\GenBank\__init__.py", line 1574, in __getitem__ raise KeyError, "I unexpectedly got back html-formatted data." KeyError: I unexpectedly got back html-formatted data. I can not find a solution, maybe NCBI has change its formats?... If somebody can help!!!!! Julio Bonis Sanz MD http://www.juliobonis.com/portal/ Biomedical Informatics Laboratory Group of Research in Biomedical Informatics (GRIB) http://www.imim.es/grib/ Municipal Institute of Medical Research (IMIM) http://www.imim.es/ Barcelona - Spain _______________________________________________ BioPython mailing list - BioPython@biopython.org http://biopython.org/mailman/listinfo/biopython From lpritc at scri.sari.ac.uk Thu May 6 05:56:08 2004 From: lpritc at scri.sari.ac.uk (Leighton Pritchard) Date: Thu May 6 06:00:12 2004 Subject: [BioPython] GenBank parser In-Reply-To: <20040505175755.GB65164@evostick.agtec.uga.edu> References: <40910B22.6040705@scri.sari.ac.uk> <20040505175755.GB65164@evostick.agtec.uga.edu> Message-ID: <409A0BB8.7060906@scri.sari.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Brad, Brad Chapman wrote: |>I've noticed an oddity in the GenBank FeatureParser (CVS installation |>19/4). | A fix for this was just checked in CVS, in which the | feature_qualifier_name tags are handled correctly. Excellent! | Thanks for the bug report! No problem; thank you for the quick fix. - -- Dr Leighton Pritchard AMRSC D104, PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK E: lpritc@scri.sari.ac.uk W: http://bioinf.scri.sari.ac.uk/lp/index.shtml T: +44 (0)1382 532761 ext.2405 F: +44 (0)1382 568578 PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFAmgu4L1gZ+OWLpBsRAsu3AJ9dzegaqiAVk8RLSOuXVzB7FSWsTwCgprq2 uh+EbyRHMZ9x/cupE0GahNM= =pV0S -----END PGP SIGNATURE----- From thamelry at binf.ku.dk Thu May 6 05:12:40 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Thu May 6 07:40:27 2004 Subject: [BioPython] Bio.PDB documentation Message-ID: <200405061112.40684.thamelry@binf.ku.dk> Hi everybody, I've added documentation about Bio.PDB (Biopython's structural bioinformatics module) to the CVS. It's a 13 page document in FAQ format. The FAQ is available in Latex and Lyx format. Typing 'make' in the Doc directory should generate a PDF file (biopdb_faq.pdf). I'd like to add some info on Bio.SCOP and Bio.FSSP as well...anyone? Cheers, -Thomas From mdehoon at ims.u-tokyo.ac.jp Thu May 6 08:35:34 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Thu May 6 08:39:18 2004 Subject: [BioPython] Lowess function for nonparametric regression In-Reply-To: <20040505190723.GG65164@evostick.agtec.uga.edu> References: <4091F915.2060101@ims.u-tokyo.ac.jp> <20040505190723.GG65164@evostick.agtec.uga.edu> Message-ID: <409A3116.7080104@ims.u-tokyo.ac.jp> Brad Chapman wrote: > The Lowess.py under Bio makes the most sense under the current > scheme, but I guess I'm not sure if that is the overall best thing. > Do you think it would be more useful to have a "Stats" module or > something which would collect some of these various useful > statistics bits into an easier to find place then scattered > throughout Bio? I don't really think we need a deep directory > structure, but maybe something analogous to Bio/SeqUtils. > > On the other hand, I guess I'm not sure if this would lead to moving > a lot of modules under Bio to there, which might be too much of a > mess. I had a look at the other modules under Bio. There are a couple of supervised learning routines there, but they wouldn't fit well as part of a Bio.Statistics module. However, there are a couple of other statistics-related routines that would be nice to have in Biopython (e.g. routines to estimate probability density functions or alternative non-parametric regression models). So I would argue for a Bio.Statistics module containing the Lowess function for now and hopefully other routines later, but keep the existing modules under Bio where they are. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chapmanb at uga.edu Thu May 6 12:03:25 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Thu May 6 12:12:27 2004 Subject: [BioPython] Problems parsing proteins In-Reply-To: <492487A64F98A94EBAC5AE2CBA7D1A18B5A170@fornells.imim.es> References: <492487A64F98A94EBAC5AE2CBA7D1A18B5A170@fornells.imim.es> Message-ID: <20040506160325.GB67146@evostick.agtec.uga.edu> Hi Julio; [The following NCBIDictionary code gives errors]: > from Bio import GenBank > rParser = GenBank.FeatureParser() > rDict = GenBank.NCBIDictionary(database='protein'),parser = rParser) > rDict[33990955] > > If you try in a browser: > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=33990955 > > It works (so the id 33990955 is available). The long and short of it is that NCBIDictionary uses old Entrez retrieval code, which really doesn't work reliably any longer. Getting just about anything about from NCBI should be done using the new EUtils interface, which is supported and much more reliable. So, I've updated the code for NCBIDictionary, search_for and download_many in Bio.GenBank to use the EUtils interfaces. This is checked into CVS, and will be available in the next release (which I hope to make soon). To get working code for yourself, you can do one of two things: 1. Update Biopython from anonymous CVS (see http://cvs.biopython.org for instructions) and use the new code. 2. Use the EUtils interface, which is in the 1.24 release. To retrieve using EUtils, your code would need to look like: # get the record from Bio.EUtils import DBIds, DBIdsClient db_ids = DBIds("protein", ["33990955"]) eutils_client = DBIdsClient.from_dbids(db_ids) result_handle = eutils_client.efetch(retmode = "text", rettype = "gp") # parse the result from Bio import GenBank parser = GenBank.FeatureParser() rec = parser.parse(result_handle) Thanks for the report. I hope one of the two solutions works for you. Brad From chapmanb at uga.edu Thu May 6 12:07:42 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Thu May 6 12:16:45 2004 Subject: [BioPython] Bio.PDB documentation In-Reply-To: <200405061112.40684.thamelry@binf.ku.dk> References: <200405061112.40684.thamelry@binf.ku.dk> Message-ID: <20040506160742.GC67146@evostick.agtec.uga.edu> Hi Thomas; > I've added documentation about Bio.PDB (Biopython's structural > bioinformatics module) to the CVS. It's a 13 page document in FAQ > format. > > The FAQ is available in Latex and Lyx format. Typing 'make' in the Doc > directory should generate a PDF file (biopdb_faq.pdf). This is great -- thanks much! I added the pdf to the documentation section of the web page. I really appreciate the work you put into it; makes me almost wish I worked on structural stuff. > I'd like to add some info on Bio.SCOP and Bio.FSSP as well...anyone? I believe SCOP code is due to the hard work of both Jeff and Gavin Crooks, and the FSSP code is credited to Iddo. I'm sure no one would mind if you helped them with documentation :-). Brad From chapmanb at uga.edu Thu May 6 12:11:21 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Thu May 6 12:20:22 2004 Subject: [BioPython] Lowess function for nonparametric regression In-Reply-To: <409A3116.7080104@ims.u-tokyo.ac.jp> References: <4091F915.2060101@ims.u-tokyo.ac.jp> <20040505190723.GG65164@evostick.agtec.uga.edu> <409A3116.7080104@ims.u-tokyo.ac.jp> Message-ID: <20040506161121.GD67146@evostick.agtec.uga.edu> Hi Michiel; > I had a look at the other modules under Bio. There are a couple of > supervised learning routines there, but they wouldn't fit well as part of a > Bio.Statistics module. Right, supervised learning stuff mostly -- you're right, my fault. > However, there are a couple of other > statistics-related routines that would be nice to have in Biopython (e.g. > routines to estimate probability density functions or alternative > non-parametric regression models). So I would argue for a Bio.Statistics > module containing the Lowess function for now and hopefully other routines > later, but keep the existing modules under Bio where they are. This sounds great to me. I just wanted to avoid having 18 different modules under Bio doing different statistical work, and also desired to make statistics code easy to find. So yeah, +1 from me on adding a Bio.Statistics module with the Lowess function. Go right on ahead and commit away. Thanks! Brad From chapmanb at uga.edu Thu May 6 12:24:29 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Thu May 6 12:33:31 2004 Subject: [BioPython] Plans for a 1.30 release next week Message-ID: <20040506162429.GE67146@evostick.agtec.uga.edu> Hello all; We've collected a lot of useful bug fixes, improvements, and new modules since the last release in mid-February, so I think it's about time for a new Biopython release. If it sounds good with everyone, I'd like to plan this for Tuesday of next week. This release has a lot more changes then normal, especially to some of the more widely used modules like the GenBank and Fasta parsers, so I'm planning on bumping this version up to 1.30 to reflect that. There may also be some issues we'll have to tackle with building the KDTree and Affy C++ extension, so we'll be dealing with those as well as any bugs that show up. Looking over the bug list, I believe we are in pretty good shape for a release. My major plans before the release (besides fixing any bugs that might come up) are pretty simple and more cosmetic then anything: 1. Remove the __all__ declarations in all of the modules. These are ugly to keep up and actually used by epydoc when figuring out which modules are public and private. I'd rather not deal with them, or only have them if a module really needs to be protected from import and use. 2. Go through code documentation again and make sure modules have at least some indication of their function and use. If anyone has code they are nearly finished with and would like to get checked in, or bugs that need to be fixed, please let the list know before next Tuesday. New releases. Woo woo. Brad From karel at javeriana.edu.co Thu May 6 12:42:52 2004 From: karel at javeriana.edu.co (=?ISO-8859-1?Q?Carlos_Manuel_Est=E9vez-Bret=F3n?=) Date: Thu May 6 12:47:13 2004 Subject: [BioPython] Count In-Reply-To: <20040506161121.GD67146@evostick.agtec.uga.edu> References: <4091F915.2060101@ims.u-tokyo.ac.jp> <409A3116.7080104@ims.u-tokyo.ac.jp> <20040506161121.GD67146@evostick.agtec.uga.edu> Message-ID: <6B008DFD-9F7C-11D8-9565-0030656749CC@javeriana.edu.co> Hi People! I'm new in the list, (also in Python) I have a tutorial of python for Biologists, from Pasteur Institute, in it is an example that use "count" command, but i'm having an error of not command not defined.. Could some one help this newby? _______ [Paradox:karel/Desktop/egenix-mx-base-2.0.5] karel# python Python 2.3 (#1, Sep 13 2003, 00:49:11) [GCC 3.3 20030304 (Apple Computer, Inc. build 1495)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> se = 'sgggggggggggggggggkljkljdiujdoiaudoiasud' >>> se 'sgggggggggggggggggkljkljdiujdoiaudoiasud' >>> long se >>> a = len(se) >>> a 40 >>> b = count(se, 'g') Traceback (most recent call last): File "", line 1, in ? NameError: name 'count' is not defined _______________________________ Carlos Manuel Est?vez-Bret?n R. Coordinador Unidad Sistemas Facultad de Ciencias Pontificia Universidad Javeriana Tel.(571) 320 8320 Ext.4033/32/75 El 06/05/2004, a las 11:11, Brad Chapman escribi?: From idoerg at burnham.org Thu May 6 12:59:00 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu May 6 13:04:39 2004 Subject: [BioPython] Count In-Reply-To: <6B008DFD-9F7C-11D8-9565-0030656749CC@javeriana.edu.co> References: <4091F915.2060101@ims.u-tokyo.ac.jp> <409A3116.7080104@ims.u-tokyo.ac.jp> <20040506161121.GD67146@evostick.agtec.uga.edu> <6B008DFD-9F7C-11D8-9565-0030656749CC@javeriana.edu.co> Message-ID: <409A6ED4.1050107@burnham.org> I guess the Pasteur Institute pages need updating, count() is a sequence method, not a function. Thus instead of: >>> count(se, 'g') use: >>> se.count('g') Iddo Carlos Manuel Est?vez-Bret?n wrote: > Hi People! > > I'm new in the list, (also in Python) > > I have a tutorial of python for Biologists, from Pasteur Institute, in > it is an example that use "count" command, but i'm having an error of > not command not defined.. > > Could some one help this newby? > > > _______ > [Paradox:karel/Desktop/egenix-mx-base-2.0.5] karel# python > Python 2.3 (#1, Sep 13 2003, 00:49:11) > [GCC 3.3 20030304 (Apple Computer, Inc. build 1495)] on darwin > Type "help", "copyright", "credits" or "license" for more information. > >>> se = 'sgggggggggggggggggkljkljdiujdoiaudoiasud' > >>> se > 'sgggggggggggggggggkljkljdiujdoiaudoiasud' > >>> long se > >>> a = len(se) > >>> a > 40 > >>> b = count(se, 'g') > Traceback (most recent call last): > File "", line 1, in ? > NameError: name 'count' is not defined > > _______________________________ > Carlos Manuel Est?vez-Bret?n R. > > Coordinador Unidad Sistemas > Facultad de Ciencias > Pontificia Universidad Javeriana > > Tel.(571) 320 8320 Ext.4033/32/75 > El 06/05/2004, a las 11:11, Brad Chapman escribi?: > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From singerg at tcd.ie Thu May 6 13:27:11 2004 From: singerg at tcd.ie (Greg Singer) Date: Thu May 6 13:32:17 2004 Subject: [BioPython] Count In-Reply-To: <409A6ED4.1050107@burnham.org> References: <4091F915.2060101@ims.u-tokyo.ac.jp> <409A3116.7080104@ims.u-tokyo.ac.jp> <20040506161121.GD67146@evostick.agtec.uga.edu> <6B008DFD-9F7C-11D8-9565-0030656749CC@javeriana.edu.co> <409A6ED4.1050107@burnham.org> Message-ID: <1083864431.409a756f0ee6b@mymail.tcd.ie> Count became a string method back around Python 2.0 if I recall correctly. Before that, you had to import it from the string module. You can still do that for backwards compatibility: from string import count print count('aaabbbccc','c') - Greg Quoting Iddo Friedberg : > I guess the Pasteur Institute pages need updating, count() is a sequence > method, not a function. Thus instead of: > > >>> count(se, 'g') > > > use: > > >>> se.count('g') > > > Iddo > From lpritc at scri.sari.ac.uk Fri May 7 06:28:42 2004 From: lpritc at scri.sari.ac.uk (Leighton Pritchard) Date: Fri May 7 06:32:43 2004 Subject: [BioPython] Ace parser Message-ID: <409B64DA.2040706@scri.sari.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Frank, One of my .ace output files had a contig whose record ended immediately after a 'QA' line. I fixed the problem locally in Ace.py at line 350 with the following after the parser checks for 'QA'. ######## ~ read_and_call(uhandle,consumer.qa,start='QA ') ~ # Changed by LP 7/5/04 ~ try: ~ read_and_call_while(uhandle,consumer.noevent,blank=1) ~ except SyntaxError: ~ consumer.end_contig ~ return ~ line = safe_peekline(uhandle) ~ if line.startswith('DS'): ~ read_and_call(uhandle,consumer.ds,start='DS ') ######## Again, you might be wanting a more elegant solution ;) The above also accounts for situations in which my last suggestion (for the absence of a 'DS' line broke. Best, - -- Dr Leighton Pritchard AMRSC D104, PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK E: lpritc@scri.sari.ac.uk W: http://bioinf.scri.sari.ac.uk/lp/index.shtml T: +44 (0)1382 532761 ext.2405 F: +44 (0)1382 568578 PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFAm2TaL1gZ+OWLpBsRAm1FAKCqv12bFyQgeD8dPwIF5MFsKmoWGgCfd+Zd RthLO14Wrj3iuMVYXLFcGY8= =SAys -----END PGP SIGNATURE----- From bioboy at uga.edu Mon May 10 03:05:52 2004 From: bioboy at uga.edu (Xian) Date: Mon May 10 03:09:48 2004 Subject: [BioPython] optimal integration of primer3 into biopython and others using swig and biomoby In-Reply-To: <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> References: <409CB249.2090900@uga.edu> <70D7B115-A117-11D8-A663-000A956845CE@stanfordalumni.org> Message-ID: <409F29D0.7010708@uga.edu> optimal integration of primer3 into biopython and others using swig and biomoby Abstract: Primer3 is the de facto open source C program for automated PCR primer selection; it is used by emboss and biopython, among others. There is no active development [last release 0.9 9/98]. I have used primer3 and python to study Arabidopsis genome function. I aim to integrate primer3 into biopython. Specifically, my goal is to develop primer3 into a set of C modules or libraries to provide: a) standardized access via python, perl, etc b) impetus to further primer3 development. I propose here an optimal development path that maximizes target audience while minimizing code rewriting. Discussion: TTBOMK, Biopython and bioperl each have a primer3 i/o parser. These multiple, unstandardized dependencies may hinder future primer3 development [such as the addition of R. Griffais's K-tuple frequency method, Nucl. Acids. Res. 1991 19: 3887-3891 ]. My aim is to develop primer3 into a maintainable and easily extendable set of C modules or libraries that are natively accessible by perl and python. Swig is a "C compiler" that provide this functionality; e.g. primer3's Tm analysis module [oligotm.h and oligotm.c] can be compiled and imported as a python module whose methods are native C functions. Once this is done adding new language support is trivial. Well-defined, standard i/o structures for these libraries will facilitate their use by the bioinformatics community from within perl or python, and should be considered in development. Biomoby is an XML-based data ontology which represents data as heirarchical objects in the ontology, e.g. the hypothetical object "PrimerPair" contains two instances of "DNASequence" along with any other data such as Tm, self-hybridization, etc. Designing a biomoby object for primer3 data i/o has the additional benefit of easing information-sharing with existing databases and other biomoby-aware services. Please reply if you are interested in using, testing, designing, or developing this project. Likewise, feel free to forward this to such people. If there is sufficient interest, I will spawn a mailing group or possibly a sourceforge project. Thanks for your time, xian References/Links: Primer3[down at time of writing]: http://www-genome.wi.mit.edu/genome_software/other/primer3.html Emboss's eprimer3 [primer3 wrapper]: http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/eprimer3.html SWIG, Simplified Wrapper and Interface Generator: http://www.swig.org/ biomoby: http://www.biomoby.org/overview.html biomoby, bioperl, and much more: http://open-bio.org/ From gec at compbio.berkeley.edu Mon May 10 15:49:23 2004 From: gec at compbio.berkeley.edu (Gavin Crooks) Date: Mon May 10 15:53:20 2004 Subject: [BioPython] Plans for a 1.30 : Re: SCOP In-Reply-To: <20040506162429.GE67146@evostick.agtec.uga.edu> References: <20040506162429.GE67146@evostick.agtec.uga.edu> Message-ID: <22A49D88-A2BB-11D8-8245-000393B63894@compbio.berkeley.edu> > Hello all; > We've collected a lot of useful bug fixes, improvements, and new > modules since the last release in mid-February, so I think it's > about time for a new Biopython release. If it sounds good with > everyone, I'd like to plan this for Tuesday of next week. A code cleanup a few months ago broke the Bio.SCOP code. I'd like to commit the bug fix, and integrate the SCOP unit tests into the biopython testing framework, preferably before the release. However, I can't seem to access the developer CVS repository. What is the current machine? dev.open-bio.org doesn't seem to exist. For that matter, do I still have an account!? Of lower priority, James Casbon has contributed some useful extensions to the SCOP module that I would like to upload in the near future. Gavin -- Gavin E. Crooks Postdoctoral Fellow tel: (510) 642-9614 461 Koshland Hall aim:notastring University of California http://threeplusone.com/ Berkeley, CA 94720-3102, USA gec@compbio.berkeley.edu From chapmanb at uga.edu Mon May 10 15:57:41 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Mon May 10 16:06:34 2004 Subject: [BioPython] Plans for a 1.30 : Re: SCOP In-Reply-To: <22A49D88-A2BB-11D8-8245-000393B63894@compbio.berkeley.edu> References: <20040506162429.GE67146@evostick.agtec.uga.edu> <22A49D88-A2BB-11D8-8245-000393B63894@compbio.berkeley.edu> Message-ID: <20040510195741.GA81206@evostick.agtec.uga.edu> Hi Gavin; > A code cleanup a few months ago broke the Bio.SCOP code. I'd like to > commit the bug fix, and integrate the SCOP unit tests into the biopython > testing framework, preferably before the release. Yeah, uh, that breakage would be me. Sorry about that. That type of cleanup to Bio.SCOP would be much appreciated -- I'll happily delay the release until you feel that the SCOP module is ready. Thanks a lot for looking at this. > However, I can't seem to access the developer CVS repository. What is > the current machine? dev.open-bio.org doesn't seem to exist. For that > matter, do I still have an account!? You do, but the machine has changed. I'll re-set your password and send you the details via a separate mail. > Of lower priority, James Casbon has contributed some useful extensions > to the SCOP module that I would like to upload in the near future. Great, also very welcome. Thanks again for your work on this! Brad From gec at compbio.berkeley.edu Mon May 10 17:14:52 2004 From: gec at compbio.berkeley.edu (Gavin Crooks) Date: Mon May 10 17:18:47 2004 Subject: [BioPython] Plans for a 1.30 : Re: SCOP In-Reply-To: <20040510195954.GB81206@evostick.agtec.uga.edu> References: <20040506162429.GE67146@evostick.agtec.uga.edu> <22A49D88-A2BB-11D8-8245-000393B63894@compbio.berkeley.edu> <20040510195954.GB81206@evostick.agtec.uga.edu> Message-ID: <143B8A5D-A2C7-11D8-8245-000393B63894@compbio.berkeley.edu> SCOP has been bug fixed, and I've integrated a bunch of tests into biopython/Tests. I'd appreciate it if someone would do a "cvs update -d", and check that the new unit tests work on a machine other than my own. Thanks, Gavin -- Gavin E. Crooks Postdoctoral Fellow tel: (510) 642-9614 461 Koshland Hall aim:notastring University of California http://threeplusone.com/ Berkeley, CA 94720-3102, USA gec@compbio.berkeley.edu From chapmanb at uga.edu Mon May 10 17:18:17 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Mon May 10 17:27:07 2004 Subject: [BioPython] Plans for a 1.30 : Re: SCOP In-Reply-To: <143B8A5D-A2C7-11D8-8245-000393B63894@compbio.berkeley.edu> References: <20040506162429.GE67146@evostick.agtec.uga.edu> <22A49D88-A2BB-11D8-8245-000393B63894@compbio.berkeley.edu> <20040510195954.GB81206@evostick.agtec.uga.edu> <143B8A5D-A2C7-11D8-8245-000393B63894@compbio.berkeley.edu> Message-ID: <20040510211817.GA81369@evostick.agtec.uga.edu> Hi Gavin; > SCOP has been bug fixed, and I've integrated a bunch of tests into > biopython/Tests. > I'd appreciate it if someone would do a "cvs update -d", and check that > the new unit tests work on a machine other than my own. All of the test_SCOP*'s pass for me. The only change I made was to remove Bio.SCOP.tests from setup.py since you got rid of that. Otherwise, worked just fine. I'll remove the long-standing bug in the database about this. Woo hoo. Thanks again. Brad From dag at sonsorol.org Mon May 10 20:25:26 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon May 10 20:32:38 2004 Subject: [BioPython] {off topic} Apple is giving away 5 workgroup sized clusters in a program for bioinformatics researchers Message-ID: <40A01D76.3010502@sonsorol.org> Hi folks, Apologies for the semi off topic posting but I think it may be appropriate because I know lots of people doing really clever informatics stuff tend to be on the open-bio.org mailing lists. I want to make sure many of the small group, individuals and DIY types hear about this as they can probably benefit the most from a influx of hardware. In short, Apple just announced a program to give away 5 fully provisioned mini-clusters (4 Xserve G5 nodes) in a judged process specifically aimed at bioinformatics types. Awards are announced on 29 June 2004. The URL is here: http://www.apple.com/science/clusteraward/ Regards, Chris From dag at sonsorol.org Tue May 11 10:01:20 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue May 11 10:05:21 2004 Subject: [BioPython] testing a new Open-Bio website and mail list archive search Message-ID: <40A0DCB0.1050207@sonsorol.org> Hello Everyone, A fantastic volunteer (Kyle Jensen) has been steathily working on a problem for us that has long been a major issue for us -- website searching and indexing. We've tried various solutions and ht://dig implementations in the past and nothing really worked well. Kyle has been setting up a search indexing system based on the code from www.swish-e.org and so far it looks very very promising. We have 2 main indexed search sites: This page is a search index for all of the open-bio hosted websites: http://search.open-bio.org/cgi-bin/obf-search.cgi This page is just for searching mailing list archives: http://search.open-bio.org/cgi-bin/mail-search.cgi Please give the pages a whirl and let me know what you think. Thanks again Kyle! -Chris open-bio.org admin team From delivery at hosyou-b.mine.nu Tue May 11 09:53:17 2004 From: delivery at hosyou-b.mine.nu (=?iso-2022-jp?Q?=1B=24B3t=3C02q=3CR7P=3AQJ88K=1B=28B?=) Date: Tue May 11 10:20:56 2004 Subject: [BioPython] =?iso-2022-jp?b?GyRCIiMjNkBpS3wxX0t4JEchIkcvPH0bKEI=?= =?iso-2022-jp?b?GyRCSVRCLSROSn0kSzQ/N14iIyMyQGlLfDFfIzEyLzFfIzQyLzFfGyhC?= =?iso-2022-jp?b?GyRCPlo1ck0tPH1GfiROSn1LISIjMj84TiRLTFkkKyRrJHJDTiRrGyhC?= =?iso-2022-jp?b?GyRCSn1LISIjGyhCMDA1MTAbJEI5ZhsoQg==?= Message-ID: <16943039.1084283597546.JavaMail.nobody@hosyou-b.mine.nu> biopython@biopython.org様 　　　[時代のめーるマガジン]更なる高収入高利益へご招待のチャンスニュース・００５１０号 　　　あなた様も景気回復に便乗！中国オリンピックの特需景気により、本格的に景気回復が始まりました。 ━━＜PR＞━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 　 http://hosyou003.orgdns.org/zaitakubuisiness10.htm　　 ┏━　売れています　━━━━━━━━━━━━━━━━━━━━━━━━━━５億９千万円ビジネス━━┓　　　　 http://hosyou003.orgdns.org/qanda11.html 　　　　　 ●２　億　円、３　億　円　以上の収入者続出しています。ネットで、はがきで、できます●　　　 ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛ 　　　　　　　　　　　　　　　 今すぐアクセス→→→http://hosyou003.orgdns.org 　　　　年収６千万円　に　不足　している方に　歓迎されています！　論より証拠で　目的収入は最高！ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━＜PR＞━━━━ 　　　■■　【　５億９千万円　証拠有収入ネットビジネス・一人で５億９千万円収入の事実　】　■■　 　　　　　　　 　 証拠は>日本の、韓国のオリンピック景気の時、周辺の国々は設備投資の恩恵を受けてバブル景気となり ました。 　 そのときに便乗した人・企業だけが巨額の収入となりました・景気に便乗しなかった個人・企業は万年不 景気の暮らしとなりました。日本と韓国の時と同じに、中国のオリンピック終了とともに不景気へ急降下 するのは当然の経済サイクルです。　　　 やっと景気回復開始■■株価高値の高額収入者続出■■これまでのように外人投資による株価上昇でなく 日本の個人投資が外人より多くなりました、これは景気回復の現象です。★満足を追求する★その材料に ３億円あるとよい★簡単、早く、達成したい★その景気に乗る時代に叶った方法は在宅ビジネスでもあり ます。 ■■問題は、確かな収入の裏付けである【証拠が有るか否か】見せるか見せないか・で真偽が確定します 確認は成功の秘訣です。　　　　　　　　　　　　　　　　　　　　（ 記：経済文庫担当中川和彦） *********************************■■●【　　目　次　　】●■■　**************************** 　 　[１] 時代メルマガ記事000419　　　　　　　　　　　　　　　　 ★ なぜ儲かる　・　儲からない □━━━━━━━━━━━━━━━【　今以上の　満足　を追求する　━━━━━━━━━━━━━━ 　　 [２]　　広　　　　　告 0675 　　　　　　　　　　〓お小遣い、満足するほど欲しい、方は歓迎 ■□━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 　　 [３] 　時代メルマガ記事000430　　　　　　　　　 　　　　　 ★ 億万長者 へ の 方法とは!! □━━━━━━━━━━━━━━━【　３　　億　円　収入証拠有　】━━━━━━━━━━━━━ 　　 [４]　広　　　　　告 0676 　　　　　 　〓２億３億円以上収入者続出、　証拠見せます ■□━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 　　 [５] 時代メルマガ記事000431　　　　　　　　　 　　　　　　 ★ 働けど　儲からないから脱出 　 ■□━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━　　　　　 <<<<<<<<<<<<<<<<<<<<<<<<<<<<■■■　　★記事　　〓広告　　■■<<<<<<<<<<<<<<<<<<<<<<<<<<< 　　■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛ 　　[１] 時代の波メルマガ記事000419　　　　　　　　 　　　　　　　★ なぜ儲かる　・儲からない！ 　　●世の中には人の何倍も働き苦労しても「儲からない」○悠々、ゆったり生活でも儲かる人がいます。 　　　　　この差は、急変する時代の波に＞便乗する・改革する・完全に切り替える・方（Aさん）・・時代 　　　　　の波を感じない、見逃す、放置する・方（Bさん）と、の差であることはどんな時代でも同じです。 　　　　　…☆…儲かる方法ーー時代の波とはーー便乗の方法はーー２億円儲ける方法は・・・ 　　　　　　　時代の波メルマガ記事000430に記事投稿します。配信停止しないでお待ちしては・・ 　　■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛　 　[２]　広　　　　　告 0675 　　　　　　　　　　〓　お小遣い、満足するほど欲しい、方は歓迎　 　　　　●在宅で、借り入れ、仕入れ、無くして　私みたいな普通の主婦が出来ちゃった多額の収入で生活向上 　　　　　し安心生活！詳しくは　 http://www.stage-one.jp/jc/ennko/　でどうぞ！ 　　■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛ 　　[３] 時代メルマガ記事000430　　　　　　　　　　　　　　　　★ 億万長者　へ　の方法とは・・　 　　　　●方法はあります。確実な証拠があります。簡単ビジネスに改善の連続で完成してあります。 　　　　成人ならできる！証拠からできる！証拠のあるのから始まると、騙されません！探せばあります！待て 　ば幸運なら舞い込みます。続編で次々お知らせ投稿いたします。 　　　　裁判は証拠主義です・金儲けも証拠主義は裁判官と同じ目線となり間違いはありません 　　　　次回投稿お待ちください。 （記事投稿者ー失敗成功の繰り返しで今成功者松原） 　　■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛ 　　[４]　広　　　　　告 0675 〓 ２億、３億円以上収入者続出、証拠見せます 　　●既に２億円３億円５億９千万円の収入者続出していますホームページをダウンロードして出来ます● 　　 　　　　　個人で出来る、在宅５億９千万円ビジネス　 　　　　◇既に、２億円、３億円、５億９千万円の収入者続出しています。 　　　　◇そんな、うまい話は今の時代に無い、本当か嘘か・・怪しい・・ 　　　　◇その通りです、何事も証拠を見て納得し十分確認するまでは当然の判断です。 　　　　◇証拠は見せます・見て下さい・見るまでは信用しないで下さい・何事も同じです！ 　　　　◇単なる証拠でなく「物的証拠」は、裁判判決の最終的決め手です。 　　　　◇銀行印有、実名有、年月日有、金額有の振込書を見てから判断してください。 　　　　　　　　　 ◇在宅で、成人男女は、ネットで、はがきで、２億３億目的で、兼業で、出来ます。 　 詳細資料【無料】請求希望の方はこちらから。 http://hosyou003.orgdns.org/page3.htm 　　 ■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛ 　 [５] 時代メルマガ記事000431　　　　　　　　　　　　　　　　　　　　 働けど儲からないから脱出 　　　●生涯型収入が得られる儲かるインターネットビジネス【無料】とは？→詳しくは語れません。 最も効果的な実証済みインターネットビジネスとは？　　 http://www.netlihe-oftice.com/ex/click □━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━□　　 ☆★☆★☆ 情報ステーション！お得な情報満載！おしらせ！☆★☆★☆★☆彡彡彡 　　　　　　　　　　提携キャンペーンがパワーアップしました。 　　　　　　　　　　クリック数＝あなたのＨＰを実際に見た方です。 　　　 　http://www.movezet.com/kurikku/afr/in.cgi?id=3 　 　　　 　アクセスアップ君 　　　 　 提携サイト１５０誌　４０万部以上に配信 　　　 　依頼があった広告を７日程度で配信します。短期決戦方の方に便利！ 　　　 　一番の人気は、複数の広告が依頼できる事！ 　　　 　三つの広告文があれば、５０誌ずつで配信！ビジネスが違ってもＯＫ！ 　　　 　とても経済的な、広告サイトです。 　　　 　　http://www.movezet.com/up/cgi/in.cgi?id=28 　　　　　 何はなくても千客万来様々な特典を受けられます。 　　　　　　　　　　ビジネスをされる方のビジネスです。 　　　 　　http://www.movezet.com/banrai/afr/in.cgi?id=72 　　　　　　　　☆★☆★☆★☆★　↓お得な情報満載！一括無料投稿↓　☆★☆★☆★☆★ 　　　　　　　　　　　　　完全無料で副収入！ホームページをプレゼント中！ 　http://www.southernclub.net/members/shimasyou.html 　完全無料で登録報酬を一気に獲得出来ます。宣伝技術のある方ならかなりの 　収入が得られます。ノーリスクで参加出来ますので損はしないと思います。 　本当に高収入！無料ビジネス参加者募集 http://www.baros.jp/net-bill/?ID=kushiyaki&PG=affili 実践すれば解る本当の無料登録高収入ビジネス！この情報を直にＧＥＴ！ すぐに、あなたの欲しがる！あの手この手を伝授して貰えます。 低リスクで高収入希望の貴方！必見ですョ！！」 http://ims326.fc2web.com/ 低リスクで気軽にビジネス開始ＯＫ！貴方の決断次第で 　 「本業の月収を超える収入獲得の絶好のチャンス！」 　　　　　　　 副収入応援団！ http://www.geocities.jp/openebluez1961/index.html 副収入応援団！！誇大広告はもう飽きた 。 在宅で、自分の時間で、できる副業。初心者の方にも簡単に取り掛かれものを重視しました。 「稼げる！」だから「辞めない！」 　　　　　　　　　　　　http://kirinkirin.fc2web.com/mikarin.htm 　　　　　　　　　　ビジネス辞退者がいない（少ない）と言うことは・・・ 　　　　　　　　　　永続的な収入が見込める！そんなビジネスを目指します！ 独占広告攻略のための実践Eメールセミナー http://1lejend.com/nouhau/1_pop.php?noumenid=000039 「どうやったら広告の効果があがるのか？」「儲かる広告・儲からない広告 その違いは？」「なぜ今まで集客できなかったのか？」が分かる！ あなたの組織が１０倍になります http://go.fc2.com/mlmsupport/ 自分から登録者を出す喜びをあなたにも。 この方法なら、間違いない！！ ちいさな島への紹介状 http://omosiro.com/~original1971/ 素敵な出会い。。　運命の出会い。。　 ちいさな島で一緒にさがしませんか？ 　ネットワーカーへ 　http://www.mlmsupport.jp/no1ryo/ 　今、組織図くりに悩まれてる方へ！ 　日本MLM総合研究所が、あなたのビジネスをサポートします★ 健康と収入アップに！！ http://www5e.biglobe.ne.jp/~kumara/au1/index.htm あなたに健康と収入を！！　 ヤンキースの選手も愛用している。 ３０日間無料仮登録でこのビジネスのすばらしさを体感して下さい。 オーダースーツ Pitty Savile Row http://www18.big.or.jp/~pitty/ オーダースーツ専門店。 １９３０年創業の高級紳士服店サポートサイト。￥２７８００〜 最強のドリーム・メール！ http://plaza.rakuten.co.jp/chicyan10151003/ 海外版リード・メールの最強版です！本当に凄いの一言です！！　　　　　　　　　　　　　　　　　　　 他には絶対にありませんよ！ Four Pillars http://fpillars99.fc2web.com/ 四つの柱（ビジネス・在宅、セキュリティ、ソフト、等など）から、 情報の提供、販売また自作ソフトの紹介、販売するサイトです。 集客のフェロモン！？ 大好評！行列を作っちゃうフェロモン集客法！ もう集客で悩みたくない方はクリック！！ http://1lejend.com/stepmail/kd.php?no=282 うそではありません。後は　私たちが　しっかりサポートします。 ■■■■『携帯かけ放題　ビジネスパートナー募集』■■■■ http://www.formzu.net/formgen.cgi?ID=b5439262 みんなが待ってた定額かけ放題の愛用者の募集のお仕事。 各地域限定　若干名募集します！チャンスを掴むのは今！！ NEW!日払い時給３万円の仕事！完全な独自手法です！ http://www.geocities.jp/randow4444/ この方法は我が社独自の方法のため、まだどこにも出回っておりません。 だいたい時給３万円程度は普通に稼げます。興味のある方のみご覧下さい。 【広告投稿随時募集中 】広告　5回掲載10日掲載で3000円　広告１７回掲載４５日掲載で４０００円 　　 　　　　　　　　　 広告１０回掲載６０日掲載で５０００円　無料投稿広告　　　　　　 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ■免責事項■　当メールマガジンに掲載している情報に関して発行者では一切の責任を負いません。一切 　　の責任を負いかねますのでご了承ください。掲載記事に関するお問い合わせは直接投稿者へお願いいたし 　　ます。 　■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━■ 　 ■　アドレスで解除　■広告申し込み■記事投稿は http://hosyou003.orgdns.org/teishi.html からお願いします。 購読お申し込みの方に配信していますがイタズラに他人のアドレスで購読申し込みと広告投稿がありご迷惑 をおかけしている場合もあり申しわけありません。 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 　発行元：ＳＢＣ通信 　　　　 サバー 管理者：株式会社ORIINTO　　めるまが編集者：K I T A 通 信 社 　配信 システム：楽々情報社使用　 発行：株式会社経済文庫　　　 発送技術事業者 ：ＤＨネトシステム社 　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　 ------------------------------------------- 5月11日17時発表 主要都市 今夜 明日 札幌 晴れ 晴れ 仙台 晴れ時々曇り 晴れ 東京 晴れ 晴れのち時々曇り 長野 晴れ 晴れ 静岡 晴れ 晴れ 名古屋 晴れ 晴れ 新潟 曇りのち時々晴れ 晴れ 金沢 曇り時々晴れ 晴れ 大阪 晴れ 晴れ 岡山 晴れ 晴れ 広島 晴れ 晴れ 高松 晴れ 晴れ 福岡 晴れ 晴れのち時々曇り 鹿児島 晴れ 晴れ 那覇 晴れ 晴れのち時々曇り From crocha at dc.uba.ar Tue May 11 12:58:15 2004 From: crocha at dc.uba.ar (Cristian S. Rocha) Date: Tue May 11 13:03:35 2004 Subject: [BioPython] Solved BioPython & Zope problem and a Bug? In-Reply-To: <20040504165538.GD602@misterbd.agtec.uga.edu> References: <1082736999.23447.67.camel@numero2> <20040504165538.GD602@misterbd.agtec.uga.edu> Message-ID: <1084294695.2235.150.camel@numero2> Brad, I tried to use the biopython in the cvs on zope but I had found my first problem: I'm working in Linux with Debian distribution, and the Zope deb package is compiled for python2.2. That the reason I had choose to compile Biopython with python2.2, but it's fail on tests! The Biopython tests are using "enumerate" function but it's only work on python2.3. I had to write the "enumerate" function to jump the problem. Can you append these function to the CVS? I'm attaching my code in the email. That's not the only problem with python2.2 compatibility, exists other tests as test_Registry.py who use the "in" operator between strings to check if exists substrings on assert functions. I had to replace a lot of asserts to make it compatible with python2.2. For example: def t_embl(self): """Retrieval of EMBL records from various sources. """ embl_db = db["embl"] for embl_location in embl_db.objs: #if embl_location.name.find("xembl") == -1: handle = embl_location[self.embl_id] first_line = handle.read(40) # --- # assert self.embl_id in first_line, \ # (embl_location.name, first_line) assert not first_line.find(self.embl_id) == -1, \ (embl_location.name, first_line) I had a Warning about the "yield" keyword. Can you check it? That's the warning line: /biopython/build/lib.linux-i686-2.2/Bio/PDB/StructureAlignment.py:84: Warning: 'yield' will become a reserved keyword in the future I feel I will find more problems. I would like to submit my changes to the cvs if you want. else, I must to check how to use Zope in python2.3... ;) Thanks, Cristian. El mar, 04-05-2004 a las 13:55, Brad Chapman escribi?: > Hi Cristian; > > > I could solve my problem with BioPython in Zope. > > Thanks for your work on this. I suspect there are not many people > out there (myself included) working with Zope and Biopython, so I > appreciate your work treading into unknown territory. > > > The main problem was > > Zope can't import some functions defined in some modules. These modules > > have other modules with relative imports and Zope can't import them. > > Okay, I guess the problem is that both Zope and Biopython are > probably playing around with import hooks. I don't know enough about > all of what Zope does to fix all of the problems, but I guess the > best way is trial and error. > > > Bio.config.FormatRegistry.py have the following relative import: > > > > import _support > > > > I change it to: > > > > from Bio.config import _support > > Fixed. > > > I do the same with FormatIO.py with ReseekFile import. > > Where specifically are these problems and I can add the relevant > full import? Do all relative imports need to be removed? > > > The second problem IS """Bio.MultiProc.copen""". I really don't know > > why, but Zope begin an infinity loop when I ask for the symbol table of > > the module. To solve these problem I commented the import on the > > Bio.config._support module. > > Okay, I moved this import into the __call__ function where it is > used. Hopefully that'll fix the import loops. > > Both of those changes are in CVS -- please let me know if that fixes > things or if other changes are needed. > > Thanks again for the work! > Brad > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- Lic. Cristian S. Rocha. Departamento de Computacin. FCEyN. UBA. Pabellon I. Cuarto 9. Ciudad Universitaria. (1428) Buenos Aires. Argentina. Tel: +54-11-4576-3390/96 int 714 Tel/Fax: +54-11-4576-3359 Cel: 15-5-607-9192 From chapmanb at uga.edu Tue May 11 13:13:46 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue May 11 13:22:33 2004 Subject: [BioPython] Solved BioPython & Zope problem and a Bug? In-Reply-To: <1084294695.2235.150.camel@numero2> References: <1082736999.23447.67.camel@numero2> <20040504165538.GD602@misterbd.agtec.uga.edu> <1084294695.2235.150.camel@numero2> Message-ID: <20040511171346.GE83225@evostick.agtec.uga.edu> Hi Cristian; > I tried to use the biopython in the cvs on zope but I had found my first > problem: > > I'm working in Linux with Debian distribution, and the Zope deb > package is compiled for python2.2. That the reason I had choose to > compile Biopython with python2.2, but it's fail on tests! Thanks for reporting these 2.2 incompatibilities. I went through and fixed all of them I could find, and just checked the changes into CVS (it may take a few moments to get through to anonymous CVS). Please let me know if the changes fix your problems. On the way I also made a few other fixes to the Tests in CVS so they should hopefully all pass more successfully this time. Thanks again for the report! Brad From venkatar at seznam.cz Tue May 11 17:14:26 2004 From: venkatar at seznam.cz (hal) Date: Tue May 11 17:13:36 2004 Subject: [BioPython] - Message-ID: <200405112113.i4BLDR6B002943@portal.open-bio.org> ????????? ???????! ?????????? ??? 18-19 ??? ????????????? ? ??????????? ???????? ?? ???? : "???????? ???????????? ???????" (?????????????????? - ?????? ? ????.) ????? ???????? ???????! ? ???? ??????? ??? ???????????? ?? ????? ???????, ????? ????????????? ???????? ??????????? ??????? ???? ?????, ? ???? ?? ????? ? ???????? ???????????????? ?????????? ????????? ??? ??????? ?????? ????????? ?????????? ???????, ????????? ?? ????????? ????????? ?? ????? ???????? ????????? ?????? ??????? ?????? ?????????? ????????? ??????????? ???????? ?????????????? ??????? ? ????? ?????????? ?????????????? ??????? ? ?????????? ??????, ?????????? ??????????? ??????????? ???????. ????? ??????????? ???????? ????????? ?????? ????? ???????????? ?????? ? ??????? ??????????? ????????? ??????, ???????? ??????? ? ????????? ?????????? ??????????????????. ?????????? ??????? ? ?????? ???????????. 1.???????? ???????????? ??????? ? ???? ???????????? ??????. ??????????? ???????????????? ??????. ? ???????????? (???????????????) ?????????????? ??????????? ???????. ? ??????????? ???? ??????? ?? ????????? ? ?????????? ????? ???????????. ? ??????????? ????????????? ????????? ??????? ?????? ? ???????? ?????????? ?????????? ????????. (? ????? ???? ? ???????? ???? ????????????) ? ???????????? ??????? ??? ?????????? ??????. (???????? ??????? ? ???????? ??????). 2.??????????????? ?????????????? ? ??????????? ?????? ? ??????? ? ?????? ???????. ? ????????????? ????? ? ???????. ? ????????? ???????????? ??????? ??????????? ???????????? ? ?????????????? ? ???????. ? ?????? ????????????? ????????? ?????? ? ?????????????? ??????????. ? ?????????? ??? ?????????????? ???????: ????????? ?????, ?????? ? ???????. 3.?????? ?????? ?????? ??????? ? ??????????? ??????????????? ????? ?????? ? ??????? ? ???????? ??????????? ????????????? ? ???????? ?????? ?????? ??????? ? ?????? ?????? ?????? ???????: ????????????????? ????????, ????????????? ?????????????? ??????? ????????, ????????????. ????????? ????? ??????????? ?????? ? ??????????? ???????. ????????? ??????? 7500 ??????, c ?????? ???. ????? ?????? ????? (???????? ??? ???????????). ? ????? ????? ??????: ??????? ? ?????? ??????,??????????? ???????? ????-?????, ????. ??????-????? ???????? ? ?????? (?. ?????????????). ?????? ??????????? ? 10 ????? ? ????????? ? 17 ?????. ???? ???? ??????? ? ??????????? ?????????? ?? ?????????? ??? ?????????? ?????? ?? ????? ????? ? ?????? ??????-???????. ? ????????????? ??????????? ??????????? ????????. ????????? ???????????? ?????????????? 4500 ???. ? ?????? ??? (095) 747-71-88 From henrik at freepage.de Thu May 13 21:18:12 2004 From: henrik at freepage.de (henrik@freepage.de) Date: Thu May 13 21:22:00 2004 Subject: [BioPython] Biopython, How do they f@k.k with snakes? In-Reply-To: References: Message-ID: <7GI000G583HIJA98@freepage.de> Looks like you've come to a real Z00 here! Yeap! We have goats, we have horses, sheep, snakes, even dogs! e have lots of @n1m@ls here and we also have lots of g1r|s who just love to have some s. e -x with these creatures? How do they do it? http://zoo-action.com/av/val/?TQptz How do they sa-ck those c0c.k-s? How do they f@kk with snakes? Snakes don't have c0c.k-s!!! Guys! Our g1r|s can do it with every creature they want! They are ready for it! They are tired from men! They do realize that wild @n1m@ls are f@kking like no man would ever f@kk them. Cause they are animals and they f@kk just like everybody did thousands and millions years ago! http://zoo-action.com/av/val/?TiuKL Stunning 1ma-.ges, v1de0s, art series, lots of @n1m@ls, y0.u-n.g horny g1r|s spre@d1ng their legs and s@kking c0c-k.s! This is a first ever -X-.-X-.-X- zoo where every g1r| can f@kk the creature she wants! LOOK AT THIS NOW! nCnptJty TLXyBMufU From mdehoon at ims.u-tokyo.ac.jp Thu May 13 23:08:19 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Thu May 13 23:11:35 2004 Subject: [BioPython] Bio.HMM Message-ID: <40A43823.3080506@ims.u-tokyo.ac.jp> Dear Biopythoneers, I was hoping to use the Hidden Markov Model routines in Bio.HMM in Biopython. Is there any documentation or (preferably) example scripts for this module available? Many thanks in advance, --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chapmanb at uga.edu Fri May 14 10:34:30 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Fri May 14 10:43:08 2004 Subject: [BioPython] Biopython 1.30 release Message-ID: <20040514143430.GC86985@evostick.agtec.uga.edu> Hello all; I'm happy to announce a new release of Biopython 1.30, available today from http://biopython.org. This release contains a number of new modules and substantial changes to older modules. As a result of the changes, we've bumped up to a brand new major number. Please do download, test with your code, and report any bugs or problems to the normal lists (biopython@biopython.org or biopython-dev@biopython.org). The substantial changes in this release include: -> Overhaul of the FASTA parser. Internally, fasta parsing now uses C libraries, so it is much faster and scalable to large files. The changes should all be internal, so that code written for the old Fasta parser will work with the new version. -> Updated GenBank parser internals. In a desire to make GenBank parsing more flexible to the numerous updates to the format, a number of underlying parser details have been improved. -> New contributed modules: Affymetrix cel parsing -- Harry Zuzan Compass output parsing -- James Casbon Melting temperature calculation -- Sebastian Bassi Reduced protein alphabets -- Iddo Friedberg Blast XML output parsing -- Bertrand Frottier -> Some duplicated and non-finished modules have been deprecated. For now you will get DeprecationWarnings with these modules, but they will eventually be removed. The effected modules are Bio/sequtils, Bio/kMeans, Bio/SVM and Bio/RecordFile. Please see the file DEPRECATED in the distribution for details of switching your code to use the new replacement modules. -> The C++ code in the KDTree and Affy modules is now compiled by default. This has been tested on a number of platforms, but is a potential source of compilation errors. If you run into any problems compiling these C++ modules, please report them to the list. -> A large assortment of bug fixes and updates to documentation. A full list of changes is included below. Please download, test, and enjoy. Thanks much for everyone's hard work that went into making this release possible. Brad May 14, 2004: Biopython 1.30 Affy package added for dealing with Affymetrix cel files -- thanks to Harry Zuzan. Added code for parsing Blast XML output -- thanks to Bertrand Frottier. Added code for parsing Compass output -- thanks to James Casbon. New melting temperature calculation module -- thanks to Sebastian Bassi. Added lowess function for non-parameteric regression -- thanks to Michiel. Reduced protein alphabet supported added -- thanks to Iddo. Added documentation for Logistic Regression and Bio.PDB -- thanks to Michiel and Thomas. Documentation added for converting between file formats. Updates to install documentation for non-root users -- thanks to Jakob Fredslund. epydoc now used for automatic generation of documentation. Fasta parser updated to use Martel for parsing and indexing, allowing better speed and dealing with large data files. Updated to Registry code. Now 'from Bio import db' gives you a number of new retrieval options, including embl, fasta, genbak, interpro, prodoc and swissprot. GenBank parser uses new Martel format. GenBank retrieval now uses EUtils instead of the old non-working entrez scripts. GenBank indexing uses standard Mindy indexing. Fix for valueless qualifiers in feature keys -- thanks to Leighton Pritchard. Numerous updated to Bio.PDB modules -- thanks to Thomas. PDB can now parse headers -- thanks to Kristian Rother. Updates to the Ace parser -- thanks to Frank Kauff and Leighton Pritchard. Added pgdb (PyGreSQL) support to BioSQL -- thanks to Marc Colosimo. Fix problems with using py2exe and Biopython -- thanks to Michael Cariaso. PSIBlast parser fixes -- thanks to Jer-Yee John Chuang and James Casbon. Fix to NCBIWWW retrieval so that HTML results are returned correctly. Fix to Clustalw to handle question marks in title names -- thanks to Ashleigh Smythe. Fix to NBRF parsing to it accepts files produced by Clustalw -- thanks to Ashleigh Smythe. Fixes to the Enyzme module -- thanks to Marc Colosimo. Fix for bugs in SeqUtils -- thanks to Frank Kauff. Fix for optional hsps in ncbiblast Martel format -- thanks to Heiko. Fix to Fasta parsing to allow # comment lines -- thanks to Karl Diedrich. Updates to the C clustering library -- thanks to Michiel. Fixes for breakage in the SCOP module and addition of regression tests to framework -- thanks to Gavin. Various fixes to Bio.Wise -- thanks to Michael. Fix for bug in FastaReader -- thanks to Micheal. Fix EUtils bug where efetch would only return 500 sequences. Updates for Emboss commandlines, water and tranalign. Fixes to the FormatIO system of file conversion. C++ code (KDTree, Affy) now compiled by default on most platforms -- thanks to Michael for some nice distutils hacks and many people for testing. Deprecated Bio.sequtils -- use Bio.SeqUtils instead. Deprecated Bio.SVM -- use libsvm instead. Deprecated Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead. Deprecated RecordFile -- doesn't appear to be finished code. From chapmanb at uga.edu Fri May 14 11:24:16 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Fri May 14 11:32:54 2004 Subject: [BioPython] Bio.HMM In-Reply-To: <40A43823.3080506@ims.u-tokyo.ac.jp> References: <40A43823.3080506@ims.u-tokyo.ac.jp> Message-ID: <20040514152416.GH86985@evostick.agtec.uga.edu> Hi Michiel; > I was hoping to use the Hidden Markov Model routines in Bio.HMM in > Biopython. Is there any documentation or (preferably) example scripts for > this module available? That code was my doing, but sadly there is really not any documentation on it. However, the tests in the test directory might be some guide: test_HMMCasino.py --> Example of code usage based on a loaded dice scenario. Basically, there are two dice, a fair and a loaded (6 comes up 1/2 of the time). The example generates rolls, and then builds a MarkovModel and tries to predict based on the roll frequencies which die is being used when. There are a couple of different trainers -- BaumWelchTrainer and a KnownStateTrainer that are used in it. test_HMMGeneral.py --> More standard test code but at least gives an idea of all the different functionality in the module. The code docs are actually semi-decent, as well: http://www.biopython.org/docs/api/public/Bio.HMM-module.html I'd be happy for you to hack away, change, do whatever to the module, as I haven't used it in a while myself. But definitely feel free to ask any questions and I'll try to help as much as possible. Brad From jchuang8 at itsa.ucsf.edu Sat May 15 02:50:38 2004 From: jchuang8 at itsa.ucsf.edu (Jer-Yee John Chuang) Date: Sat May 15 02:54:26 2004 Subject: [BioPython] PSIBlastParser error Message-ID: Hi, I am some difficulty with the NCBIStandalone.PSIBlastParser. After running blastpgp, I use the parser and get the error message: chuang@Poggi ~/blast/workbench $ python psiBlastHomologues.py ./275proteins_allEnteroBact/allEntero ./275prote ins_allEnteroBact/all275seeds 1 100 1e-3 0 1 Traceback (most recent call last): File "psiBlastHomologues.py", line 89, in ? myRecord= myIterator.next() File "NCBIStandalone.py", line 1342, in next File "NCBIStandalone.py", line 581, in parse File "NCBIStandalone.py", line 96, in feed File "NCBIStandalone.py", line 154, in _scan_rounds File "NCBIStandalone.py", line 279, in _scan_descriptions File "c:\python23\lib\site-packages\Bio\ParserSupport.py", line 340, in read_a nd_call_until method(line) File "NCBIStandalone.py", line 647, in description File "NCBIStandalone.py", line 704, in _parse File "NCBIStandalone.py", line 1612, in _safe_int ValueError: invalid literal for float(): round I've traced this problem to the following line in the blast output: "Sequences not found previously or not previously below threshold:" It appears that the parser complains when this line is not followed by any sequences AND there is another round afterwards. This is kind of odd, since I thought that when there are no sequences following that line, psiblast should have converged. However, this is not the case, as I have additional rounds (i.e. iterations) afterwards. I can forward the actual psiblast output file if it helps. Thank you for your time. Sincerely, John Chuang From chapmanb at uga.edu Sat May 15 07:20:05 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat May 15 11:27:57 2004 Subject: [BioPython] PSIBlastParser error In-Reply-To: References: Message-ID: <20040515112005.GC40622@misterbd.agtec.uga.edu> Hi John; > I am some difficulty with the NCBIStandalone.PSIBlastParser. After > running blastpgp, I use the parser and get the error message: > > $ python psiBlastHomologues.py ./275proteins_allEnteroBact/allEntero > ./275prote > ins_allEnteroBact/all275seeds 1 100 1e-3 0 1 [...] > ValueError: invalid literal for float(): round > > I've traced this problem to the following line in the blast output: > "Sequences not found previously or not previously below threshold:" It > appears that the parser complains when this line is not followed by any > sequences AND there is another round afterwards. This is kind of odd, > since I thought that when there are no sequences following that line, > psiblast should have converged. However, this is not the case, as I have > additional rounds (i.e. iterations) afterwards. Hmmm, that is very strange. But, if blastpgp produces it, we should be able to parse it. > I can forward the actual psiblast output file if it helps. That would be a big help if you could either send me the file directly, or post it as a bug in the bug database (http://bugzilla.open-bio.org/) and then attach it there. Either way we'll have a look and try to get it fixed up. Thanks for the report. Brad From corky at seznam.cz Sun May 16 04:53:28 2004 From: corky at seznam.cz (ivy) Date: Sun May 16 14:04:58 2004 Subject: [BioPython] =?windows-1251?b?zuHz9+Xt6OU=?= Message-ID: <200405161804.i4GI4rKr002767@portal.open-bio.org> ????????? ???????! ?????????? ??? 20 ??? ?????? ????????????? ? ??????????? ???????? ?? ???? : ??????? ?????????????? ????????. ??????? ?????????????: ???????????? ?? ?????? ? ??????????, ????????????? ??????????? ????????, ???????????? ?? ??????????? ???????????, ?????????? ?????????????, ???????????? ?? ??????? ????????. ????????? ????????: 1. ?????? ????????????? ???????? ?? ?????? ? ? ??????. ??????, ?????????? ?? ????????? ????????????? ???????. ??????? ????????????? ????????? ??????? ?? ????????????? ???????. ??????? ??????????? ????? ? ???????. 2. ????????????? ??????? ??????????? ????????. ??????? ?????? ????? ????????. ??????????????? ?????? ??????? ????????. ????????? ????????? ????? ???????? ???????????. ???????. 3. ????????????? ??????? ???????? ????????. ??????? ?????? ????? ????????. ??????????????? ?????? ??????? ???????? ??? ????????. ??????????? ???????? ???????? ????? ????????. 4. ????????????? ??????? ????????? ????????. ??????? ?????? ????? ???????? . ??????????????? ??????. ??????????? ???????? ???????? ????? ?????????. ???????. 5. ????????????? ??????? ??????????? ????????. ??????? ?????? ????? ????????. ??????????????? ??????. ??????????? ???????? ???????? ?????? ????????????. ??????? ??????? ?????? ?????????? ????????. 6. ??????-?????: "???????????? ?????????? ???????? ??????? ????????????? ????????. ???????? ? ???? ????????". ??????? ????. ?????????? ????????????? ???????? ??????? ? ??????????? ??????????? ?????????????? ???????. ???????? ???????????? ??? ?????? ? ??????? ?????????????. ?????????? ??? ??? ????????. ????????? ?????? ???? ??????? ??????? ?????? ??? ?????? ???????? ????????? ??????? 3900 ??????, c ?????? ???. ????? ?????? ????? (???????? ??? ???????????). ? ????? ????? ??????: ??????? ? ???????????,?????????????? ???????? ????????? ????-?????, ????. ????? ?????????? ??????-?????? ?????? ?. ?????????????.?????? ??????????? ? 10 ????? ? ????????? ? 17 ?????. ??? ??????? ? ???????? ?????????? ????????????????. ??????? ??? ??????? 747-71-88 From joec at quintanaroo.com Mon May 17 16:14:37 2004 From: joec at quintanaroo.com (Patel I. Curvature) Date: Sun May 16 16:38:21 2004 Subject: [BioPython] Have a nice day! //absent in body, let us be present with each other in spirit; and Message-ID: <001001c43b82$426ae672$4a475f1d@quintanaroo.com> Get easy money! http://members.lycos.co.uk/lancer131/1/ --- since they were baptized, yet because they have been From crocha at dc.uba.ar Mon May 17 09:28:57 2004 From: crocha at dc.uba.ar (Cristian S. Rocha) Date: Mon May 17 09:34:13 2004 Subject: [BioPython] BioSql: Checking if exists a database. Message-ID: <1084800537.27844.12.camel@numero2> Hi, I need to check if exists a database before to create it. I write the following but it doesn't work. """ server = BioSeqDatabase.open_database(driver='MySQLdb', user='bio', passwd='secret', host='localhost', db='bio') if database in server: db = server[database] else: db = server.new_database(database) """ The traceback output is: """ File "BioTools.py", line 160, in ? SequenceStoreFile(open('example.fasta'), 'estC', 'fasta') File "BioTools.py", line 103, in SequenceStoreFile if database in server: File "/home/crocha/Tmp/biopython/biopython/build/lib.linux-i686-2.2/BioSQL/BioSeqDatabase.py", line 78, in __getitem__ return BioSeqDatabase(self.adaptor, name) File "/home/crocha/Tmp/biopython/biopython/build/lib.linux-i686-2.2/BioSQL/BioSeqDatabase.py", line 308, in __init__ self.dbid = self.adaptor.fetch_dbid_by_dbname(name) File "/home/crocha/Tmp/biopython/biopython/build/lib.linux-i686-2.2/BioSQL/BioSeqDatabase.py", line 168, in fetch_dbid_by_dbname raise KeyError("Cannot find biodatabase with name %r" % dbname) """ I feel it's not implemented these feature or it's not the best way to check it. If it's the last case, How can I do it? thxs, Cristian. -- Lic. Cristian S. Rocha. Departamento de Computacin. FCEyN. UBA. Pabellon I. Cuarto 9. Ciudad Universitaria. (1428) Buenos Aires. Argentina. Tel: +54-11-4576-3390/96 int 714 Tel/Fax: +54-11-4576-3359 Cel: 15-5-607-9192 From sbassi at asalup.org Mon May 17 11:22:23 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Mon May 17 11:26:32 2004 Subject: [BioPython] BioSql: Checking if exists a database. In-Reply-To: <1084800537.27844.12.camel@numero2> References: <1084800537.27844.12.camel@numero2> Message-ID: <40A8D8AF.6040500@asalup.org> Cristian S. Rocha wrote: > Hi, > > I need to check if exists a database before to create it. I write the > following but it doesn't work. You could use Try and except: Try: HERE THE "NORMAL" CODE THAT COULD RISE AN EXCEPTION Except: HERE THE CODE THAT YOU WOULD USE IF THERE IS AN ERROR. -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From crocha at dc.uba.ar Mon May 17 14:54:25 2004 From: crocha at dc.uba.ar (Cristian S. Rocha) Date: Mon May 17 14:59:34 2004 Subject: [BioPython] MARTEL parser & FASTA Message-ID: <1084820065.10155.20.camel@numero2> Hi, I would like to parse FASTA files with NCBI description header. I see some reference about it in the Bio.expression.fasta module, but when I use it by the SeqRecord.io module it assign None and "" values to the 'id' and 'name' attribs. What's wrong? SeqFile = open('example.fasta') r = SeqRecord.io.readFile(SeqFile, debug_level=0) for i in r: print i.id print i.name print i.description Thxs, Cristian. -- Lic. Cristian S. Rocha. Departamento de Computacin. FCEyN. UBA. Pabellon I. Cuarto 9. Ciudad Universitaria. (1428) Buenos Aires. Argentina. Tel: +54-11-4576-3390/96 int 714 Tel/Fax: +54-11-4576-3359 Cel: 15-5-607-9192 From hlapp at gnf.org Mon May 17 22:22:24 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon May 17 22:26:10 2004 Subject: [BioPython] FW: [BioSQL-l] BioSQL&Python&SwissProt Message-ID: <833E32F61B9F8746878F2A1865BECE60430B6C@EXCHCLUSTER01.lj.gnf.org> Tamas, I'm forwarding this to the biopython people who may be able to help you. -hilmar -----Original Message----- From: Hegedus, Tamas . [mailto:Hegedus.Tamas@mayo.edu] Sent: Monday, May 17, 2004 5:39 PM To: 'biosql-l@open-bio.org' Subject: [BioSQL-l] BioSQL&Python&SwissProt Dear All, I tried to load swissprot.dat file into the biosql schema. It resulted in AttributeError. (I am using BioPython-1.24; and the most recent biosql.tarball) It seems for me that the Loader try to find the record.id, but SProt.Record does not have an 'id'. What is the solution? How can I load the SwissProt into BioSQL (I prefer Python vs. Perl)? Thanks for your help, Tamas #-------------------- #!python parser = SProt.RecordParser() iterator = SProt.Iterator(open("path_to/uniprot_sprot.dat"), parser) server = BioSeqDatabase.open_database(driver="psycopg", user="bioroot", passwd="pwd", host="localhost", database="biosql") db = server.new_database("bup") n_prt = db.load(iterator) print "Number of loaded PRT: ", n_prt --------------- n_prt = db.load(iterator) File "/home/src/biopython-1.24/build/lib.linux-i686-2.3/BioSQL/BioSeqDatabase .py", line 414, in load db_loader.load_seqrecord(cur_record) File "/home/src/biopython-1.24/build/lib.linux-i686-2.3/BioSQL/Loader.py", line 37, in load_seqrecord bioentry_id = self._load_bioentry_table(record) File "/home/src/biopython-1.24/build/lib.linux-i686-2.3/BioSQL/Loader.py", line 209, in _load_bioentry_table if record.id.find('.') >= 0: # try to get a version from the id AttributeError: Record instance has no attribute 'id' _______________________________________________ BioSQL-l mailing list BioSQL-l@open-bio.org http://open-bio.org/mailman/listinfo/biosql-l From chapmanb at uga.edu Tue May 18 06:11:46 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue May 18 10:19:29 2004 Subject: [BioPython] Re: [BioSQL-l] BioSQL&Python&SwissProt In-Reply-To: References: Message-ID: <20040518101146.GA34051@misterbd.agtec.uga.edu> Hi Tamas; > I tried to load swissprot.dat file into the biosql schema. > It resulted in AttributeError. [...] > It seems for me that the Loader try to find the record.id, but > SProt.Record does not have an 'id'. > What is the solution? The BioSQL loader uses an iterator of generic SeqRecord objects to load the database. You are using the RecordParser, which generates Swissprot specific Record objects. The solution is to use the SequenceParser instead, so you should just need to modify one line of your code: > parser = SProt.RecordParser() to: parser = SProt.SequenceParser() This should work better for you. Another option, which is less well tested, is to use the SeqRecord.io system to get an iterator: from Bio import SeqRecord iterator = SeqRecord.io.readFile(open("path_to/uniprot_sprot.dat")) Just another option. We appreciate the report on this -- to be honest BioSQL has not been well tested with Swissprot entries, so we are happy to hear about people working on this and reporting problems. Hope this helps. Brad From chapmanb at uga.edu Tue May 18 06:04:27 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue May 18 10:39:03 2004 Subject: [BioPython] MARTEL parser & FASTA In-Reply-To: <1084820065.10155.20.camel@numero2> References: <1084820065.10155.20.camel@numero2> Message-ID: <20040518100427.GA34006@misterbd.agtec.uga.edu> Hi Cristian; > I would like to parse FASTA files with NCBI description header. I see > some reference about it in the Bio.expression.fasta module, but when I > use it by the SeqRecord.io module it assign None and "" values > to the 'id' and 'name' attribs. What's wrong? > > SeqFile = open('example.fasta') > r = SeqRecord.io.readFile(SeqFile, debug_level=0) > for i in r: > print i.id > print i.name > print i.description Thanks for this report. The problem is basically that the io system is still under development and not completely finished. We really do appreciate people testing on it and reporting problems. I updated Bio/builders/SeqRecord/sequence.py so that it not tries to handle setting the name and id attributes in a smarter fashion. I've committed the changes into CVS and also am attaching a patch with the changes made. Let me know if this works better for you. Thanks again for the report. Brad -------------- next part -------------- Index: sequence.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/builders/SeqRecord/sequence.py,v retrieving revision 1.6 retrieving revision 1.8 diff -c -r1.6 -r1.8 *** sequence.py 18 Mar 2004 00:53:24 -0000 1.6 --- sequence.py 18 May 2004 13:58:35 -0000 1.8 *************** *** 32,37 **** --- 32,39 ---- Dispatch.Dispatcher.__init__(self) self.acquire(StdHandler.Handle_dbid(self.add_dbid), prefix = Std.NS) + self.acquire(StdHandler.Handle_dbxref(self.add_dbxref_dbids), + prefix = Std.NS) self.acquire(StdHandler.Handle_description(self.add_description), prefix = Std.NS) self.acquire(StdHandler.Handle_sequence(self.add_sequence), *************** *** 44,60 **** def start_record(self, tag, attrs): self.dbname = None self.id_text = None self.description = None self.alphabet = None self.seq = None self.features = None self.dbxrefs = [] - def add_dbid(self, text, attrs): if attrs.get("type") == "primary": self.dbname = attrs.get("dbname", "unknown") self.id_text = text def add_description(self, text): self.description = text --- 46,83 ---- def start_record(self, tag, attrs): self.dbname = None self.id_text = None + self.name_text = '' self.description = None self.alphabet = None self.seq = None self.features = None self.dbxrefs = [] def add_dbid(self, text, attrs): if attrs.get("type") == "primary": self.dbname = attrs.get("dbname", "unknown") self.id_text = text + # use the first accession/secondary id as the name + # this should be equivalent to what Biopython does + elif attrs.get("type") in ["accession", "secondary"]: + self.name_text = text + + def add_dbxref_dbids(self, dbname_style, dbname, idtype, dbid, negate): + """Handle setting name and id attributes from the dbxref ids. + + Likely we'll either have a dbid or dbxref dbids to use. We default + to using the dbid if it exists. + """ + # first deal with the primary id: SeqFeature.id + # set the id if we haven't yet set an id (take the first id we get) + # and if we have a primary id + if (self.id_text is None and idtype == "primary"): + self.id_text = dbid + + # now deal with secondary ids: SeqFeature.name + if idtype == "secondary": + self.name_text = dbid + def add_description(self, text): self.description = text *************** *** 65,70 **** --- 88,95 ---- self.seq = Seq.Seq(seq, alphabet) def add_dbxref(self, dbname_style, dbname, idtype, dbid, negate): + """Store all id cross references. + """ self.dbxrefs.append(DBXRef.from_parser(dbname_style, dbname, idtype, dbid, negate)) *************** *** 80,85 **** --- 105,111 ---- self.document = SeqRecord.SeqRecord( seq = self.seq, id = self.id_text, + name = self.name_text, description = self.description, dbxrefs = self.dbxrefs, features = self.features, From prabhu at seznam.cz Tue May 18 17:48:25 2004 From: prabhu at seznam.cz (evan) Date: Tue May 18 18:02:19 2004 Subject: [BioPython] =?windows-1251?b?zuHz9+Xt6OU=?= Message-ID: <200405182202.i4IM24Kr032431@portal.open-bio.org> ????????? ???????! ?????????? ??? 24 ??? ??????? ??????? ? ??????????? ???????? ?? ???? : ????? ??????????????? ?????????? ??????? ????????????? ??????? ???????????, ????????? ?????????????, ????????????? ???6????????. ????????? ????????. 1. ??????? ??????????????? ?????????. ???????? ? ????????????: ????????? ?????????, ??????????????? ???????, ??????????????? ??????????. ??? ?????????, ???? ????????? ???????????????? ?? ???????? ?????????? ??????????? ??????? ? ????? ????? ??????????????? ?????????. 2. ????? ? ????? ??????????????? ????????? ??? ????? ????????? ??????? ?? ??????? 3. ???? ??????????? ? ??????? ???????? ??????????????? ????????? ??? ????? ???????????????. ?????? ??????????????? ????????? ? ????????? ?????. 4. ????????? ???????? ???????? ??????? ? ?????????????? ??????? ? ??????????????? ?????????. ?????????? ??????????? ? ????????? ?? ? ????????? ????? 5. ????????? ???? ???????? ?? ?????? ??????????????? ????????? 6. ??????????? ?????????? ????? ???????? ??????????????? ?????????, ????????? ? ???????????? ?? 1 ?????? 2002 ?. 7. ????????????? ????????? ???????? ??? ????? ??????????????? ????????? ? ????????, ????????? ? ??? ????????????? 8. ?????????? ? ?????? ??????? ???????? ??????????????? ????????? ????????? ??????? ? ????????, ???????? ??????? ?? ?????? ? ????????? ?????. ????????? ??????? 3900 ??????, ? ?.?. ???. ????? ?????? ????? (???????? ??? ???????????). ? ????????? ??????: ??????? ? ???????????,?????????????? ???????? ????????? ????-?????, ????. ????? ?????????? ??????-?????? ?????? ?. ?????????????.????? ?????????? ? 10 ?? 17.30. ??????????? ?????????? ???????????. ???? ?? ?? ?????? ???????? ??????-????? ?? ?????????? ??? ?????????? ?????? ?? ????? ???????????.? ??????????????? ??????????? ??????????? ????????. ????????? ???????????? ???????????? 2600 ???. ? ??? ??????? ??? ??????? 747-71-88 From hlapp at gmx.net Mon May 24 00:20:46 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon May 24 00:24:25 2004 Subject: [BioPython] Re: [Bioperl-l] testing a new Open-Bio website and mail list archive search In-Reply-To: <40A0DCB0.1050207@sonsorol.org> Message-ID: There's one thing that I noticed at least for searches against the bioperl mailing lists: the first pages of hits is commit messages from bioperl-guts. The guts list should be excluded from the index I think. Seldom will you want to search for a commit message through this interface. -hilmar On Tuesday, May 11, 2004, at 07:01 AM, Chris Dagdigian wrote: > Hello Everyone, > > A fantastic volunteer (Kyle Jensen) has been steathily working on a > problem for us that has long been a major issue for us -- website > searching and indexing. > > We've tried various solutions and ht://dig implementations in the past > and nothing really worked well. > > Kyle has been setting up a search indexing system based on the code > from www.swish-e.org and so far it looks very very promising. > > We have 2 main indexed search sites: > > This page is a search index for all of the open-bio hosted websites: > http://search.open-bio.org/cgi-bin/obf-search.cgi > > This page is just for searching mailing list archives: > http://search.open-bio.org/cgi-bin/mail-search.cgi > > > Please give the pages a whirl and let me know what you think. > > Thanks again Kyle! > > -Chris > open-bio.org admin team > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From trisha at seznam.cz Wed May 26 00:23:19 2004 From: trisha at seznam.cz (maurice) Date: Wed May 26 00:36:52 2004 Subject: [BioPython] =?windows-1251?b?zuHz9+Xt6OU=?= Message-ID: <200405260436.i4Q4ajKr013063@portal.open-bio.org> ????????? ???????! ?????????? ??? 31.05 ??????? ??????? ? ??????????? ???????? ?? ???? : "??????? ?????????? ?????????? ?? ??????????? ???? ??????????? ?????? ????????, ??????? ?? ???????????? ????????? ? ?????????? ?????????????? ?????????????, ???????????? ? ?????????????? ?????????? ????????? ? ??????? ????????. ????????? - ???????? ???????????? ?????? ?????????? ? ???????????? ?????? ?????????????? ? ??????????? ????????. ? ?????????, ????????? ???????? ?????????? ?????? ?????? ??????????????, ??? ??????????? ????????? ????????? ?????????? ? ?????????? ?????????. ?????????? ???????? ???????????? ????????? ?????????: 1. ????????? ????????? - ???????? ???? ????????? - ???????????? ????????? - ????? ????????? - ?????????? ????????? 2. ?????????? ? ?????????. - ?????????? ???? ????????? - ????? ??????? ????????? ?????????. - ?????? ?????????? ? ?????????? - ??????? ????????? ?????????? ?? ??????????. - ???????? ???, ????????? ?????????. ?????????? ????????. 3. ?????????? ?????????. - ?????? ?????????? ???????? ? ?????????. - ??? ?????? ???????????? ??????????? - ??????? ??????????. - ??????????????? ??????? - ?????????????? ???????? ????? - ???????? ??????? ?????????. - ?????? ??????????? ?? ?????????? ????? - ????? ???????? ???????, ?????????? ?????? ????????? ???????. - ????????? ?????????? ???????? ???????, ????????? ??????????? ???????. - ??????????. ??????????, ?????????????? ? ???????? ????????. - ????????? ? ????????. 4. ?????? ???????????? ????????. ???????? ?????????? ???????? ???????. ?? ????????? ???????? ????????? ??????: - ?????????? ??????????? ? ???????????? ?????, ?????????? ?? ????????? - ???????????? ? ????????? ???? ?????????? ? ????????? ?????????????? ? ??????? ? ??????? ???????? - ?????? ???????? ?????? ?????????? ? ????????????? ?? ? ????? ????????? ????????? - ????????? ??????????? ????????? ???, ????? ????????? ???????????? ??????????? - ????????? ????? ? ???? ??? ??????? ??? ?????????? ?????????. C???????? ??????? ? ??????-?????? 3900 ??????, c ?????? ???. ????? ?????? ????? (???????? ??? ???????????). ? ????? ????? ??????: ??????? ? ???????????,?????????????? ???????? ????????? ????-?????, ????. ????? ?????????? ??????-?????? ?????? ?. ?????????????.?????? ??????????? ? 10 ????? ? ????????? ? 17 ?????. ??? ??????? ? ???????? ?????????? ????????????????. ???? ?? ?? ?????? ???????? ??????-????? ?? ?????????? ??? ?????????? ?????? ?? ????? ???????????.? ??????????????? ??????????? ?????????????? ????????? ?????????????? ???????. ????????? ???????????? ???????????? 2600 ???. ? ?????? ??? ??????? ??? ??????? 788-73-28 From dougalld at cbmi.pitt.edu Wed May 26 15:45:26 2004 From: dougalld at cbmi.pitt.edu (Dougall, David) Date: Wed May 26 15:47:33 2004 Subject: [BioPython] Problem importing Bio.PDB Message-ID: <09D04633DAED5F489FFEB6A0EAF22C164B105D@pikachu.health.pitt.edu> When I try to import Bio.PDB I get the following message: >>> from Bio.PDB import * Traceback (most recent call last): File "", line 1, in ? File "D:\Python23\Lib\site-packages\Bio\PDB\__init__.py", line 10, in ? from PDBParser import PDBParser File "D:\Python23\Lib\site-packages\Bio\PDB\PDBParser.py", line 10, in ? from Numeric import array, Float0 File "D:\Python23\Numeric\Numeric.py", line 91, in ? import multiarray ImportError: Module use of python20.dll conflicts with this version of Python. I am using Python version 2.3.2 Biopython version 1.3 Numeric version 23.1 for Python 2.3 Numarray version 0.9 for Python 2.3 In my C:\WINNT\system32 folder I had three python--.dll versions python20.dll python21.dll python23.dll Any suggestions???? Dave David S. Dougall Center for Biomedical Informatics University of Pittsburgh 8084 Forbes Tower 200 Lothrop Street Pittsburgh, PA 15213-2582 412-246-5643 (REALLY NEW) fax 412-383-3072 dougalld@cbmi.pitt.edu (Note: change from upmc to pitt) "If we don't succeed, we run the risk of failure." -Dan Quayle From chapmanb at uga.edu Wed May 26 12:18:24 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed May 26 16:26:09 2004 Subject: [BioPython] Problem importing Bio.PDB In-Reply-To: <09D04633DAED5F489FFEB6A0EAF22C164B105D@pikachu.health.pitt.edu> References: <09D04633DAED5F489FFEB6A0EAF22C164B105D@pikachu.health.pitt.edu> Message-ID: <20040526161824.GH73563@misterbd.agtec.uga.edu> Hi Dave; > When I try to import Bio.PDB I get the following message: > > >>> from Bio.PDB import * > Traceback (most recent call last): > File "", line 1, in ? > File "D:\Python23\Lib\site-packages\Bio\PDB\__init__.py", line 10, in ? > from PDBParser import PDBParser > File "D:\Python23\Lib\site-packages\Bio\PDB\PDBParser.py", line 10, in ? > from Numeric import array, Float0 > File "D:\Python23\Numeric\Numeric.py", line 91, in ? > import multiarray > ImportError: Module use of python20.dll conflicts with this version of > Python. This error comes from multiarray, which is part of the Numeric package. What it indicates is that the multiarray module was built against Python 2.0, instead of the Python 2.3.2 version that you are using. Shared libaries built with one version of Python are often not compatible across multiple versions, especially as far as from 2.0 to 2.3. > I am using > Python version 2.3.2 > Biopython version 1.3 > Numeric version 23.1 for Python 2.3 > Numarray version 0.9 for Python 2.3 > > In my C:\WINNT\system32 folder I had three python--.dll versions > python20.dll > python21.dll > python23.dll Okay, I can't say for sure without knowing the whole history of the three python versions and how everything was installed, but it looks like at least part of Numeric was build against the Python 2.0. A couple things I would look at: 1. When you type 'python' at a DOS command prompt, do you get the Python version you expect (2.3.2)? If there are PATH confusions and multiple versions of Python on a machine, you can very often end up using versions you don't mean to. 2. How was Numeric built and installed? If you got a Windows installer from somewhere, you may want to check the source of that to make sure it was built correctly. If you built it yourself, you'll need to supply us with more information before we can make any guesses -- what compiler did you use? What was the process? In general, the best thing to do to try and get things working is to get rid of Numeric in your site-packages and reinstall the Python 2.3 version from a Windows installer. There are some available at the numpy sourceforge page (http://sourceforge.net/projects/numpy). Hope this helps. Brad From thamelry at binf.ku.dk Wed May 26 16:50:48 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Wed May 26 16:45:37 2004 Subject: [BioPython] Problem importing Bio.PDB In-Reply-To: <09D04633DAED5F489FFEB6A0EAF22C164B105D@pikachu.health.pitt.edu> References: <09D04633DAED5F489FFEB6A0EAF22C164B105D@pikachu.health.pitt.edu> Message-ID: <33643.80.63.229.248.1085604648.squirrel@www.binf.ku.dk> > When I try to import Bio.PDB I get the following message: [X] > ImportError: Module use of python20.dll conflicts with this version of > Python. [X] > In my C:\WINNT\system32 folder I had three python--.dll versions > python20.dll > python21.dll > python23.dll Judged from a quick Google search and the above three dlls, this is due to old stuff hanging around... My advice is a fresh python install. Cheers, -Thomas From mauriceling at acm.org Fri May 28 03:58:46 2004 From: mauriceling at acm.org (Maurice Ling) Date: Fri May 28 03:57:48 2004 Subject: [BioPython] how to be a participant? Message-ID: <40B6F136.9080505@acm.org> Hi, I've just finished my honours year in University of Melbourne. During my studies, I had used python as a data analysis and filtering tool for my experiments. Hence, I'll be interested to be a participant in BioPython project. How can I do that? Thanks, Maurice Ling From bernie526 at mac.com Fri May 28 06:30:05 2004 From: bernie526 at mac.com (Bernadette Sullivan) Date: Fri May 28 06:33:11 2004 Subject: [BioPython] Your website Message-ID: The DNA is left-handed; it should be right-handed. Thanks, B. Sullivan From hoffman at ebi.ac.uk Fri May 28 07:40:46 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Fri May 28 07:44:13 2004 Subject: [BioPython] WU-BLAST Message-ID: Does anyone have some example code for parsing WU-BLAST output? I see the Bio.expressions["wu-blastn"] but I'm not really sure how to use it... -- Michael Hoffman European Bioinformatics Institute From hoffman at ebi.ac.uk Fri May 28 07:36:51 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Fri May 28 07:44:50 2004 Subject: [BioPython] GFF parser? In-Reply-To: References: Message-ID: On Tue, 23 Mar 2004, Andrew Nunberg wrote: > Hi, > I was looking through Biopython looking for a GFF library that does parsing > and creates a seq feature object. > > I did find a GFF module but I wasn?t sure what it was doing I don't usually read this mailing list so I missed your question before. Bio.GFF gets its information out of a MySQL database loaded from a GFF file with tools in Bioperl. -- Michael Hoffman European Bioinformatics Institute From thamelry at binf.ku.dk Fri May 28 15:48:53 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Fri May 28 15:43:46 2004 Subject: [BioPython] Your website In-Reply-To: References: Message-ID: <32995.80.63.229.248.1085773733.squirrel@www.binf.ku.dk> > The DNA is left-handed; it should be right-handed. Naah, it _is_ right-handed. Besides, there is biologically relevant LH DNA :-) (see http://www-lmmb.ncifcrf.gov/~toms/LeftHanded.DNA.html). Cheers, -Thomas