From xgtl@eth.net Tue Sep 4 12:44:43 2001 From: xgtl@eth.net (G. DEEPAK REDDY) Date: Tue, 4 Sep 2001 11:44:43 -0000 Subject: [BioPython] Bioinformatics & Molecular Modeling Message-ID: <000601c13536$ff4c9680$b1bf09ca@xgt15> This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C13536.FF4C9680 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear Members, We have recently started a training division in Bioinformatics & Molecular Modeling. We are looking for feedback from experts about including Biophython as part of the curriculum in the course. Please send your suggestions as to what topics, exercises and applications to be included. Regards Jupudi Srinivas Director-Technical, Xpert Global Tech Limited, INDIA Jupudi@xpertglobaltech.com http://www.xpertglobaltech.com ------=_NextPart_000_0007_01C13536.FF4C9680 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Members,

 

We have recently started a training division in Bioinformatics & Molecular Modeling.=A0 We are looking for feedback from experts about including Biophython as part of the curriculum in the = course.=A0 Please send your suggestions as to = what topics, exercises and applications to be = included.

 

Regards

 

Jupudi Srinivas

Director-Technical,

Xpert Global Tech = Limited,

INDIA

Jupudi@xpertglobaltech.com=

http://www.xpertglobaltech.com

 

------=_NextPart_000_0007_01C13536.FF4C9680-- From jchang@SMI.Stanford.EDU Tue Sep 4 19:45:13 2001 From: jchang@SMI.Stanford.EDU (Jeffrey Chang) Date: Tue, 4 Sep 2001 11:45:13 -0700 Subject: [BioPython] Biopython 1.00a3 release now available Message-ID: Hello everybody, A new release of Biopython is now available. It fixes a major bug in File.UndoHandle that affects many components of the system, so we recommend all users of version a2 upgrade right away. Sept 3, 2001: Biopython1.00a3 added package to support KEGG added sequtils module for computations on sequences added pairwise sequence alignment algorithm major bug fixes in UndoHandle format updates in PubMed Tk interface to kMeans clustering As usual, report bugs online at: http://www.biopython.org/biopython-bugs/ Flames and comments go to this mailing list. Development issues go to biopython-dev@biopython.org. Enjoy! Jeff From Y.Benita@pharm.uu.nl Tue Sep 11 11:56:28 2001 From: Y.Benita@pharm.uu.nl (Yair Benita) Date: Tue, 11 Sep 2001 12:56:28 +0200 Subject: [BioPython] String instead of file Message-ID: Fasta files can be easily parsed like this: parser = Fasta.RecordParser() iterator = Fasta.Iterator(File.txt, parser) cur_record = iterator.next() But, how do I parse strings and not a file with this parser? I am creating sequences and I want to write the in a Fasta format. Simply making a handle does not work, the error is: ValueError: I expected a file handle of file-like object Thanks, Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From ploukasm@fantti.btk.utu.fi Tue Sep 11 13:18:18 2001 From: ploukasm@fantti.btk.utu.fi (Petri Loukasmaki (Genomics)) Date: Tue, 11 Sep 2001 15:18:18 +0300 (EEST) Subject: [BioPython] String instead of file In-Reply-To: Message-ID: On Tue, 11 Sep 2001, Yair Benita wrote: > Fasta files can be easily parsed like this: > > parser = Fasta.RecordParser() > iterator = Fasta.Iterator(File.txt, parser) > cur_record = iterator.next() > > But, how do I parse strings and not a file with this parser? > I am creating sequences and I want to write the in a Fasta format. > Simply making a handle does not work, the error is: > > ValueError: I expected a file handle of file-like object If I remeber correct, the parameter must be a file-interface satisfying object. With string, this can be archieved by using memoryfiles. In python, this is implemented by StringIO class, which handles strings as file-like objects. So (in theory) following should work: import StringIO mystring="a fasta string..." mystringfile=StringIO.StringIO(mystring) iterator = Fasta.Iterator(mystringfile, parser) ... cheers; ------ ---- --- -- -- -- - - - - Petri Loukasmäki petri.loukasmaki@btk.utu.fi Research Assistant / BioInformatics tel +358 (0)2 333 8622 Turku Centre for Biotechnology Tykistökatu 6B, 5th floor P.O.Box 123, BioCity Turku, FIN-20521 FINLAND From chapmanb@arches.uga.edu Tue Sep 11 13:20:49 2001 From: chapmanb@arches.uga.edu (Brad Chapman) Date: Tue, 11 Sep 2001 08:20:49 -0400 Subject: [BioPython] String instead of file In-Reply-To: References: Message-ID: <20010911082049.A22424@ci350185-a.athen1.ga.home.com> Hi Yair; > But, how do I parse strings and not a file with this parser? > I am creating sequences and I want to write the in a Fasta format. > Simply making a handle does not work, the error is: > > ValueError: I expected a file handle of file-like object Basically, you need to convert the string into a handle using the StringIO module. I wrote a little about handles in general (and handles with strings specifically) in the biopython documentation: http://www.bioinformatics.org/bradstuff/bp/tut/Tutorial006.html#toc29 Here's a concrete example of doing what you want to do in the interpreter: >>> fasta_string = "> First Fasta\nGATCGATC\n> Second Fasta\nAAAATTTT\n" >>> print fasta_string > First Fasta GATCGATC > Second Fasta AAAATTTT >>> import StringIO >>> fasta_handle = StringIO.StringIO(fasta_string) >>> from Bio import Fasta >>> parser = Fasta.RecordParser() >>> iterator = Fasta.Iterator(fasta_handle, parser) >>> record = iterator.next() >>> print record > First Fasta GATCGATC Hopefully this helps -- let us know if this isn't clear! Brad From rick@bioinformatics.org Fri Sep 14 18:25:20 2001 From: rick@bioinformatics.org (Rick Ree) Date: 14 Sep 2001 10:25:20 -0700 Subject: [BioPython] Python bindings for the Nexus Class Library Message-ID: <1000488320.2538.23.camel@pedic> I've (finally) put together some python bindings to Paul Lewis' Nexus Class Library. Nexus is a data format widely used in phylogenetics, and these bindings allow Nexus files to be parsed, and expose an object-oriented framework for accessing the data. It uses the Boost::Python C++ library. The package can be obtained from: Any comments and suggestions are welcome. regards, Rick -- Section of Evolution and Ecology University of California Davis, CA 95616 From alexl@users.sourceforge.net Sat Sep 15 03:45:26 2001 From: alexl@users.sourceforge.net (Alex Lancaster) Date: 14 Sep 2001 19:45:26 -0700 Subject: [BioPython] Biopython and population genetics Message-ID: <7u3d5prx2x.fsf@allele2.biol.berkeley.edu> Hi folks, Let me introduce myself: I'm a recently converted Pythoneer/Pythonista working in computational biology/bioinformatics in several different areas, but most recently focused on bioinformatics in the context of population genetics analysis. As part of an NIH funded study we are currently implementing a Python-based framework for analysing population genetics data files and generating statistics such as linkage disequilibrium, and Hardy-Weinberg tests based on the parsing of these files. At this stage it is not 100% certain that we will be able to release this as an open source effort, although it is more than likely that we will be able to. Our university has an license policy that most closely resembles the XFree86-style license (i.e. BSD without the "advertising clause"). A typical "population genetics" data file, consists of multi-locus genotyped data, which is to say a series of lines, each consisting of an individual with a tab- or space-delimited series of loci (with two alleles per loci). e.g.: Individual_ID Locus_A Locus_B Locus_C 10323 A32 A12 B3 B4 C9 C10 10324 A2 A12 B5 B1 C1 C10 ... etc. The alleles ("A32", "A12", "B3", etc.) can sometimes consist of high-resolution data (e.g. actual DNA or RNA sequences) or lower-level data (such as "DQP1003", which are simply nomenclature strings, often termed "allele calls", because the molecular typing techniques using "kits", as they need to be carried out on large numbers of individuals, aren't as accurate as full-sequencing, or at least that's my understanding of the in-vitro aspect, being a strictly in-silico person myself ;-)). Unfortunately unlike the NCBI/Genbank and other formats there are no generally accepted formats for pop-gen multi-locus data for many individuals (please correct me if I'm wrong), however there are a few attempts at standardisation, most notably the PGDB project at the University of Louisiana: http://seahorse.louisiana.edu/PGDB/ which has attempted a tentative XML file-format standard. Currently I'm implementing a parser for the fairly simple-minded, but reasonably common format as described above, but it currently is independent of biopython. Ideally, it would be a subclass of "AbstractParser" or somesuch (and would ultimately recognise the XML version, when one hopefully becomes standard), and could return appropriate Sequence or SeqFeature objects. If not all of our code can be released, then at the very least, perhaps some of our modules could be contributed directly to biopython or be made as "optional" add-ons to biopython. In any case, I have been investigating biopython and would like to get some feedback from the community: * pointers to existing work in Python (or elsewhere) along these lines (if there is any); * suggestions about how such parsing modules might be most elegantly integrated into the biopython framework; * comments from others who deal in pop. genetics analysis and have experience and/or suggestions for data formats in pop. genetics and other multi-locus genotype data, and whether there is sufficient interest in such a parser to warrant the effort to generalise it. Thanks, Alex From jchang@SMI.Stanford.EDU Mon Sep 17 06:27:18 2001 From: jchang@SMI.Stanford.EDU (Jeffrey Chang) Date: Sun, 16 Sep 2001 22:27:18 -0700 Subject: [BioPython] Biopython and population genetics In-Reply-To: <7u3d5prx2x.fsf@allele2.biol.berkeley.edu> References: <7u3d5prx2x.fsf@allele2.biol.berkeley.edu> Message-ID: >If not all of our code can be released, then at the very least, >perhaps some of our modules could be contributed directly to biopython >or be made as "optional" add-ons to biopython. Yep, it would be really cool if your code could be released. However, getting permission to release code as open source can be difficult. See the open source authors mailing list: http://open-bio.org/mailman/listinfo/authors >* suggestions about how such parsing modules might be most elegantly > integrated into the biopython framework; The proper way to do it would be to create a subdirectory under Bio/ with a name that's descriptive of the data file. There's an ad-hoc standard that parsers have a method called "parse" that takes a handle and returns some sort of object. I don't work in population genetics, so will leave it to you and the community to find a good solution that's generalizable for others' needs. Jeff From Y.Benita@pharm.uu.nl Thu Sep 20 13:01:33 2001 From: Y.Benita@pharm.uu.nl (Yair Benita) Date: Thu, 20 Sep 2001 14:01:33 +0200 Subject: [BioPython] Kill blast Message-ID: Hi all, I use local BLAST for many genes. For some genes it takes 30sec to complete and for others hours. How can I kill the blast process if it takes too long (more than 3 min or so)? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From Andrew Dalke" Yair Benita : > How can I kill the blast process if it takes too long (more > than 3 min or so)? On most unix systems, the easiest way is to define a ulimit on the spawned off BLAST run. See the man page for bash or whatever your /bin/sh is for details on how to specific ulimit. For example, % ulimit -t 300 % python Python 2.0 (#4, Dec 8 2000, 21:23:00) [GCC egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)] on linux2 Type "copyright", "credits" or "license" for more information. >>> while 1: pass ... CPU time limit exceeded % sets a cpu runtime limit of 5 minutes to any new process. Then you would run blast and let the OS kill it if it takes too long. 'Course, you would have to have the code to check if BLAST exists without output. I'm not checked how the current biopython code deals with it. To make things more complicated, if you use an csh based shell (like tcsh) then the command is called "limit", as in [dalke@pw600a Blast]$ limit cputime 1 But popen3, which NCBIStandalone uses, runs /bin/sh. What does this all mean? Try using blastcmd = "limit -t 300 && blastall" in the call to run BLAST. Andrew dalke@dalkescientific.com From chapmanb@arches.uga.edu Thu Sep 27 03:14:53 2001 From: chapmanb@arches.uga.edu (Brad Chapman) Date: Wed, 26 Sep 2001 22:14:53 -0400 Subject: [BioPython] Biopython-corba 0.3.0 release available Message-ID: <20010926221453.B27721@ci350185-a.athen1.ga.home.com> Hello all; I'm very happy to announce the release of biopython-corba 0.3.0. Biopython-corba provides a python library implementing the BioCorba specificiations, and allows you to easily make Biopython objects available through CORBA, and access CORBA objects through a Biopython-like interface. As normal, the release is available from the download page: http://biopython.org/Download/ This version of biopython-corba reimplements the library for the new BioCorba interfaces worked out at BOSC/ISMB this year (the Tivoli IDLs). There are many good reasons to try out this module, including: => Allows you to easily make Biopython objects like GenBank Dictionaries available as CORBA servers, which allows people to access them across a network from their language of choice. => You can access BioCorba objects through a Biopython-like interface, so if you understand biopython you can understand biopython-corba. => Works interchangably with omniORBpy, ORBit-python, and Fnorb ORB implementations, so you can pick your python ORB o' choice. => Includes documentation and example scripts to help get started. => It would make Brad happy :-) As always, I'm more than happy to answer any questions here or on the dev mailing list. Thanks for listening and enjoy! Brad -- PGP public key available from http://pgp.mit.edu/ From Andrew Dalke" Hello, As most of you know, my company is looking for companies interested in having us further develop Biopython. As a software consulting and development shop, we've been looking for people who need those sorts of services. We've also heard from people who don't need specific software written but are interested in helping further the Biopython community. For example, one company I've been talking to uses Python in-house. They would like to support the community as a way to show their appreciation, with the indirect benefit that they will be able to draw from a larger pool of people and software. I'm coming up with a list of things that might be funded. I'm trying to emphasize tasks that people don't really volunteer doing, but are willing to work on in exchange for some payment. web site maintainer - make sure the web pages stay up to date - add new items (news, releases, etc.) as available - keep things in synch with the other bio* projects documentation - high-level descriptions - documenting the various APIs teaching materials - pay for what's needed to clean up in-house materials - help pay for development materials I don't know how to renumerate for the following: format tracking - make sure Biopython parsers and client code stays up-to-date (not sure how to charge answering questions on the mailing list Any other suggestions? Andrew dalke@dalkescientific.com From o.hofmann@Smail.Uni-Koeln.de Fri Sep 28 16:10:04 2001 From: o.hofmann@Smail.Uni-Koeln.de (Oliver Hofmann) Date: Fri, 28 Sep 2001 17:10:04 +0200 Subject: [BioPython] Blast results in XML Message-ID: 'lo everyone! Just a quick question before I probably start writing one.. as of now, there is no parser for the XML blast results? Ie, all parsers in the BioPython project expect the results to be in regular flatfile format? Thanks a lot, Oliver -- Oliver Hofmann - University of Cologne (temporarily at deCode Iceland) PGP Fingerprint - 3B91 E308 2E5D D2A4 4E8D 633B F628 488D 8ECF 3893 Reality continues to ruin my live. -- Calvin From msterman@exceloncorp.com Fri Sep 28 19:40:10 2001 From: msterman@exceloncorp.com (Martin Sterman) Date: Fri, 28 Sep 2001 14:40:10 -0400 Subject: [BioPython] Blast results in XML References: Message-ID: <00e601c1484d$012f6710$171103c6@exceloncorp.com> Do you require the parser source code to be in Python or are you just looking for an XML parser? As long as the blast results are well formed XML, there are plenty of parsers out there. SAX for read only or DOM for read/write. You need only write a handler for an existing parser. Don't want to advertise anyone's parser in particular, so try http://www.oasis-open.org/cover/publicSW.html for a full set of links. Martin Sterman eXcelon Corp. ----- Original Message ----- From: "Oliver Hofmann" To: Sent: Friday, September 28, 2001 11:10 AM Subject: [BioPython] Blast results in XML > 'lo everyone! > > > Just a quick question before I probably start writing one.. as of > now, there is no parser for the XML blast results? Ie, all parsers > in the BioPython project expect the results to be in regular > flatfile format? > > > Thanks a lot, > > Oliver > > > -- > Oliver Hofmann - University of Cologne (temporarily at deCode Iceland) > PGP Fingerprint - 3B91 E308 2E5D D2A4 4E8D 633B F628 488D 8ECF 3893 > > Reality continues to ruin my live. > -- Calvin > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From jchang@SMI.Stanford.EDU Fri Sep 28 19:46:50 2001 From: jchang@SMI.Stanford.EDU (Jeffrey Chang) Date: Fri, 28 Sep 2001 11:46:50 -0700 Subject: [BioPython] Blast results in XML In-Reply-To: References: Message-ID: Yep, no parser for the XML format. It would be a good idea to have one, so if you do develop one, please consider submitting it to the project! Jeff At 5:10 PM +0200 9/28/01, Oliver Hofmann wrote: >'lo everyone! > > >Just a quick question before I probably start writing one.. as of >now, there is no parser for the XML blast results? Ie, all parsers >in the BioPython project expect the results to be in regular >flatfile format? > > >Thanks a lot, > > Oliver > > >-- >Oliver Hofmann - University of Cologne (temporarily at deCode Iceland) >PGP Fingerprint - 3B91 E308 2E5D D2A4 4E8D 633B F628 488D 8ECF 3893 > >Reality continues to ruin my live. > -- Calvin > >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython