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Subject: Re: [BioPython] Need help parsing Blastoutput - msg#00006List: python.bio.generalMichiel De Hoon wrote: > A general question is if anybody still needs the parser for Blast text > output. Currently, we are confusing our users by having a Blast text parser > that tends to break. A broken parser may be worse than no parser. I still do think it is worth the effort to keep it in the tree, for study purposes and for the fact that not everybody uses XML formatted output yet. ;-) Martin _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython Thread at a glance:
Previous Message by Date: click to view message preview[BioPython] Google Summer of CodeProposals are due by May 8, 2006 13:00 PDT. Proposals made before this period may get comments and permit you to update to reflect feedback on what you submitted. ----- Forwarded message from Neal Norwitz <nnorwitz@xxxxxxxxx> ----- Date: Thu, 20 Apr 2006 00:32:56 -0700 From: "Neal Norwitz" <nnorwitz@xxxxxxxxx> To: python-list@xxxxxxxxxx Subject: Python Software Foundation seeks mentors and students for Google Summer of Code This spring and summer, Google will again provide stipends for students (18+, undergraduate thru PhD programs) to write new open-source code. The Python Software Foundation (PSF) http://www.python.org/psf/ will again act as a sponsoring organization in Google's Summer of Code, matching mentors and projects benefiting Python and Python users. Projects can include work on the core Python language, programmer utilities, libraries, packages, frameworks related to Python, or other Python implementations like Jython, PyPy, or IronPython. Please add your project ideas to the existing set at http://wiki.python.org/moin/SummerOfCode Mentoring instructions are also on this page. The deadline is soon, so please sign up as a mentor early. If you are a student considering a project, you should start deciding now. Feel free to ask questions on python-dev@xxxxxxxxxx The main page for the Summer of Code is http://code.google.com/summerofcode.html At the bottom are links to StudentFAQ, MentorFAQ, and TermsOfService. The first two have the timeline. Note that student applications are due between May 1, 17:00 PST and May 8, 17:00 PST. People interested in mentoring a student though PSF are encouraged to contact me, Neal Norwitz at nnorwitz@xxxxxxxxxx People unknown to Guido or myself should find a couple of people known within the Python community who are willing to act as references. Feel free to contact me if you have any questions. I look forward to meeting many new mentors and students. Let's improve Python! ----- End forwarded message ----- _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython Next Message by Date: click to view message previewRe: [BioPython] Need help parsing BlastoutputOn 5/4/06, Martin MOKREJŠ <mmokrejs@xxxxxxxxxxxxxxxxxxxxxx> wrote: > I still do think it is worth the effort to keep it in the tree, for > study purposes and for the fact that not everybody uses XML formatted output > yet. ;-) While I agree that nobody is using XML output by default (I also use text or HTML output), I think people will use the XML output if they BLAST knowing that they will parse it using Biopython. So I think that text parser should stay in Biopython, but examples in documentation should be in XML. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython Previous Message by Thread: click to view message preview[BioPython] Google Summer of CodeProposals are due by May 8, 2006 13:00 PDT. Proposals made before this period may get comments and permit you to update to reflect feedback on what you submitted. ----- Forwarded message from Neal Norwitz <nnorwitz@xxxxxxxxx> ----- Date: Thu, 20 Apr 2006 00:32:56 -0700 From: "Neal Norwitz" <nnorwitz@xxxxxxxxx> To: python-list@xxxxxxxxxx Subject: Python Software Foundation seeks mentors and students for Google Summer of Code This spring and summer, Google will again provide stipends for students (18+, undergraduate thru PhD programs) to write new open-source code. The Python Software Foundation (PSF) http://www.python.org/psf/ will again act as a sponsoring organization in Google's Summer of Code, matching mentors and projects benefiting Python and Python users. Projects can include work on the core Python language, programmer utilities, libraries, packages, frameworks related to Python, or other Python implementations like Jython, PyPy, or IronPython. Please add your project ideas to the existing set at http://wiki.python.org/moin/SummerOfCode Mentoring instructions are also on this page. The deadline is soon, so please sign up as a mentor early. If you are a student considering a project, you should start deciding now. Feel free to ask questions on python-dev@xxxxxxxxxx The main page for the Summer of Code is http://code.google.com/summerofcode.html At the bottom are links to StudentFAQ, MentorFAQ, and TermsOfService. The first two have the timeline. Note that student applications are due between May 1, 17:00 PST and May 8, 17:00 PST. People interested in mentoring a student though PSF are encouraged to contact me, Neal Norwitz at nnorwitz@xxxxxxxxxx People unknown to Guido or myself should find a couple of people known within the Python community who are willing to act as references. Feel free to contact me if you have any questions. I look forward to meeting many new mentors and students. Let's improve Python! ----- End forwarded message ----- _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython Next Message by Thread: click to view message previewRe: [BioPython] Need help parsing BlastoutputOn 5/4/06, Martin MOKREJŠ <mmokrejs@xxxxxxxxxxxxxxxxxxxxxx> wrote: > I still do think it is worth the effort to keep it in the tree, for > study purposes and for the fact that not everybody uses XML formatted output > yet. ;-) While I agree that nobody is using XML output by default (I also use text or HTML output), I think people will use the XML output if they BLAST knowing that they will parse it using Biopython. So I think that text parser should stay in Biopython, but examples in documentation should be in XML. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 _______________________________________________ BioPython mailing list - BioPython@xxxxxxxxxxxxxxxxxx http://lists.open-bio.org/mailman/listinfo/biopython Loading Comments...
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