From j.a.casbon at qmul.ac.uk Mon Dec 6 10:09:31 2004 From: j.a.casbon at qmul.ac.uk (James Casbon) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... Message-ID: <200412061509.31127.j.a.casbon@qmul.ac.uk> Is biopython dead? I counted 4 patches in bugzilla (before I got bored) that have not been applied to cvs, without any response from developers. In addition, no-one responded to this offer of code: http://portal.open-bio.org/pipermail/biopython-dev/2004-November/002713.html or the repeated calls to sort out the dev mailing list, eg: http://portal.open-bio.org/pipermail/biopython-dev/2004-October/002571.html Is anyone still out there? James From idoerg at burnham.org Mon Dec 6 13:02:41 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412061509.31127.j.a.casbon@qmul.ac.uk> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> Message-ID: <41B49EC1.6090006@burnham.org> James Casbon wrote: >Is biopython dead? > No but it sure smells funny. I apologize for that, our day jobs seem to get the better of us. Brad, Jeff: if you guys are busy, I can take over for a while. I'll need some guidance with a couple of issues. Ping me, please. Cheers, Iddo >I counted 4 patches in bugzilla (before I got bored) that >have not been applied to cvs, without any response from developers. > >In addition, no-one responded to this offer of code: >http://portal.open-bio.org/pipermail/biopython-dev/2004-November/002713.html > >or the repeated calls to sort out the dev mailing list, eg: >http://portal.open-bio.org/pipermail/biopython-dev/2004-October/002571.html > >Is anyone still out there? > >James >_______________________________________________ >Biopython-dev mailing list >Biopython-dev@biopython.org >http://biopython.org/mailman/listinfo/biopython-dev > > > > -- 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 biopython-dev at maubp.freeserve.co.uk Mon Dec 6 14:42:11 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Parsing RPS-Blast output with BioPython Message-ID: <41B4B613.80803@maubp.freeserve.co.uk> Has anyone looked at using BioPython with the NCBI's (standalone) RPS-Blast program? RPSBLAST = Reverse Position Specific BLAST, used to query a protein sequence against the Conserved Domain Database, Pfam, SMART etc. I've had a little look at the NCBIStandalone.py, and can see how a function rpsblast could be added, based on the existing blastall or blastpgp functions. (i.e. Make a copy of blastpgp and called it rpsblast) However, it would appear that the output parser will need some additional work to understand the RPS-BLAST output... Thanks Peter MOAC Doctoral Training Centre University of Warwick, UK From biopython-dev at maubp.freeserve.co.uk Mon Dec 6 16:57:05 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Parsing RPS-Blast output with BioPython In-Reply-To: <41B4B613.80803@maubp.freeserve.co.uk> References: <41B4B613.80803@maubp.freeserve.co.uk> Message-ID: <41B4D5B1.60704@maubp.freeserve.co.uk> Peter wrote: > Has anyone looked at using BioPython with the NCBI's (standalone) > RPS-Blast program? > > RPSBLAST = Reverse Position Specific BLAST, used to query a protein > sequence against the Conserved Domain Database, Pfam, SMART etc. > > I've had a little look at the NCBIStandalone.py, and can see how a > function rpsblast could be added, based on the existing blastall or > blastpgp functions. > > (i.e. Make a copy of blastpgp and called it rpsblast) > > However, it would appear that the output parser will need some > additional work to understand the RPS-BLAST output... It looks like its not as much work as I had feared. With Blast 2.2.9 at least, the RPS-BLAST output is just a slightly reduced version of the BLASTP output. [I know BLAST 2.2.10 has been released. I should really update my machine] I think I have got the existing code to work, by making the parser aware that some sections of the "header" and "database report" sections are now "optional". Bug logged and rough solution submitted: http://bugzilla.open-bio.org/show_bug.cgi?id=1715 Please note that my changes have only received minimal testing, and in particular I have only checked the classic Blast support still works for a simple blastp query. I'm hoping that a BioPython developer will now volunteer to take a look at this, make sure the style etc is acceptable, and hopefully merge it into CVS. Do you guys have semi-automatic test scripts/unit tests? Thanks Peter MOAC Doctoral Training Centre University of Warwick, UK From edwina.roth_xr at acer.com.sg Mon Dec 6 17:16:15 2004 From: edwina.roth_xr at acer.com.sg (Edwina Roth) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] New product! Cialis soft tabs. Message-ID: Hi! We have a new product that we offer to you, C_I_A_L_I_S soft tabs, Cialis Soft Tabs is the new impotence treatment drug that everyone is talking about.Soft Tabs acts up to 36 hours, compare this to only two or three hours of Viagra action! The active ingredient is Tadalafil, same as in brand Cialis. Simply disolve half a pill under your tongue, 10 min before sex, for the best erections you've ever had! Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them). You can get it at: http://the-rxsite.com/soft/ No thanks: http://the-rxsite.com/rr.php From bugzilla-daemon at portal.open-bio.org Mon Dec 6 16:46:31 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412062146.iB6LkVaH010275@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-06 16:46 ------- Created an attachment (id=182) --> (http://bugzilla.open-bio.org/attachment.cgi?id=182&action=view) Edited version of NCBIStandalone.py as shipped with BioPython 1.30 ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 6 16:47:31 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412062147.iB6LlVF7010289@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-06 16:47 ------- Created an attachment (id=183) --> (http://bugzilla.open-bio.org/attachment.cgi?id=183&action=view) Example script using rpsblast support ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 6 16:44:59 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] New: Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412062144.iB6LixkW010251@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 Summary: Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk The NCBI's standalone RPS-Blast program (Reverse Position Specific BLAST) can be used to query a protein sequence against the Conserved Domain Database, or Pfam, or SMART etc. The commandline program rpsblast(.exe) is very similar in use to the existing blastall(.exe), and the resulting output file simply seems to omit some lines. I have been able to modify the NCBIStandalone.py as shipped with BioPython 1.30 to support rpsblast as well. Attachments to follow. See also this email and any follow ups: http://www.biopython.org/pipermail/biopython-dev/2004-December/002795.html ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From jeffrey.chang at duke.edu Mon Dec 6 21:57:19 2004 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412061509.31127.j.a.casbon@qmul.ac.uk> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> Message-ID: Hi James, and everyone else, As the ex-leader for the Biopython project, I should probably say something, since no one (except for Iddo :) has responded on the list. As many of you are aware, I still follow the project on a day to day basis, but I no longer have the time to maintain the project, and a little over a year ago, I handed the project off. However, since then, Brad seems to have disappeared at some point, and messages to the list have gone unanswered. However, I would like to point out, that as a community-based open source project, it is not Brad's, or anyone else's, responsibility to answer every question on the list, check every patch, and investigate every bug report. Biopython's grown to be too big a project for one person to manage, while maintaining their day jobs. While the traffic on the mailing lists is low to middling, stuff does happen off the list that eats away at time too. Even though Iddo has graciously agreed to step up and help out in a lead role for a while, and I think he would do a fantastic job, it is becoming clear to me that that is not a sustainable solution. I think it is time for the project to move to a group managed system, where the responsibilities are distributed out to more people, and also more clearly. While currently there are people roughly responsible for different sections of the code, possible other important "jobs" include making releases, checking in patches, fixing bug reports, responding to help requests on the mailing lists, and slightly lower priority, maintaining regression tests, documentation, updating the web page. Currently, Brad does the lion's share of all this, and with (very roughly counting) nearly 600 *.py files in the repository now, it's getting hard. It's time for people to step up and volunteer to take on more of these responsibilities. So what are your thoughts? Does this make sense, and is there any interest in the community for trying to spread out the work? The idea would be to give more people a stake and responsibility in the project, and someone (Iddo :) to oversee and help out where he can. Maintaining the project is too large a task for someone with a day job, and it's too hard for one person to be responsible for the majority of the work anymore. Jeff From hisahikosatou at hotmail.com Mon Dec 6 22:25:49 2004 From: hisahikosatou at hotmail.com (Hisahiko Sato) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] PubMed module Message-ID: I am considering using pubmed class of BioPython to access Pubmed. I have a question for using this. Is there any limitation for using this class? I am afraid too much use of this class would recognize as traffic attack to ncbi site from my company. I heard ncbi would limit the internet access if there are too much access. Sincerely, Hisahiko Sato From mdehoon at ims.u-tokyo.ac.jp Tue Dec 7 03:00:12 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Building biopython 1.30 on Windows with MSCV In-Reply-To: <419AB67D.7050703@ims.u-tokyo.ac.jp> References: <27816144.1100627287997.JavaMail.www@wwinf3001> <419AB67D.7050703@ims.u-tokyo.ac.jp> Message-ID: <41B5630C.30808@ims.u-tokyo.ac.jp> Finally, I found out how to update the Biopython web page. On the download page, you will now find a Windows installer for Biopython 1.30 for Python versions 2.2, 2.3, and 2.4. Sorry for the delay. Please let me know if there are any problems. --Michiel. Michiel Jan Laurens de Hoon wrote: > There *is* a Windows installer for Biopython 1.30, for some reason it is > not visible now on the Biopython website. I have updated the biopython > webpage in CVS, but I cannot find the setup.py on the biopython > webserver to install the new webpage. Does anybody know what happened > with this setup.py? > > --Michiel. > > Peter wrote: > >> I'm trying to build and/or install BioPython 1.30 on Windows XP. >> >> I would guess that since there isn't a Windows installer for Biopython >> 1.30 (yet) that most development occurs on linux/unix. >> >> Furthermore, the only instructions in the documentation are for >> Borland's free C++ compiler: >> >> http://www.bioinformatics.org/bradstuff/bp/tut/Tutorial001.html#sec:windows_install >> >> >> I have Microsoft Visual C++ 6.0 (MSVC) which I have successfully used >> to compile other python extensions (both a simple install, and >> creation of a windows installation program). >> >> In theory using MSVC 6.0 should actually be easier, but it looks like >> no-one has tried this recently as there is a library problem of some >> sort. If I try this for BioPython 1.30: >> >> python setup.py bdist_wininst >> >> After a few warnings, it fails here: >> >> building 'Bio.PDB.mmCIF.MMCIFlex' extension >> C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo >> /Ox /MD /W3 >> /GX /DNDEBUG -IBio -Ic:\Python23\include -Ic:\Python23\PC >> /TcBio/PDB/mmCIF/lex.yy.c >> /Fobuild\temp.win32-2.3\Release\Bio/PDB/mmCIF/lex.yy.obj >> lex.yy.c >> Bio/PDB/mmCIF/lex.yy.c(12) : fatal error C1083: Cannot open include >> file: 'unistd.h': No such file or directory >> error: command '"C:\Program Files\Microsoft Visual >> Studio\VC98\BIN\cl.exe"' fail >> ed with exit status 2 >> >> Before I can too carried away, does anyone on the list have any >> experience of building BioPython on windows? >> >> Thank you >> >> Peter >> > -- 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 ymasuda at ethercube.com Tue Dec 7 03:24:54 2004 From: ymasuda at ethercube.com (Yasushi MASUDA) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] PubMed module In-Reply-To: References: Message-ID: <200412070824.iB78OwvO031349@www216.sakura.ne.jp> As far as I know/believe, PubMed.py, which handles communication with Entrez/PubMed, imports Bio.WWW.RequestLimiter. It seems to limit your access to NCBI based on time delay. The default delays are 5.0 seconds for Dictionary(), 2.0 seconds for search_for(), 120.0 seconds for download_many(). Those delays are injected just *before* each iterative request (even in single query) by RequestLimitter so that your program will sleep before retriving individual entry every time. Thus, if you write your program in well-behaved manner (no parallelize of requests by threading, no use of broken system timer, etc.), there should be no problem. If you are interested in reading Python code doing it, please take a look into $pythonlib/site-packages/Bio/WWW/__init__.py or $ptyhonlib/site-packages/Bio/PubMed.py. "Hisahiko Sato" wrote: > I am considering using pubmed class of BioPython to access Pubmed. > > I have a question for using this. > Is there any limitation for using this class? > I am afraid too much use of this class would recognize as traffic attack to > ncbi site from my company. > I heard ncbi would limit the internet access if there are too much access. --- Yasushi Masuda http://www.cubelab.com/ymasuda/ From bugzilla-daemon at portal.open-bio.org Tue Dec 7 03:48:07 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1675] complement() returns string instead of Seq object Message-ID: <200412070848.iB78m73t016059@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1675 mdehoon@ims.u-tokyo.ac.jp changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biopython-dev@biopython.org |mdehoon@ims.u-tokyo.ac.jp ------- Additional Comments From mdehoon@ims.u-tokyo.ac.jp 2004-12-07 03:48 ------- This has been fixed in the CVS version of Biopython. For a Seq object, there is currently no reverse() function. You can use s[-1::-1] instead, but that will still give you a string instead of a new Seq object. >>> from Bio.Seq import * >>> s = Seq('ATCGACTG') >>> s.reverse_complement() Seq('CAGTCGAT', Alphabet()) >>> s.complement() Seq('TAGCTGAC', Alphabet()) >>> m = MutableSeq('ATCGACTAG') >>> m.reverse() >>> m MutableSeq(array('c', 'GATCAGCTA'), Alphabet()) >>> m.complement() >>> m MutableSeq(array('c', 'CTAGTCGAT'), Alphabet()) >>> m.reverse_complement() >>> m MutableSeq(array('c', 'ATCGACTAG'), Alphabet()) ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mike at maibaum.org Tue Dec 7 05:24:30 2004 From: mike at maibaum.org (Michael Maibaum) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: References: <200412061509.31127.j.a.casbon@qmul.ac.uk> Message-ID: <2E834FCA-483A-11D9-80F4-000D93C8D9CE@maibaum.org> On 7 Dec 2004, at 02:57, Jeffrey Chang wrote: > Hi James, and everyone else, > > I think it is time for the project to move to a group managed system, > where the responsibilities are distributed out to more people, and > also more clearly. While currently there are people roughly > responsible for different sections of the code, possible other > important "jobs" include making releases, checking in patches, fixing > bug reports, responding to help requests on the mailing lists, and > slightly lower priority, maintaining regression tests, documentation, > updating the web page. Currently, Brad does the lion's share of all > this, and with (very roughly counting) nearly 600 *.py files in the > repository now, it's getting hard. It's time for people to step up > and volunteer to take on more of these responsibilities. > > So what are your thoughts? Does this make sense, and is there any > interest in the community for trying to spread out the work? The idea > would be to give more people a stake and responsibility in the > project, and someone (Iddo :) to oversee and help out where he can. > Maintaining the project is too large a task for someone with a day > job, and it's too hard for one person to be responsible for the > majority of the work anymore. I agree absolutely - one person (with other jobs) will not have enough time to be able to cope with the demands of a successful project. If there is anything I can do to help I'd certainly be interested (probably in one of the patches/bugs/mailing list parts, I don't think I know biopython well enough yet to write documentation or managing releases). I think a short term priority has to be to clean up the mailing list. As a newcomer to biopython I reviewed the mailing list archives and very nearly abandoned ideas of using it. The first impression it gives is of a dead project, with so much spam that the lists are very hard to search for past information. I think the lists should switch over to subscription only, while I understand the utility of non-members being able to post that benefit is swamped by the spam problem in the archives and the negative first impression. Michael From j.a.casbon at qmul.ac.uk Tue Dec 7 06:41:40 2004 From: j.a.casbon at qmul.ac.uk (James Casbon) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <2E834FCA-483A-11D9-80F4-000D93C8D9CE@maibaum.org> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <2E834FCA-483A-11D9-80F4-000D93C8D9CE@maibaum.org> Message-ID: <200412071141.40822.j.a.casbon@qmul.ac.uk> > > So what are your thoughts? Does this make sense, and is there any > > interest in the community for trying to spread out the work? The idea > > would be to give more people a stake and responsibility in the > > project, and someone (Iddo :) to oversee and help out where he can. > > Maintaining the project is too large a task for someone with a day > > job, and it's too hard for one person to be responsible for the > > majority of the work anymore. This sounds like a good way forward. I didn't realise that it was all up to one person to manage everything. I suppose we need to identify people interested in particular areas of the project who could focus on maintaining parts relevant to them. I would be willing to help maintain the modules I have experience with. > I think a short term priority has to be to clean up the mailing list. I agree, according to the homepage, these people run the list: jchang at smi.stanford.edu, dag at sonsorol.org, mailteam at open-bio.org so Jeffrey, can you make the list subscriber only from here: http://biopython.org/mailman/admin/biopython-dev James From jeffrey.chang at duke.edu Tue Dec 7 07:48:03 2004 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412071141.40822.j.a.casbon@qmul.ac.uk> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <2E834FCA-483A-11D9-80F4-000D93C8D9CE@maibaum.org> <200412071141.40822.j.a.casbon@qmul.ac.uk> Message-ID: <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> On Dec 7, 2004, at 6:41 AM, James Casbon wrote: >> [Michael] >> I think a short term priority has to be to clean up the mailing list. > I agree, according to the homepage, these people run the list: > jchang at smi.stanford.edu, dag at sonsorol.org, mailteam at > open-bio.org > so Jeffrey, can you make the list subscriber only from here: > http://biopython.org/mailman/admin/biopython-dev Sure, I can do that. I'll give people 24 hours to voice their concerns about this, and if I don't hear anything, and if we don't change our minds, I'll switch biopython-dev over to subscriber only tomorrow. Jeff From chapmanb at 50mail.com Tue Dec 7 08:17:30 2004 From: chapmanb at 50mail.com (Brad Chapman) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: References: <200412061509.31127.j.a.casbon@qmul.ac.uk> Message-ID: <20041207131730.GE39850@lebowski.bos.east.verizon.net> Hey all; > However, since then, > Brad seems to have disappeared at some point, and messages to the list > have gone unanswered. Heh, yeah. I have been sadly absent, for which I apologize. Right now I'm still in the unfortunate situation of not having a real job. This leaves me working 50+ hours a week at my throwaway catering job, and the rest of the week trying to actually get a position. Sadly, this means I have very rarely been touching a computer this past few months (except to right yet another cover letter, ugh). I keep hoping that the situation will change soon and I will go back to both having more time, and also having a current job where Biopython is useful to me again (somehow, it doesn't really come into play too much when waiting tables :-). But yeah, I've been living job hope to job hope thinking that soon I'd be back in the game without much success so far. Enough whining on and on. Surely whatever is right for moving things forward is fine by me. I hope soon I will be able to contribute more, but until then I don't want to give the impression Biopython is dead, which it most assuredly is not. Thanks guys, and I will try to be of as much help as I can. Now-wishing-to-go-back-to-the-warm-confines-of-grad-school-ly yr's, Brad From longlill at yahoo.com Tue Dec 7 10:58:50 2004 From: longlill at yahoo.com (Long Li) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: Message-ID: <20041207155851.68246.qmail@web52808.mail.yahoo.com> --- Jeffrey Chang wrote: > However, I would like to point out, that as a > community-based open > source project, it is not Brad's, or anyone else's, > responsibility to > answer every question on the list, check every > patch, and investigate > every bug report. Maybe Debian GNU/Linux is good example for us. Many volunteers maintain it successfully. By the way, BioPython has been a formal package of Debian GNU/Linux now, its maintainer is Philipp Benner . http://packages.debian.org/testing/python/python-biopython >Biopython's grown to be too big a > project for one > person to manage Yes, this project need more maintainers. For each module or package, it at lease need two or more maintainers. But there is no limit to ecah person, he or she can maintain one or more modules/packages. Another thing is that the maintains MUST post the message to the bipython-dev list if he or she update one module/package. In fact, I think any technique problem should be posted to the biopython-dev first, after discussion, then modify the source code or write new modules. BioPython should also have more documents,especially more examples, for biologists who want write some simple source code to solve their problems. Best regards, Long __________________________________ Do you Yahoo!? Take Yahoo! Mail with you! Get it on your mobile phone. http://mobile.yahoo.com/maildemo From mit2005 at vreme.yubc.net Wed Dec 8 00:05:11 2004 From: mit2005 at vreme.yubc.net (IPSI-2005 MIT and Belgrade) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Invitation to MIT and Belgrade 2005, c/ba Message-ID: <200412080505.iB855BuG001759@vreme.yubc.net> Dear potential Speaker: On behalf of the organizing committee, I would like to extend a cordial invitation for you to attend one or both of the upcoming IPSI BgD multidisciplinary, interdisciplinary, and transdisciplinary conferences. The first one will be in Belgrade, Serbia and Montenegro: IPSI-2005 BELGRADE University of Belgrade (arrival: 2 June 05 / departure: 5 June 05) Deadlines: 1 March 05 (abstract) & 15 April 05 (full paper) The second one will be in Massachusetts, USA : IPSI-2005 USA Hotel@MIT, Cambridge (arrival: 7 July 05 / departure: 10 July 05) Deadlines: 20 February 05 (abstract) / 20 March 05 (full paper) All IPSI BgD conferences are non-profit. They bring together the elite of the world of science; so far, we have had seven Nobel Laureates speaking at the opening ceremonies. The conferences always take place in some of the most attractive places of the world. All those who come to IPSI conferences once, always love to come back (because of the unique professional quality and the extremely creative atmosphere); lists of past participants are on the web, as well as details of future conferences. These conferences are in line with the newest recommendations of the US National Science Foundation and of the EU research sponsoring agencies, to stress multidisciplinary, interdisciplinary, and transdisciplinary research (M.I.T. research). The speakers and activities at the conferences truly support this type of scientific interaction. Topics of interest include, but are not limited to: * Internet * Computer Science and Engineering * Mobile Communications/Computing for Science and Business * Management and Business Administration * Education * e-Medicine * e-Oriented Bio Engineering/Science and Molecular Engineering/Science * Environmental Protection * e-Economy * e-Law * Technology Based Art and Art to Inspire Technology Developments * Internet Psychology If you would like more information on either conference, please reply to this e-mail message. If you plan to submit an abstract and paper, please let us know immediately for planning purposes. Sincerely Yours, Prof. V. 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From bugzilla-daemon at portal.open-bio.org Wed Dec 8 06:55:35 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412081155.iB8BtZ5J001662@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #184 is|0 |1 obsolete| | ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-08 06:55 ------- Created an attachment (id=185) --> (http://bugzilla.open-bio.org/attachment.cgi?id=185&action=view) RPS-BLAST 2.2.10 output file for testing rpsblast support Updated test file, the only difference between this (rpsblast 2.2.10) and the 2.2.9 output is the version number at the start of the file. [As an aside, the next free Blast test file number is actually bt072, bt071 has been used to test a PSIBlast parser fix ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Dec 8 05:45:12 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412081045.iB8AjCwI031927@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-08 05:45 ------- Created an attachment (id=184) --> (http://bugzilla.open-bio.org/attachment.cgi?id=184&action=view) RPS-BLAST 2.2.9 output file for testing rpsblast support I am pleased to report that with my proposed changes, the Bio/Tests/test_NCBIStandalone.py program still runs without error. The attachment (bt071) is an additional test file (currently the next free slot is bt071) to go here Bio/Tests/Blast/bt071 It is the output of RPS-BLAST 2.2.9 [May-01-2004] when fed a KdpE (225 letters) from E.coli against the Pfam database from the NCBI. Adding bt071 to Bio/Tests/test_NCBIStandalone.py works as expected. Note - With rpsblast 2.2.9 and 2.2.10, the output file DOES NOT appear to include any reference to the database used. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Dec 8 08:01:12 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412081301.iB8D1COO003129@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #182 is|0 |1 obsolete| | ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-08 08:01 ------- Created an attachment (id=186) --> (http://bugzilla.open-bio.org/attachment.cgi?id=186&action=view) Edited version of NCBIStandalone.py based on CVS revision 1.57 Replacement to my previous file, this time based on the current code from CVS. Changes: (1) Removed some print statements left in by mistake (2) Changes to _scan_database_report made in CVS by Jeff Chang for a BLASTN 2.2.9 problem reported by Sameet Mehta also cope with RPSBLAST output, so my similar change is not needed. See also CVS revision 1.55 (3) Did the doc string and parameters dictionary for the new rpsblast function properly, trying to use the same names where possible from either blastall or blastpgp. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From jeffrey_chang at stanfordalumni.org Wed Dec 8 09:36:29 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <2E834FCA-483A-11D9-80F4-000D93C8D9CE@maibaum.org> <200412071141.40822.j.a.casbon@qmul.ac.uk> <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> Message-ID: <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> Hi all, I've switched the biopython-dev mailing list to subscriber only. Please let me know if something doesn't look right! Jeff From biopython-dev at maubp.freeserve.co.uk Wed Dec 8 10:09:52 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Parsing RPS-Blast output with BioPython Message-ID: <41B71940.7030003@maubp.freeserve.co.uk> As you might have noticed from the flood of emails onto the mailing list from the bugzilla-daemon (is this deliberate by the way?) I have done some more work on supporting the NCBI's (standalone) RPS-Blast program. http://bugzilla.open-bio.org/show_bug.cgi?id=1715 I have tested my changes with rpsblast 2.2.9 and 2.2.10 (which gives identical output except for the version number). I have tested my changes do not alter the results of the existing test collection (bt001 to bt071) used by test_NCBIStandalone.py, and have submitted a new test file of rpsblast 2.2.10 output. [So far all this was done on Windows, I am going to try and setup RPS-Blast on a linux machine as well] So what happens now? There doesn't seem to be any guidelines on the website for this... e.g. preferred format of patches/diff files - my code is just an edited version of the current CVS copy of NCBIStandalone.py Do I have to wave at the core-developers to give it the once over? Or would someone else on the list volunteer to double check my changes seem to work on their system? Ideally someone familiar with all the parameters for RPS-Blast, as I have just been using the default settings. Thanks again Peter MOAC Doctoral Training Centre University of Warwick, UK From bugzilla-daemon at portal.open-bio.org Wed Dec 8 16:03:33 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412082103.iB8L3Xup009561@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #186 is|0 |1 obsolete| | ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-08 16:03 ------- Created an attachment (id=187) --> (http://bugzilla.open-bio.org/attachment.cgi?id=187&action=view) Edited version of NCBIStandalone.py based on CVS revision 1.57 As per attachment 186 except for a one word change: database name in the header was being dealt with as a "noevent" instead of a "database_info" event. Sorry for not spotting this last time round, I have been running test_NCBIStandalone.py on its own and doing file comparison on the output by hand. I couldn't workout how to use the GUI run_test.py to do this for me. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Dec 8 18:40:16 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1717] New: Fasta.Dictionary should support has_key Message-ID: <200412082340.iB8NeGZ4010722@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1717 Summary: Fasta.Dictionary should support has_key Product: Biopython Version: Not Applicable Platform: All OS/Version: Windows 2000 Status: NEW Severity: enhancement Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk The Fasta.Dictionary is designed to let a fasta file be accessed like a Python dictionary. With this in mind, it would be nice to support the has_key(key) method. See also (slightly related) Bug 1716 - Fasta.Dictionary should throw KeyError for invalid keys ---------------------------------------------------------------- Possible implementation, based on how the keys() method is implemented. The doc string is that used for the standard Python dictionary method: def has_key(self, key) : """D.has_key(k) -> True if D has a key k, else False """ return key in self._index['id'].keys() There may be a far more efficient way of doing this, someone with more knowledge about Mindy may be able to help. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Dec 8 18:27:14 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1716] New: Fasta.Dictionary should throw KeyError for invalid keys Message-ID: <200412082327.iB8NREuY010621@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1716 Summary: Fasta.Dictionary should throw KeyError for invalid keys Product: Biopython Version: Not Applicable Platform: All OS/Version: Windows 2000 Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk Product: BioPython Version: 1.30 Component: Bio.Fasta OS: Windows and Linux, assume all The Fasta.Dictionary object can be used to access sequences by key: fasta_dict = Fasta.Dictionary(...) my_seq = fasta_dict[my_key] Try doing this for an invalid key (e.g. a gene not present in the Fasta file). Actual result: The Fasta.Dictionary appears to raise a ZeroDivisionError exception (from Bio\Mindy\FlatDB.py). Expected Result: By analogy with the Python dictionary, a KeyError exception should occur. -------------------------------------------------------- Detailed reproduction steps: (1) Create and change to an empty test directory (2) Create the file test.faa as below (3) Create the file test.py as below (4) Run the test script, test.py (5) Check you get the following output: Building FASTA index file using gene name as index, Done Loading FASTA index file, Done Valid keys: ['Alpha', 'Beta', 'Delta', 'Gamma'] About to try an use a non-existant key! Traceback (most recent call last): File "C:\Temp\fasta_dict_bug\test.py", line 42, in ? seq = fasta_dict['non_existant_key'] File "c:\python23\Lib\site-packages\Bio\Fasta\__init__.py", line 190, in __getitem__ seqs = self._index.lookup(aliases = key) File "c:\python23\Lib\site-packages\Bio\Mindy\BaseDB.py", line 118, in lookup return self[namespace][name] File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 351, in __getitem__ primary_keys = _lookup_alias(id_filename, name) File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 264, in _lookup_alias lines = _find_range(id_filename, word) File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 243, in _find_range bf = BisectFile(infile, size) File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 216, in __init__ assert (size - 4) % self.record_size == 0, "record size is wrong" ZeroDivisionError: long division or modulo by zero ------------------------------------------------------- test.faa ------------------------------------------------------- >Alpha This is the first sample AAAAAAAAAAAA >Beta Second sample [sensible data!] GVMNMTISFLSEHIFI >Gamma Third sample, with a silly sequence CASTLEINTHESKY >Delta Fourth sample, again with a silly sequence LITTLE ------------------------------------------------------- test.py ------------------------------------------------------- import os import string import Bio from Bio import Fasta from Bio.Alphabet import IUPAC filename_faa="test.faa" filename_idx="test.idx" if os.path.isfile(filename_idx) : # The index is a file on older versions of BioPython, # mind you Fasta.Dictionary seemed to be broken on # BioPython 1.24 so there isn't much point trying. pass elif os.path.isdir(filename_idx) : #The index files should exist pass else : print "Building FASTA index file using gene name as index,", Fasta.index_file(filename_faa, filename_idx, \ lambda seq : string.split(seq.title)[0]) print "Done" print "Loading FASTA index file,", fasta_dict = Fasta.Dictionary(filename_idx, Fasta.SequenceParser(IUPAC.ambiguous_dna)) print "Done" print "Valid keys:" print fasta_dict.keys() print "About to try an use a non-existant key!" seq = fasta_dict['non_existant_key'] print "Done" ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Dec 8 19:00:15 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1718] New: Fasta.Dictionary should support "in" (the __contains__ method) Message-ID: <200412090000.iB900Fs6010822@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1718 Summary: Fasta.Dictionary should support "in" (the __contains__ method) Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: biopython-bugzilla@maubp.freeserve.co.uk With a real Python dictionary you can do this: dictionary = {'A' : 'Apple', 'B' : 'Bananna', 'C' : 'Cherry'} print 'A' in dictionary print 'D' in dictionary The Fasta.Dictionary does not support this. It fails with a TypeError exception from Mindy which is very confusing to a novice (full traceback below). Possible implementation in Bio/Fasta/__init__.py is as follows: def __contains__(self, key) : """key in D -> True if D has a key k, else False """ return key in self._index['id'].keys() A Mindy expert may have a more efficient way of doing this. ---------------------------------------------------------------- Traceback (most recent call last): File "C:\Temp\fasta_dict_bug\test.py", line 33, in ? print 'Alpha' in fasta_dict File "C:\Python23\lib\site-packages\Bio\Fasta\__init__.py", line 187, in __getitem__ seqs = self._index.lookup(id = key) File "c:\python23\Lib\site-packages\Bio\Mindy\BaseDB.py", line 118, in lookup return self[namespace][name] File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 329, in __getitem__ loc = _lookup_location(self.db.key_filename, name) File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 258, in _lookup_location line = _find_entry(key_filename, word) File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 235, in _find_entry if not line.startswith(wantword): TypeError: expected a character buffer object ---------------------------------------------------------------- See also the related: Bug 1716 - Fasta.Dictionary should throw KeyError for invalid keys Bug 1717 - Fasta.Dictionary should support has_key ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Fri Dec 10 07:00:38 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] BioPython Homepage: Links not easily seen In-Reply-To: <20040915111839.38739.qmail@web52805.mail.yahoo.com> References: <20040915111839.38739.qmail@web52805.mail.yahoo.com> Message-ID: <41B98FE6.6080500@ims.u-tokyo.ac.jp> I agree with Long. I have trouble finding the links myself. So if nobody objects, I'll change the colors of the links to some visible color. Like python-green. --Michiel. Long Li wrote: > Hi, > > It is not easy to see the links when browsing > BioPython homepage. I have to move the mouse to the > text to know if it is a link. Could those links be > underlined like BioPerl homepage or be displayed in > another color? > > Best regards, > Long > > > > _______________________________ > Do you Yahoo!? > Declare Yourself - Register online to vote today! > http://vote.yahoo.com > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- 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 bugzilla-daemon at portal.open-bio.org Fri Dec 10 07:27:07 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412101227.iBACR7bI008187@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #187 is|0 |1 obsolete| | ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-10 07:26 ------- Created an attachment (id=188) --> (http://bugzilla.open-bio.org/attachment.cgi?id=188&action=view) Edited version of NCBIStandalone.py based on CVS revision 1.57 As per attachment 187 with a further refinement to cope with an error condition: If blastall 2.2.10 is given an empty input file (0 bytes) it produces no ouput. However, rpsblast 2.2.10 will produce a single line of output, the version string. This means that while parsing the header we should check for this possible end of file, and issue a helpful error message. This revision has been tested on both Linux, Windows 2000 and Windows XP. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From james.casbon at a4internet.com Sat Dec 11 07:28:23 2004 From: james.casbon at a4internet.com (James Casbon) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> Message-ID: <200412111228.26941.james.casbon@a4internet.com> On Wednesday 08 December 2004 14:36, Jeffrey Chang wrote: > Hi all, > > I've switched the biopython-dev mailing list to subscriber only. > Please let me know if something doesn't look right! > OK, well that's a a step in the right direction, but now comes the hard part: getting more people involved in looking after parts of the project. I suppose a good place to start is finding out how many of the original authors of modules are still maintaining them. A quick and dirty search reveals the list below. So my question is, from the list who is still out there, and who is still interested in maintaining their code? This way we can find the orphaned modules. James Bio $ grep Copyright * */* */*/* | perl -e 'while(<>){/Copyright (.+)/; print "$1\n"}'| sort| uniq (C) 1992-2001 HHMI/Washington University School of Medicine (C) 2002 Michiel Jan Laurens de Hoon. (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be) (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk) (C) 2004. Frederic Sohm. (C) 2004. Frederic Sohm.\n\ (c) 1998-2000 John Aycock (c) 1999, 2000, 2001 Steve Purcell (c) 1999-2000, The University of Chicago 1999 by Jeffrey Chang. All rights reserved. 1999-2000 by Jeffrey Chang. All rights reserved. 2000 by Andrew Dalke. All rights reserved. 2000 by Jeffrey Chang, Brad Chapman. All rights reserved. 2000 by Jeffrey Chang. All rights reserved. 2000 by Katharine Lindner. All rights reserved. 2001 Tarjei Mikkelsen. All rights reserved. 2001 by Gavin E. Crooks. All rights reserved. 2001 by Jeffrey Chang. All rights reserved. 2001 by Katharine Lindner. All rights reserved. 2001 by Katharine Lindner. All rights reserved. 2001 by Tarjei Mikkelsen. All rights reserved. 2001 by Tarjei Mikkelsen. All rights reserved. 2001 by Tarjei Mikkelsen. All rights reserved. 2001 by Tarjei Mikkelsen. All rights reserved. 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark. 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved. 2002 by Jeffrey Chang, Brad Chapman. All rights reserved. 2002 by Jeffrey Chang. All rights reserved. 2002 by Katharine Lindner. All rights reserved. 2002 by Katharine Lindner. All rights reserved. 2002 by Michael Hoffman. All rights reserved. 2002 by Tarjei Mikkelsen. All rights reserved. 2002-2003 by Michael Hoffman. All rights reserved. 2003 Iddo Friedberg. All rights reserved. 2003 by Bartek Wilczynski. All rights reserved. 2003 by Sebastian Bassi. sbassi@genesdigitales.com 2004 by Harry Zuzan. All rights reserved. 2004 by James Casbon. All rights reserved. Iddo Friedberg idoerg@cc.huji.ac.il Yair Benita Y.Benita@pharm.uu.nl notice must be evident to users From biopython-dev at maubp.freeserve.co.uk Sat Dec 11 08:14:44 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Fasta Module [was: To the core developers...] In-Reply-To: <200412111228.26941.james.casbon@a4internet.com> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> <200412111228.26941.james.casbon@a4internet.com> Message-ID: <41BAF2C4.4040602@maubp.freeserve.co.uk> James wrote: > OK, well that's a a step in the right direction, but now comes > the hard part: getting more people involved in looking after > parts of the project. > > I suppose a good place to start is finding out how many of the > original authors of modules are still maintaining them. A quick > and dirty search reveals the list below. So my question is, from > the list who is still out there, and who is still interested in > maintaining their code? This way we can find the orphaned > modules. You may have noticed from the recent stream of emails from the bug tracking system, that I've suggested some improvements to the Bio.Fasta module's FastaDictionary support. This file (Bio/Fasta/__init__.py) does not have a copyright statement at the top. Looking back in the CVS logs, Jeffrey Chang used to do most of the maintenance. However, in 2004, Brad Chapman seems to have done a major overhaul to use the Mindy. I'm guessing either of these two lucky people are the de facto owners of Bio.Fasta and would be best qualified to comment on my suggestions. Basically I want to make the FastaDictionary act more like a Python Dictionary, and not throw weird errors when an invalid key is used. http://bugzilla.open-bio.org/show_bug.cgi?id=1716 Fasta.Dictionary should throw KeyError for invalid keys http://bugzilla.open-bio.org/show_bug.cgi?id=1717 Fasta.Dictionary should support has_key http://bugzilla.open-bio.org/show_bug.cgi?id=1718 Fasta.Dictionary should support "in" (the __contains__ method) [I'm not ready to volunteer myself as the module owner, as I still have no idea what Martel and Mindy do, which would probably be a drawback] Peter -- PhD Student MOAC Doctoral Training Centre University Of Warwick, UK http://www.warwick.ac.uk/go/moac From bugzilla-daemon at portal.open-bio.org Sat Dec 11 08:47:46 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] [Bug 1716] Fasta.Dictionary should throw KeyError for invalid keys Message-ID: <200412111347.iBBDlkph029747@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1716 biopython-bugzilla@maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- OS/Version|Windows 2000 |All ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-11 08:47 ------- Further investigation reveals that the __getitem__ function checks for an invalid key by exception, and in this case attempts to "try and fetch by alias". I'm not sure what that is meant to do, but if this also fails, I think a KeyError should be raised rather than whatever went wrong with the alias fetch. An except from old code in Bio/Fasta/__init.py__ from the class Dictionary: ---------------------------------------------------------------------------- def __getitem__(self, key): # first try to retrieve by the base id try: seqs = self._index.lookup(id = key) # if we can't do that, we have to try and fetch by alias except KeyError: seqs = self._index.lookup(aliases = key) ... ---------------------------------------------------------------------------- My suggested code: ---------------------------------------------------------------------------- def __getitem__(self, key): # first try to retrieve by the base id try: seqs = self._index.lookup(id = key) # if we can't do that, we have to try and fetch by alias except KeyError: try : seqs = self._index.lookup(aliases = key) except : #That failed too. Rather than returning some #cryptic ZeroDivisionError from Mindy, do this: raise KeyError("Key (%s) not found, not even as an alias" % key) ... ---------------------------------------------------------------------------- This would appear to fix my original problem of a miss-leading error message. The actual wording I have suggested could probably be improved... ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Sun Dec 12 03:17:20 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412111228.26941.james.casbon@a4internet.com> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> <200412111228.26941.james.casbon@a4internet.com> Message-ID: <41BBFE90.5030401@ims.u-tokyo.ac.jp> James Casbon wrote: > So my question is, from the list who is still out there, and who is still > interested in maintaining their code? This way we can find the orphaned > modules. > > (C) 2002 Michiel Jan Laurens de Hoon. > .... I'm still around. Maintaining Bio.Cluster and Bio.Statistics, also I did some work on Bio.LogisticRegression. I'd be interested in cleaning up Bio.Seq. I've built the Windows installers for recent Biopython releases, so I'm also interested in maintaining Biopython's portability. --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 idoerg at burnham.org Sun Dec 12 17:17:40 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412111228.26941.james.casbon@a4internet.com> Message-ID: Well, I'm here. FFAS and SubsMat module. Also played around enough with Align to be able to maintain it. ./I -- 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) 646 3171 http://ffas.ljcrf.edu/~iddo On Sat, 11 Dec 2004, James Casbon wrote: > On Wednesday 08 December 2004 14:36, Jeffrey Chang wrote: > > Hi all, > > > > I've switched the biopython-dev mailing list to subscriber only. > > Please let me know if something doesn't look right! > > > OK, well that's a a step in the right direction, but now comes the hard part: > getting more people involved in looking after parts of the project. > > I suppose a good place to start is finding out how many of the original > authors of modules are still maintaining them. A quick and dirty search > reveals the list below. So my question is, from the list who is still out > there, and who is still interested in maintaining their code? This way we > can find the orphaned modules. > > James > > Bio $ grep Copyright * */* */*/* | perl -e 'while(<>){/Copyright (.+)/; print > "$1\n"}'| sort| uniq > (C) 1992-2001 HHMI/Washington University School of Medicine > (C) 2002 Michiel Jan Laurens de Hoon. > (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be) > (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk) > (C) 2004. Frederic Sohm. > (C) 2004. Frederic Sohm.\n\ > (c) 1998-2000 John Aycock > (c) 1999, 2000, 2001 Steve Purcell > (c) 1999-2000, The University of Chicago > 1999 by Jeffrey Chang. All rights reserved. > 1999-2000 by Jeffrey Chang. All rights reserved. > 2000 by Andrew Dalke. All rights reserved. > 2000 by Jeffrey Chang, Brad Chapman. All rights reserved. > 2000 by Jeffrey Chang. All rights reserved. > 2000 by Katharine Lindner. All rights reserved. > 2001 Tarjei Mikkelsen. All rights reserved. > 2001 by Gavin E. Crooks. All rights reserved. > 2001 by Jeffrey Chang. All rights reserved. > 2001 by Katharine Lindner. All rights reserved. > 2001 by Katharine Lindner. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark. > 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved. > 2002 by Jeffrey Chang, Brad Chapman. All rights reserved. > 2002 by Jeffrey Chang. All rights reserved. > 2002 by Katharine Lindner. All rights reserved. > 2002 by Katharine Lindner. All rights reserved. > 2002 by Michael Hoffman. All rights reserved. > 2002 by Tarjei Mikkelsen. All rights reserved. > 2002-2003 by Michael Hoffman. All rights reserved. > 2003 Iddo Friedberg. All rights reserved. > 2003 by Bartek Wilczynski. All rights reserved. > 2003 by Sebastian Bassi. sbassi@genesdigitales.com > 2004 by Harry Zuzan. All rights reserved. > 2004 by James Casbon. All rights reserved. > Iddo Friedberg idoerg@cc.huji.ac.il > Yair Benita Y.Benita@pharm.uu.nl > notice must be evident to users > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > From bartek at rezolwenta.eu.org Sun Dec 12 17:55:31 2004 From: bartek at rezolwenta.eu.org (bartek wilczynski) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: References: Message-ID: <1102892131.41bccc6351fd4@imp.rezolwenta.eu.org> Hi, I'm silent, but nonetheless interested. A do keep an eye on my AlignACE code, I'm also still planning to do something about the Gene Ontology code, but It will have to wait untill I have some spare time. -- cheers Bartek Wilczynski Cytowanie Iddo Friedberg : > > Well, I'm here. FFAS and SubsMat module. Also played around enough with > Align to be able to maintain it. > > ./I > > -- > 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) 646 3171 > http://ffas.ljcrf.edu/~iddo > > On Sat, 11 Dec 2004, James Casbon wrote: > > > On Wednesday 08 December 2004 14:36, Jeffrey Chang wrote: > > > Hi all, > > > > > > I've switched the biopython-dev mailing list to subscriber only. > > > Please let me know if something doesn't look right! > > > > > OK, well that's a a step in the right direction, but now comes the hard > part: > > getting more people involved in looking after parts of the project. > > > > I suppose a good place to start is finding out how many of the original > > authors of modules are still maintaining them. A quick and dirty search > > reveals the list below. So my question is, from the list who is still out > > > there, and who is still interested in maintaining their code? This way we > > > can find the orphaned modules. > > > > James > > > > Bio $ grep Copyright * */* */*/* | perl -e 'while(<>){/Copyright (.+)/; > print > > "$1\n"}'| sort| uniq > > (C) 1992-2001 HHMI/Washington University School of Medicine > > (C) 2002 Michiel Jan Laurens de Hoon. > > (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be) > > (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk) > > (C) 2004. Frederic Sohm. > > (C) 2004. Frederic Sohm.\n\ > > (c) 1998-2000 John Aycock > > (c) 1999, 2000, 2001 Steve Purcell > > (c) 1999-2000, The University of Chicago > > 1999 by Jeffrey Chang. All rights reserved. > > 1999-2000 by Jeffrey Chang. All rights reserved. > > 2000 by Andrew Dalke. All rights reserved. > > 2000 by Jeffrey Chang, Brad Chapman. All rights reserved. > > 2000 by Jeffrey Chang. All rights reserved. > > 2000 by Katharine Lindner. All rights reserved. > > 2001 Tarjei Mikkelsen. All rights reserved. > > 2001 by Gavin E. Crooks. All rights reserved. > > 2001 by Jeffrey Chang. All rights reserved. > > 2001 by Katharine Lindner. All rights reserved. > > 2001 by Katharine Lindner. All rights reserved. > > 2001 by Tarjei Mikkelsen. All rights reserved. > > 2001 by Tarjei Mikkelsen. All rights reserved. > > 2001 by Tarjei Mikkelsen. All rights reserved. > > 2001 by Tarjei Mikkelsen. All rights reserved. > > 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark. > > 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved. > > 2002 by Jeffrey Chang, Brad Chapman. All rights reserved. > > 2002 by Jeffrey Chang. All rights reserved. > > 2002 by Katharine Lindner. All rights reserved. > > 2002 by Katharine Lindner. All rights reserved. > > 2002 by Michael Hoffman. All rights reserved. > > 2002 by Tarjei Mikkelsen. All rights reserved. > > 2002-2003 by Michael Hoffman. All rights reserved. > > 2003 Iddo Friedberg. All rights reserved. > > 2003 by Bartek Wilczynski. All rights reserved. > > 2003 by Sebastian Bassi. sbassi@genesdigitales.com > > 2004 by Harry Zuzan. All rights reserved. > > 2004 by James Casbon. All rights reserved. > > Iddo Friedberg idoerg@cc.huji.ac.il > > Yair Benita Y.Benita@pharm.uu.nl > > notice must be evident to users > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > ------------------------------ > Scanned for viruses by MKS_Vir > Last update: > ------------------------------ > From fkauff at duke.edu Sun Dec 12 20:40:12 2004 From: fkauff at duke.edu (Frank Kauff) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412111228.26941.james.casbon@a4internet.com> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> <200412111228.26941.james.casbon@a4internet.com> Message-ID: <1102902012.2156.2.camel@osiris.biology.duke.edu> Hi all, I'm not on the list but I'm also still alive and eager to take care of Ace and Phd parsers. And, early next year, might be able to add (finally) a nexus parser. Frank On Sat, 2004-12-11 at 07:28, James Casbon wrote: > On Wednesday 08 December 2004 14:36, Jeffrey Chang wrote: > > Hi all, > > > > I've switched the biopython-dev mailing list to subscriber only. > > Please let me know if something doesn't look right! > > > OK, well that's a a step in the right direction, but now comes the hard part: > getting more people involved in looking after parts of the project. > > I suppose a good place to start is finding out how many of the original > authors of modules are still maintaining them. A quick and dirty search > reveals the list below. So my question is, from the list who is still out > there, and who is still interested in maintaining their code? This way we > can find the orphaned modules. > > James > > Bio $ grep Copyright * */* */*/* | perl -e 'while(<>){/Copyright (.+)/; print > "$1\n"}'| sort| uniq > (C) 1992-2001 HHMI/Washington University School of Medicine > (C) 2002 Michiel Jan Laurens de Hoon. > (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be) > (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk) > (C) 2004. Frederic Sohm. > (C) 2004. Frederic Sohm.\n\ > (c) 1998-2000 John Aycock > (c) 1999, 2000, 2001 Steve Purcell > (c) 1999-2000, The University of Chicago > 1999 by Jeffrey Chang. All rights reserved. > 1999-2000 by Jeffrey Chang. All rights reserved. > 2000 by Andrew Dalke. All rights reserved. > 2000 by Jeffrey Chang, Brad Chapman. All rights reserved. > 2000 by Jeffrey Chang. All rights reserved. > 2000 by Katharine Lindner. All rights reserved. > 2001 Tarjei Mikkelsen. All rights reserved. > 2001 by Gavin E. Crooks. All rights reserved. > 2001 by Jeffrey Chang. All rights reserved. > 2001 by Katharine Lindner. All rights reserved. > 2001 by Katharine Lindner. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Tarjei Mikkelsen. All rights reserved. > 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark. > 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved. > 2002 by Jeffrey Chang, Brad Chapman. All rights reserved. > 2002 by Jeffrey Chang. All rights reserved. > 2002 by Katharine Lindner. All rights reserved. > 2002 by Katharine Lindner. All rights reserved. > 2002 by Michael Hoffman. All rights reserved. > 2002 by Tarjei Mikkelsen. All rights reserved. > 2002-2003 by Michael Hoffman. All rights reserved. > 2003 Iddo Friedberg. All rights reserved. > 2003 by Bartek Wilczynski. All rights reserved. > 2003 by Sebastian Bassi. sbassi@genesdigitales.com > 2004 by Harry Zuzan. All rights reserved. > 2004 by James Casbon. All rights reserved. > Iddo Friedberg idoerg@cc.huji.ac.il > Yair Benita Y.Benita@pharm.uu.nl > notice must be evident to users > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- Frank Kauff Dept. of Biology Duke University Box 90338 Durham, NC 27708 USA Phone 919-660-7382 Fax 919-660-7293 Web http://www.lutzonilab.net/member/frankkauff.shtml From f.sohm at whsmithnet.co.uk Mon Dec 13 06:04:32 2004 From: f.sohm at whsmithnet.co.uk (f.sohm@whsmithnet.co.uk) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developpers ... Message-ID: Hi, I have recently moved so I have been a bit absent recently, but I still maintain the Restriction packages. I have no write access to the biopython CVS though, I think a few of the patches that have not been inserted in CVS are actually mine (well all those referring to the Restriction modules at least). Either I will have to be granted a write access to CVS or somebody with write access will have to take over this part for me, whatever is the easiest for you. I can't engage myself to more than maintaining the Restriction package at the moment but I will try to help with bugs whenever I can. Bye Frederic Sohm From hoffman at ebi.ac.uk Mon Dec 13 06:28:16 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <200412111228.26941.james.casbon@a4internet.com> References: <200412061509.31127.j.a.casbon@qmul.ac.uk> <3BE30E2A-484E-11D9-8677-000A956845CE@duke.edu> <8C225DF0-4926-11D9-A806-000A956845CE@stanfordalumni.org> <200412111228.26941.james.casbon@a4internet.com> Message-ID: On Sat, 11 Dec 2004, James Casbon wrote: > OK, well that's a a step in the right direction, but now comes the hard part: > getting more people involved in looking after parts of the project. I'm still here and can maintain Bio.Wise. I'm no longer maintaining Bio.GFF. (I usually use my own GTF module that is not in Biopython instead now). Perhaps it should be deprecated if you are going to deprecate unmaintained modules. -- Michael Hoffman European Bioinformatics Institute From longlill at yahoo.com Mon Dec 13 08:09:30 2004 From: longlill at yahoo.com (Long Li) Date: Sat Mar 5 14:43:55 2005 Subject: [Biopython-dev] Do we need a new page for displaying the module name and its developers/maintainers? Message-ID: <20041213130930.73532.qmail@web52808.mail.yahoo.com> James collected part of maintainers' names, and some maintains has replied to him. I think we had better have a new page under the BioPython homepage to display the module names and their developers/maintainers. It will be convenient for new volunteers who want to be BioPython developers/maintainers. If your guys agree, please reply to this messeage and give some suggestions. Best, Long __________________________________ Do you Yahoo!? Dress up your holiday email, Hollywood style. Learn more. http://celebrity.mail.yahoo.com From biopython-dev at maubp.freeserve.co.uk Mon Dec 13 13:56:02 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Using BLAST et al with multiple queries Message-ID: <41BDE5C2.70508@maubp.freeserve.co.uk> In short: does anyone else use FASTA files containing multiple sequences as input queries to standalone Blast? How do you parse the output? ----------------------------------------------------------------------- I have recently been doing a lot of repeated blast searches on the same database, using a succession of different protein queries. I have been using the standalone blast programs, and suspect that the database is reloaded from the disc each time blast is run. This would explain the rather heavy disc usage. From the NCBI's FAQ, http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.shtml#Batch > Q: How can I search a batch of sequences with BLAST? > > There are three options for "Batch" BLAST searches: > > 1) Web MegaBLAST EST analysis tool... I want to use protein sequences, so this is N/A to me. > 3) BLAST Network Client 'blastcl3' I want to use local databases, so this is N/A to me. > 2) Standalone BLAST executables:The Standalone BLAST executables are > command line programs which run BLAST searches against local > downloaded copies of the NCBI BLAST databases. The programs will > handle either a single large file with multiple FASTA query > sequences, This is what I would like to do, but the current version of Bio/Blast/NCBIStandalone only appears to look at the output for the first query. [In fact, I would argue that silently ignoring the results for the subsequent queries is a bug...] In the case of blastp (and I would therefore expect for blastall in general), the second and subsequent queries are almost the same format, but with the database information omitted from their headers. i.e. First record header has: * Version string * Reference * Query= ... (NNN letters) * Database Subsequent records have: * Version string * Reference * Query= ... (NNN letters) For blastn and tblastn (blastall) these is also the -B option which may complicate things. The rpslast output is similar. First record has header of: * Version string * Query= ... (NNN letters) Subsequent records have just header of: * Query= ... (NNN letters) Incidentally, I have emailed the NCBI about the missing reference and database information, but got an automated reply that the recipient was on holiday until late December. See also Bug 1715 where I have got rpsblast support working in BioPython: http://bugzilla.open-bio.org/show_bug.cgi?id=1715 > or you can create a script to send multiple files one at a time... This is effectively what I have been doing with BioPython at the moment. It works fine, but the speed is rather poor due to all the disc access. Peter -- PhD Student MOAC Doctoral Training Centre University of Warwick From biopython-dev at maubp.freeserve.co.uk Mon Dec 13 15:28:16 2004 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Using BLAST et al with multiple queries In-Reply-To: <41BDE5C2.70508@maubp.freeserve.co.uk> References: <41BDE5C2.70508@maubp.freeserve.co.uk> Message-ID: <41BDFB60.3010507@maubp.freeserve.co.uk> Peter wrote: > In short: does anyone else use FASTA files containing multiple > sequences as input queries to standalone Blast? How do you parse the > output? Ahem. The answer is to use the NCBIStandalone.Iterator, which does appear to work as expected for blastp at least. It doesn't (yet) work for RPS-BLAST output (see previous email), and I am looking at that. I don't know how I missed this this object... its even in the cookbook: 3.1.6 Parsing a file full of BLAST runs Sorry! Peter -- PhD Student MOAC Doctoral Training Centre University of Warwick, UK From bugzilla-daemon at portal.open-bio.org Wed Dec 15 08:24:53 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output Message-ID: <200412151324.iBFDOrar032164@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1715 ------- Additional Comments From biopython-bugzilla@maubp.freeserve.co.uk 2004-12-15 08:24 ------- Created an attachment (id=189) --> (http://bugzilla.open-bio.org/attachment.cgi?id=189&action=view) RPS-BLAST 2.2.10 multi query output file for testing iterator support This is another test file, again using RPS-BLAST 2.2.10 results on the Pfam database, but with MULTIPLE INPUT QUERIES. As can be seen from this sample output, unlike blastall, rpsblast does not repeat the version string at the start of the second and subsequent queries. As a result the NCBIStandalone.Iterator currently fails to spot multiple queries. The "Query= " line must be used instead. The input queries were these three genes from Vibrio cholerae, extracted from NC_002506.gbk, available here: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Vibrio_cholerae/NC_002506.gbk The first entry, gi|15640033, is a small hypothetical protein (44 residues). This gives no hit results. The second query, gi|15600773, is a larger hypothetical protein (658 residues), giving ten poor hits. The third query, also a hypothetical protein (204 letters) gives four poor hits. See also: http://www.biopython.org/pipermail/biopython-dev/2004-December/002841.html http://www.biopython.org/pipermail/biopython-dev/2004-December/002842.html ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mdehoon at ims.u-tokyo.ac.jp Wed Dec 15 20:30:39 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Do we need a new page for displaying the module name and its developers/maintainers? In-Reply-To: <20041213130930.73532.qmail@web52808.mail.yahoo.com> References: <20041213130930.73532.qmail@web52808.mail.yahoo.com> Message-ID: <41C0E53F.3080804@ims.u-tokyo.ac.jp> +1 Long Li wrote: >James collected part of maintainers' names, and some >maintains has replied to him. > >I think we had better have a new page under the >BioPython homepage to display the module names and >their developers/maintainers. It will be convenient >for new volunteers who want to be BioPython >developers/maintainers. If your guys agree, please >reply to this messeage and give some suggestions. > >Best, >Long > > > >__________________________________ >Do you Yahoo!? >Dress up your holiday email, Hollywood style. Learn more. >http://celebrity.mail.yahoo.com >_______________________________________________ >Biopython-dev mailing list >Biopython-dev@biopython.org >http://biopython.org/mailman/listinfo/biopython-dev > > > > From idoerg at burnham.org Wed Dec 15 21:03:10 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Do we need a new page for displaying the module name and its developers/maintainers? In-Reply-To: <41C0E53F.3080804@ims.u-tokyo.ac.jp> References: <20041213130930.73532.qmail@web52808.mail.yahoo.com> <41C0E53F.3080804@ims.u-tokyo.ac.jp> Message-ID: <41C0ECDE.5000105@burnham.org> +2 Michiel Jan Laurens de Hoon wrote: > +1 > > Long Li wrote: > >> James collected part of maintainers' names, and some >> maintains has replied to him. >> >> I think we had better have a new page under the >> BioPython homepage to display the module names and >> their developers/maintainers. It will be convenient >> for new volunteers who want to be BioPython >> developers/maintainers. If your guys agree, please >> reply to this messeage and give some suggestions. >> >> Best, >> Long >> >> >> >> __________________________________ Do you Yahoo!? Dress up your >> holiday email, Hollywood style. Learn more. >> http://celebrity.mail.yahoo.com >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev >> >> >> >> > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- 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 jeffrey.chang at duke.edu Wed Dec 15 22:25:14 2004 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Do we need a new page for displaying the module name and its developers/maintainers? In-Reply-To: <41C0ECDE.5000105@burnham.org> References: <20041213130930.73532.qmail@web52808.mail.yahoo.com> <41C0E53F.3080804@ims.u-tokyo.ac.jp> <41C0ECDE.5000105@burnham.org> Message-ID: <19EF6080-4F12-11D9-B9D9-000A956845CE@duke.edu> Sounds good to me too. Jeff On Dec 15, 2004, at 9:03 PM, Iddo Friedberg wrote: > +2 > > Michiel Jan Laurens de Hoon wrote: > >> +1 >> >> Long Li wrote: >> >>> James collected part of maintainers' names, and some >>> maintains has replied to him. >>> >>> I think we had better have a new page under the >>> BioPython homepage to display the module names and >>> their developers/maintainers. It will be convenient >>> for new volunteers who want to be BioPython >>> developers/maintainers. If your guys agree, please >>> reply to this messeage and give some suggestions. >>> >>> Best, >>> Long >>> >>> >>> >>> __________________________________ Do you Yahoo!? Dress up your >>> holiday email, Hollywood style. Learn more. >>> http://celebrity.mail.yahoo.com >>> _______________________________________________ >>> Biopython-dev mailing list >>> Biopython-dev@biopython.org >>> http://biopython.org/mailman/listinfo/biopython-dev >>> >>> >>> >>> >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev >> >> > > > -- > 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 > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From ajoshi at cse.unsw.edu.au Wed Dec 15 22:57:52 2004 From: ajoshi at cse.unsw.edu.au (Ajinkya Joshi) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Do we need a new page for displaying the module name and its developers/maintainers? In-Reply-To: <19EF6080-4F12-11D9-B9D9-000A956845CE@duke.edu> References: <20041213130930.73532.qmail@web52808.mail.yahoo.com> <41C0E53F.3080804@ims.u-tokyo.ac.jp> <41C0ECDE.5000105@burnham.org> <19EF6080-4F12-11D9-B9D9-000A956845CE@duke.edu> Message-ID: +4 On Wed, 15 Dec 2004, Jeffrey Chang wrote: > Sounds good to me too. > > Jeff > > > On Dec 15, 2004, at 9:03 PM, Iddo Friedberg wrote: > >> +2 >> >> Michiel Jan Laurens de Hoon wrote: >> >>> +1 >>> >>> Long Li wrote: >>> >>>> James collected part of maintainers' names, and some >>>> maintains has replied to him. >>>> >>>> I think we had better have a new page under the >>>> BioPython homepage to display the module names and >>>> their developers/maintainers. It will be convenient >>>> for new volunteers who want to be BioPython >>>> developers/maintainers. If your guys agree, please >>>> reply to this messeage and give some suggestions. >>>> >>>> Best, >>>> Long >>>> >>>> >>>> >>>> __________________________________ Do you Yahoo!? Dress up your holiday >>>> email, Hollywood style. Learn more. http://celebrity.mail.yahoo.com >>>> _______________________________________________ >>>> Biopython-dev mailing list >>>> Biopython-dev@biopython.org >>>> http://biopython.org/mailman/listinfo/biopython-dev >>>> >>>> >>>> >>>> >>> >>> _______________________________________________ >>> Biopython-dev mailing list >>> Biopython-dev@biopython.org >>> http://biopython.org/mailman/listinfo/biopython-dev >>> >>> >> >> >> -- >> 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 >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > Ajinkya Joshi 3rd Year Bioinformatics Engineering Student Mobile Phone: 0417063485 CSE login/email: ajoshi From thomas at cbs.dtu.dk Thu Dec 16 03:11:28 2004 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Do we need a new page for displaying the module name and its developers/maintainers? In-Reply-To: <41C0E53F.3080804@ims.u-tokyo.ac.jp> (Michiel Jan Laurens de Hoon's message of "Thu, 16 Dec 2004 10:30:39 +0900") References: <20041213130930.73532.qmail@web52808.mail.yahoo.com> <41C0E53F.3080804@ims.u-tokyo.ac.jp> Message-ID: Sounds like a good idea to me ... /T Long Li wrote: >James collected part of maintainers' names, and some >maintains has replied to him. > >I think we had better have a new page under the >BioPython homepage to display the module names and >their developers/maintainers. It will be convenient >for new volunteers who want to be BioPython >developers/maintainers. If your guys agree, please >reply to this messeage and give some suggestions. > >Best, >Long -- Sicheritz-Ponten Thomas, Ph.D, thomas@cbs.dtu.dk ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From idoerg at burnham.org Fri Dec 17 12:25:22 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] New (mis)managemanet Message-ID: Hi folks, I guess I'll be taking over some admin duties in Biopython for a while. Some problems have been building up over time, and need to be addressed. Also, a new version rollout can't hurt, once we address the backlogged CVS submissions, and bugzilla entries. Watch this space, Iddo -- 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) 646 3171 http://ffas.ljcrf.edu/~iddo From jonathan.taylor at utoronto.ca Sun Dec 19 17:38:18 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Call to change Biopython website to use fastcgi Message-ID: <1103495898.4527.69.camel@localhost.localdomain> Hi, I am glad to see the project getting back on its feet. I think that making this a members only list is an incredible step in that direction. As long as we are doing baby steps here, I think we should change the quixote (the framework the biopython website is using) driving script to use fastcgi instead of cgi. I just finished another project that uses quixote. Moving from cgi to fastcgi results in an INCREDIBLE increase in responsiveness. I think the current page is a little slow especially when you are browsing documentation. I am willing to give any help necessary to get this done. It should, however, be as easy as installing mod_fastcgi, setting the apache conf to use it on .fcgi files, renaming biopython-website/cgi/biopython.cgi to biopython-website/cgi/biopython.fcgi and changing its last line from app.publish_cgi() to app.publish_fcgi() Cheers. Jon. P.S. Could people in favour (or not) please "vote" on this? From hoffman at ebi.ac.uk Sun Dec 19 19:16:19 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Call to change Biopython website to use fastcgi In-Reply-To: <1103495898.4527.69.camel@localhost.localdomain> References: <1103495898.4527.69.camel@localhost.localdomain> Message-ID: On Sun, 19 Dec 2004, Jonathan Taylor wrote: > P.S. Could people in favour (or not) please "vote" on this? +1 if you're volunteering to give the web site some TLC. After that I don't care what you do ;) -- Michael Hoffman European Bioinformatics Institute From idoerg at burnham.org Sun Dec 19 21:54:47 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Call to change Biopython website to use fastcgi In-Reply-To: <1103495898.4527.69.camel@localhost.localdomain> Message-ID: Yes, please do! :) ./I -- 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) 646 3171 http://ffas.ljcrf.edu/~iddo On Sun, 19 Dec 2004, Jonathan Taylor wrote: > Hi, > > I am glad to see the project getting back on its feet. I think that > making this a members only list is an incredible step in that > direction. As long as we are doing baby steps here, I think we should > change the quixote (the framework the biopython website is using) > driving script to use fastcgi instead of cgi. > > I just finished another project that uses quixote. Moving from cgi to > fastcgi results in an INCREDIBLE increase in responsiveness. I think > the current page is a little slow especially when you are browsing > documentation. > > I am willing to give any help necessary to get this done. It should, > however, be as easy as installing mod_fastcgi, setting the apache conf > to use it on .fcgi files, renaming biopython-website/cgi/biopython.cgi > to biopython-website/cgi/biopython.fcgi and changing its last line > > from > > app.publish_cgi() > > to > > app.publish_fcgi() > > Cheers. > Jon. > > P.S. Could people in favour (or not) please "vote" on this? > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > From jonathan.taylor at utoronto.ca Sun Dec 19 22:35:42 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Call to change Biopython website to use fastcgi In-Reply-To: References: Message-ID: <1103513742.10810.2.camel@localhost.localdomain> We need someone with access to the server to 1 - install mod_fastcgi 2 - update the config file to execute fcgi scripts with mod_fastcgi 3 - change the scriptalias to point to the .fcgi instead The actual code change is just app.publish_fcgi() instead of app.publish_cgi() Who has the access to do this? Jon. On Sun, 2004-12-19 at 21:54, Iddo Friedberg wrote: > Yes, please do! :) > > ./I > > > -- > 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) 646 3171 > http://ffas.ljcrf.edu/~iddo > > On Sun, 19 Dec 2004, Jonathan Taylor wrote: > > > Hi, > > > > I am glad to see the project getting back on its feet. I think that > > making this a members only list is an incredible step in that > > direction. As long as we are doing baby steps here, I think we should > > change the quixote (the framework the biopython website is using) > > driving script to use fastcgi instead of cgi. > > > > I just finished another project that uses quixote. Moving from cgi to > > fastcgi results in an INCREDIBLE increase in responsiveness. I think > > the current page is a little slow especially when you are browsing > > documentation. > > > > I am willing to give any help necessary to get this done. It should, > > however, be as easy as installing mod_fastcgi, setting the apache conf > > to use it on .fcgi files, renaming biopython-website/cgi/biopython.cgi > > to biopython-website/cgi/biopython.fcgi and changing its last line > > > > from > > > > app.publish_cgi() > > > > to > > > > app.publish_fcgi() > > > > Cheers. > > Jon. > > > > P.S. Could people in favour (or not) please "vote" on this? > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > > From bugzilla-daemon at portal.open-bio.org Mon Dec 20 13:19:51 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1667] PUBMED key collision in dbxref table Message-ID: <200412201819.iBKIJpF7014048@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1667 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From idoerg@burnham.org 2004-12-20 13:19 ------- Fixed Loader.py as suggested and committed to CVS ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 20 13:44:17 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1678] NCBIXML error in 1.30 Message-ID: <200412201844.iBKIiH8j014251@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1678 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From idoerg@burnham.org 2004-12-20 13:44 ------- Fixed per bug submitter's recommendation, and committed to CVS Iddo ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 20 13:32:28 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1669] SwissProt Parser error - cannot read recent SwissProt entries Message-ID: <200412201832.iBKIWS8u014167@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1669 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 20 15:01:34 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1678] NCBIXML error in 1.30 Message-ID: <200412202001.iBKK1Ygp015162@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1678 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |CLOSED ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 20 15:00:36 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1706] Problem with the Swiss Prot parser Message-ID: <200412202000.iBKK0aZI015131@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1706 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |WORKSFORME ------- Additional Comments From idoerg@burnham.org 2004-12-20 15:00 ------- CVS version handles this ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 20 15:01:17 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1667] PUBMED key collision in dbxref table Message-ID: <200412202001.iBKK1HNC015153@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1667 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |CLOSED ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Dec 20 14:59:35 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1669] SwissProt Parser error - cannot read recent SwissProt entries Message-ID: <200412201959.iBKJxZNT015107@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1669 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |WORKSFORME ------- Additional Comments From idoerg@burnham.org 2004-12-20 14:59 ------- Works in latest CVS version. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From JBonis at imim.es Mon Dec 13 09:36:45 2004 From: JBonis at imim.es (BONIS SANZ, JULIO) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Memory problems with eutils.efetch_using_dbids ... Message-ID: <66373AD054447F47851FCC5EB49B36110610FD@basquet.imim.es> I have tried the following code (see at the end). It is a function that retrieves information about a given SNP from pubmed. I use: snpInfoFile = eutils.efetch_using_dbids(...) and then: snpInfoFile.readline() and store this in a list (local memory). My problem is that I do it for several SNPs and each time some is stored in the RAM. At the end the system hungs up. Do you know how to free this memory? I have tried to snpInfoFile.close() and del snpInfoFile but seems not to work!!!! Help please!!!!! Regards, Julio Bonis Sanz def getSNPInfo(self,rs): # """ given a rs return the contig and the position in it """ eutils = self.GenBank.EUtils.ThinClient.ThinClient() snpdbi = self.GenBank.DBIds("snp",[str(rs)]) #print "getSNPInfo(" + str(rs) + ")" + ": " + str(len(gc.garbage)) snpInfoFile = eutils.efetch_using_dbids(snpdbi,rettype = 'flt',retmode = 'html') del eutils del snpdbi snpInfoLines = [] while 1: cLine = snpInfoFile.readline() if (cLine == ''): break else: snpInfoLines.append(cLine) snpInfoFile.close() del snpInfoFile print "getSNPInfo(" + str(rs) + ")" + ": " + str(len(gc.garbage)) return snpInfoLines From thomas at genome.cbs.dtu.dk Mon Dec 13 02:54:22 2004 From: thomas at genome.cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] To the core developers... In-Reply-To: <1102892131.41bccc6351fd4@imp.rezolwenta.eu.org> Message-ID: Silent, but still lurking in the background and keeping an occasional eye on my code. cheers -thomas > Hi, > > I'm silent, but nonetheless interested. A do keep an eye on my AlignACE code, > I'm also still planning to do something about the Gene Ontology code, but It > will have to wait untill I have some spare time. > > -- > cheers > Bartek Wilczynski > > > Cytowanie Iddo Friedberg : > > > > > Well, I'm here. FFAS and SubsMat module. Also played around enough with > > Align to be able to maintain it. > > > > ./I > > > > -- > > 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) 646 3171 > > http://ffas.ljcrf.edu/~iddo > > > > On Sat, 11 Dec 2004, James Casbon wrote: > > > > > On Wednesday 08 December 2004 14:36, Jeffrey Chang wrote: > > > > Hi all, > > > > > > > > I've switched the biopython-dev mailing list to subscriber only. > > > > Please let me know if something doesn't look right! > > > > > > > OK, well that's a a step in the right direction, but now comes the hard > > part: > > > getting more people involved in looking after parts of the project. > > > > > > I suppose a good place to start is finding out how many of the original > > > authors of modules are still maintaining them. A quick and dirty search > > > reveals the list below. So my question is, from the list who is still out > > > > > there, and who is still interested in maintaining their code? This way we > > > > > can find the orphaned modules. > > > > > > James > > > > > > Bio $ grep Copyright * */* */*/* | perl -e 'while(<>){/Copyright (.+)/; > > print > > > "$1\n"}'| sort| uniq > > > (C) 1992-2001 HHMI/Washington University School of Medicine > > > (C) 2002 Michiel Jan Laurens de Hoon. > > > (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be) > > > (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk) > > > (C) 2004. Frederic Sohm. > > > (C) 2004. Frederic Sohm.\n\ > > > (c) 1998-2000 John Aycock > > > (c) 1999, 2000, 2001 Steve Purcell > > > (c) 1999-2000, The University of Chicago > > > 1999 by Jeffrey Chang. All rights reserved. > > > 1999-2000 by Jeffrey Chang. All rights reserved. > > > 2000 by Andrew Dalke. All rights reserved. > > > 2000 by Jeffrey Chang, Brad Chapman. All rights reserved. > > > 2000 by Jeffrey Chang. All rights reserved. > > > 2000 by Katharine Lindner. All rights reserved. > > > 2001 Tarjei Mikkelsen. All rights reserved. > > > 2001 by Gavin E. Crooks. All rights reserved. > > > 2001 by Jeffrey Chang. All rights reserved. > > > 2001 by Katharine Lindner. All rights reserved. > > > 2001 by Katharine Lindner. All rights reserved. > > > 2001 by Tarjei Mikkelsen. All rights reserved. > > > 2001 by Tarjei Mikkelsen. All rights reserved. > > > 2001 by Tarjei Mikkelsen. All rights reserved. > > > 2001 by Tarjei Mikkelsen. All rights reserved. > > > 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark. > > > 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved. > > > 2002 by Jeffrey Chang, Brad Chapman. All rights reserved. > > > 2002 by Jeffrey Chang. All rights reserved. > > > 2002 by Katharine Lindner. All rights reserved. > > > 2002 by Katharine Lindner. All rights reserved. > > > 2002 by Michael Hoffman. All rights reserved. > > > 2002 by Tarjei Mikkelsen. All rights reserved. > > > 2002-2003 by Michael Hoffman. All rights reserved. > > > 2003 Iddo Friedberg. All rights reserved. > > > 2003 by Bartek Wilczynski. All rights reserved. > > > 2003 by Sebastian Bassi. sbassi@genesdigitales.com > > > 2004 by Harry Zuzan. All rights reserved. > > > 2004 by James Casbon. All rights reserved. > > > Iddo Friedberg idoerg@cc.huji.ac.il > > > Yair Benita Y.Benita@pharm.uu.nl > > > notice must be evident to users > > > _______________________________________________ > > > Biopython-dev mailing list > > > Biopython-dev@biopython.org > > > http://biopython.org/mailman/listinfo/biopython-dev > > > > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > > > ------------------------------ > > Scanned for viruses by MKS_Vir > > Last update: > > ------------------------------ > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > Sicheritz-Ponten Thomas, Ph.D, thomas@cbs.dtu.dk ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From bugzilla-daemon at portal.open-bio.org Mon Dec 20 17:51:33 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1680] Problems with the GenBank indexing Message-ID: <200412202251.iBKMpXCD017140@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1680 ------- Additional Comments From jchang@biopython.org 2004-12-20 17:51 ------- This is because the Martel/Mindy iterator does not recognize spaces between the records in the file. If you remove the spaces from the file, the code will index the file without complaint. Where did you get this record? Did you get it directly from NCBI, or did you create or edit it yourself? One fix might be to modify the system to ignore whitespaces between records. But that may cause problems if the system were applied to a format where the number of blank lines were important. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From dalke at dalkescientific.com Tue Dec 21 01:38:29 2004 From: dalke at dalkescientific.com (Andrew Dalke) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Memory problems with eutils.efetch_using_dbids ... In-Reply-To: <66373AD054447F47851FCC5EB49B36110610FD@basquet.imim.es> References: <66373AD054447F47851FCC5EB49B36110610FD@basquet.imim.es> Message-ID: BONIS SANZ, JULIO wrote: > I have tried the following code (see at the end). > My problem is that I do it for several SNPs and each time some > is stored in > the RAM. At the end the system hungs up. > > Do you know how to free this memory? I can't think of anything in what you do that would cause EUtils to accumulate memory. If you always get the OpenerDirector at the same memory location then that means there's no memory leak at all because that means it's always using the same memory. All the efetch_using_dbids function does is create the properly formated URL and pass the right data to NCBI. What it returns is the open network connection as a file handle. Nothing more is stored in the EUtils package. How many snpInfoLines are you reading? Does the network pause as you reading it? How does the system hang up? Could you enable debugging by setting ThinClient.DUMP_URL = 1 ThinClient.DUMP_RESULT = 1 ? The first shows the URL/POST data sent to NCBI and the second shows all of the data returned from the server. Andrew dalke@dalkescientific.com