From biopython-bugs at bioperl.org Sun Dec 1 13:14:37 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/107 Message-ID: <200212011814.gB1IEb6J001944@pw600a.bioperl.org> JitterBug notification new message incoming/107 Message summary for PR#107 From: senthilcoumar@hotmail.com Subject: BLAST parser fails... Date: Sun, 1 Dec 2002 13:14:36 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From senthilcoumar@hotmail.com Sun Dec 1 13:14:36 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gB1IEa6J001939 for ; Sun, 1 Dec 2002 13:14:36 -0500 Date: Sun, 1 Dec 2002 13:14:36 -0500 Message-Id: <200212011814.gB1IEa6J001939@pw600a.bioperl.org> From: senthilcoumar@hotmail.com To: biopython-bugs@bioperl.org Subject: BLAST parser fails... Full_Name: senthil Module: Version: OS: win98 Submission from: 12-249-77-218.client.attbi.com (12.249.77.218) looks like the blast result format has been changed by NCBI. the blast parser fails. can you please fix the problem, or have any suggestions so that i can fix it myself ? thanks, -senthil. From Yves.Bastide at irisa.fr Mon Dec 2 05:09:11 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] [patch] NCBIWWW parser Message-ID: <3DEB3147.3060503@irisa.fr> Hi, here's some patching and a testcase for the NCBI parser, if not already corrected; could people try it? Thanks, yves -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biopython-dev/attachments/20021202/4dd9489c/b.htm From thamelry at vub.ac.be Mon Dec 2 05:53:05 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <20021122075202.GD11726@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> <200211210813.gAL8D2010716@durendal.skynet.be> <20021122075202.GD11726@springfield.stanford.edu> Message-ID: <200212021047.gB2AlO020458@durendal.skynet.be> On Friday 22 November 2002 08:52 am, Jeffrey Chang wrote: > Hey Thomas, > > I'm getting an error when trying to link the KDTree module (attached). > This is on Solaris 2.6, gcc 2.95.3, and python 2.2. Do you know where > these errors are coming from? It's most likely an error with > distutil's compiling options, but we need a workaround. I think I found the reason and a solution for this problem (take a look at http://mail.python.org/pipermail/python-bugs-list/2001-July/005951.html): If you have CC set to "gcc", then the "setup.py" script compiles the extensions incorrectly (in particular, the "-fPIC" on the compile is not used). If you don't have "CC=gcc" set in your environment, then things work fine I don't have access to Solaris so somebody will have to check this.... Cheers, -Thomas From DJaeggi at imim.es Mon Dec 2 09:54:14 2002 From: DJaeggi at imim.es (Jaeggi, Daniel M.) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Gentoo Linux port Message-ID: <3DEB7416.7040102@imim.es> Hi Is anyone else out there using Gentoo Linux? If so, have you written an ebuild (port) for it? If not, I'll probably be writing one in the next couple of days. Thanks, Dan From gontran at gontran.net Mon Dec 2 14:04:07 2002 From: gontran at gontran.net (Gontran Zepeda) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Gentoo Linux port In-Reply-To: <3DEB7416.7040102@imim.es> References: <3DEB7416.7040102@imim.es> Message-ID: <20021202190407.GC10575@rythm.gontran.net> # Jaeggi, Daniel M. (DJaeggi@imim.es), # on 2002-12-02 at 15:54:14 +0100 wrote: > Is anyone else out there using Gentoo Linux? If so, have you written an > ebuild (port) for it? If not, I'll probably be writing one in the next > couple of days. I'm just finishing a couple for bioperl and bioperl-cvs and dependencies that I'll be submitting today, with the understanding of the dev-perl/ maintainer. If you'd like copies of what I've got let me know -- not that it's _a lot_ of help, but there you go. I'd like to see biopython in portage too. Gontran From jchang at smi.stanford.edu Mon Dec 2 15:11:33 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Gentoo Linux port In-Reply-To: <3DEB7416.7040102@imim.es> References: <3DEB7416.7040102@imim.es> Message-ID: <20021202201133.GC46025@springfield.stanford.edu> On Mon, Dec 02, 2002 at 03:54:14PM +0100, Jaeggi, Daniel M. wrote: > Is anyone else out there using Gentoo Linux? If so, have you written an > ebuild (port) for it? If not, I'll probably be writing one in the next > couple of days. Great! Let us know when it is finished. Also, be aware that we are working on putting out a new release of Biopython. The build process won't change much, though. Jeff From jchang at smi.stanford.edu Mon Dec 2 16:06:04 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] [patch] NCBIWWW parser In-Reply-To: <3DEB3147.3060503@irisa.fr> References: <3DEB3147.3060503@irisa.fr> Message-ID: <20021202210604.GF46025@springfield.stanford.edu> Good patch! I've committed it. Thanks. Jeff On Mon, Dec 02, 2002 at 11:09:11AM +0100, Yves Bastide wrote: > Hi, > > here's some patching and a testcase for the NCBI parser, if not already > corrected; could people try it? > > Thanks, > > yves From jchang at SMI.Stanford.EDU Mon Dec 2 16:09:05 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <200212021047.gB2AlO020458@durendal.skynet.be> References: <20021121043244.GA7777@springfield.stanford.edu> <200211210813.gAL8D2010716@durendal.skynet.be> <20021122075202.GD11726@springfield.stanford.edu> <200212021047.gB2AlO020458@durendal.skynet.be> Message-ID: <20021202210905.GG46025@springfield.stanford.edu> Hi Thomas, Thanks for the workaround. Unfortunately, it still doesn't compile on Solaris. My CC environment variable isn't set, and distutils is compiling with the -fPIC option (output is attached). Any other ideas? Jeff On Mon, Dec 02, 2002 at 11:53:05AM +0100, Thomas Hamelryck wrote: > On Friday 22 November 2002 08:52 am, Jeffrey Chang wrote: > > Hey Thomas, > > > > I'm getting an error when trying to link the KDTree module (attached). > > This is on Solaris 2.6, gcc 2.95.3, and python 2.2. Do you know where > > these errors are coming from? It's most likely an error with > > distutil's compiling options, but we need a workaround. > > I think I found the reason and a solution for this problem (take a look at > http://mail.python.org/pipermail/python-bugs-list/2001-July/005951.html): > > If you have CC set to "gcc", then the "setup.py" script > compiles the extensions incorrectly (in particular, the "-fPIC" > on the compile is not used). > > If you don't have "CC=gcc" set in your environment, then things work fine > > I don't have access to Solaris so somebody will have to check this.... > > Cheers, > > -Thomas > > -------------- next part -------------- A non-text attachment was scrubbed... Name: build.out.gz Type: application/x-gunzip Size: 11858 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20021202/bf21c928/build.out.bin From jchang at SMI.Stanford.EDU Mon Dec 2 23:36:43 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do In-Reply-To: <20021121043244.GA7777@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> Message-ID: <20021203043643.GA47748@springfield.stanford.edu> Hello everybody, Thanks for everybody who has been helping getting Biopython ready for another release! Here's a check-list of stuff we still have left to do, along with names of who is signed up to do it. Please send a quick progress update on the status of the task, or at least an email saying it's not getting done. Thanks, Jeff Biopython Release To-Do ======================= - dalke BUGZILLA: BerkeleyDB.py Problem? - katel BUGZILLA: Tests/MetaTool/Meta9.out conflicts with meta9.out - katel BUGZILLA: potential conflict between Bio/Rebase/Rebase.py and Bio/Rebase/__init__.py - katel test_locuslink regression test fails - gec BUGZILLA: Bio/SCOP/tests should be integrated with rest of regression tests - chapmanb make sure tutorial is still current - chapmanb make sure example scripts still work - jchang update the NEWS file - chapmanb DocSQL regression test fails - grouse test_GFF regression test fails - grouse test_easy regression test fails - grouse move easy.py and GenericTools.py out of Bio namespace From grouse at mail.utexas.edu Tue Dec 3 14:53:29 2002 From: grouse at mail.utexas.edu (Michael Hoffman) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: Biopython release To-Do In-Reply-To: <20021203043643.GA47748@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> <20021203043643.GA47748@springfield.stanford.edu> Message-ID: On Mon, 2 Dec 2002, Jeffrey Chang wrote: > - chapmanb DocSQL regression test fails Mine. Fixed. There is still a failure in the distinct BioSQL regression test for me because I do not have psycopg installed. This is not listed as a dependency in the README. > - grouse test_GFF regression test fails > - grouse test_easy regression test fails > - grouse move easy.py and GenericTools.py out of Bio namespace Fixed, fixed, and fixed. Of course, these require having MySQLdb installed (not in the README either--should I update it?). -- Michael Hoffman The University of Texas at Austin From jchang at smi.stanford.edu Tue Dec 3 15:47:18 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: Biopython release To-Do In-Reply-To: References: <20021121043244.GA7777@springfield.stanford.edu> <20021203043643.GA47748@springfield.stanford.edu> Message-ID: <20021203204718.GA50310@springfield.stanford.edu> On Tue, Dec 03, 2002 at 01:53:29PM -0600, Michael Hoffman wrote: > On Mon, 2 Dec 2002, Jeffrey Chang wrote: > > > - chapmanb DocSQL regression test fails > > Mine. Fixed. > > There is still a failure in the distinct BioSQL regression test for me > because I do not have psycopg installed. This is not listed as a > dependency in the README. > > > - grouse test_GFF regression test fails > > - grouse test_easy regression test fails > > - grouse move easy.py and GenericTools.py out of Bio namespace > > Fixed, fixed, and fixed. Of course, these require having MySQLdb > installed (not in the README either--should I update it?). Awesome! Yep, update away. Jeff From grouse at mail.utexas.edu Tue Dec 3 16:13:19 2002 From: grouse at mail.utexas.edu (Michael Hoffman) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: Biopython release To-Do In-Reply-To: <20021203204718.GA50310@springfield.stanford.edu> Message-ID: On Tue, 3 Dec 2002, Jeffrey Chang wrote: > On Tue, Dec 03, 2002 at 01:53:29PM -0600, Michael Hoffman wrote: > > > [Bio.GFF requires] having MySQLdb installed (not in the README > > either--should I update it?). > > Awesome! Yep, update away. I also updated it for psycopg. $ cvs diff -u -r 1.37 -r 1.38 README Index: README =================================================================== RCS file: /home/repository/biopython/biopython/README,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- README 2002/12/03 04:12:55 1.37 +++ README 2002/12/03 20:58:06 1.38 @@ -42,7 +42,11 @@ of chromosomes. If you do not need this functoinality, you will not need to install this package. +o psycopg:http://initd.org/software/psycopg/ (optional) + This package is only used by BioSQL to access a PostgreSQL database. +o MySQLdb:http://sourceforge.net/projects/mysql-python (optional) + This package is only used by Bio.GFF to access a MySQL database. These version numbers indicate the earliest tested versions. Later versions of these packages may work as well. =================================================================== Please let me know if there are further problems. -- Michael Hoffman The University of Texas at Austin From katel at worldpath.net Tue Dec 3 17:38:23 2002 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do Message-ID: <54360-220021223223823780@M2W032.mail2web.com> I just downloaded a new Ssh from sourceforge and connected to dev.open-bio.org. I see the file I want to check in but when I run a cvs command the OS says cvs: not found. Cayte Hello everybody, Thanks for everybody who has been helping getting Biopython ready for another release! Here's a check-list of stuff we still have left to do, along with names of who is signed up to do it. Please send a quick progress update on the status of the task, or at least an email saying it's not getting done. Thanks, Jeff . -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From jchang at SMI.Stanford.EDU Wed Dec 4 01:35:25 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do In-Reply-To: <54360-220021223223823780@M2W032.mail2web.com> References: <54360-220021223223823780@M2W032.mail2web.com> Message-ID: <20021204063525.GA52633@springfield.stanford.edu> Did you get a new copy of the CVS repository? Try using the instructions at: http://bio.perl.org/UserInfo/CVShelp.shtml substitute "biopython" for "bioperl", and "dev.open-bio.org" for "bio.perl.org". Is "cvs: not found" exactly the error message you are getting? Also, what cvs commands cause it? Does "cvs update" do it? Jeff On Tue, Dec 03, 2002 at 05:38:23PM -0500, katel@worldpath.net wrote: > > > I just downloaded a new Ssh from sourceforge and connected to > dev.open-bio.org. I see the file I want to check in but when I run a cvs > command the OS says cvs: not found. > > Cayte > Hello everybody, > > Thanks for everybody who has been helping getting Biopython ready for > another release! Here's a check-list of stuff we still have left to > do, along with names of who is signed up to do it. Please send a > quick progress update on the status of the task, or at least an email > saying it's not getting done. > > Thanks, > Jeff > > > . > > -------------------------------------------------------------------- > mail2web - Check your email from the web at > http://mail2web.com/ . > From jchang at SMI.Stanford.EDU Wed Dec 4 01:58:37 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Fwd: User Groups Can Win a Pass to an O'Reilly Conference Message-ID: <20021204065837.GE52633@springfield.stanford.edu> Anybody interested in doing this? Jeff ----- Forwarded message from Marsee Henon ----- From: Marsee Henon To: jchang@SMI.Stanford.EDU Date: Tue, 3 Dec 2002 17:35:18 -0800 (PST) Subject: User Groups Can Win a Pass to an O'Reilly Conference Enter your group to win one pass to: The O'Reilly Bioinformatics Technology Conference Westin Horton Plaza February 3-6, 2003--San Diego, CA http://conferences.oreilly.com/biocon The lucky winning group will be given a "conference sessions only" pass to attend the conference, valued at $1175.00. O'Reilly assumes that if your group is the lucky winner, as the user group representative, you will distribute the winning pass to a group member, using a method appropriate for your group (drawing, raffle, etc.) The winning pass* includes: -Access to all conference sessions February 4, 5, 6 including keynotes* -Admission to Exhibit Hall -Admission to all on-site evening events -All conference handouts (excluding tutorial materials) *Pass does not include tutorial fees, lodging, food, and transportation. Please email your entry to Marsee Henon at marsee@oreilly.com. Deadline for entries is December 12, 2002. In the subject line of your email, please say "Raffle Entry." The winning group leader will be contacted on December 13, 2002 by email--unless a phone call is requested (phone number must be provided). Only one attendee per pass will be allowed. Two people cannot share the same pass to attend the conference on separate days. 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Now for the Rules and Regulations--I apologize for the length, they're really quite simple: ***These rules constitute the official rules of this raffle. By participating in the raffle, entrants agree to be bound by the official rules and the decision of the judges, which are final and binding in all respects.*** 1. Entry: No purchase is necessary to enter the raffle. To enter the raffle, Please email Marsee Henon at marsee@oreilly.com and tell her to enter your group for the raffle. Entries must be received at O'Reilly & Associates by December 12, 2002. Limit one entry per group, per email address. O'Reilly & Associates and its agents are not responsible for lost, late, misdirected, incomplete, illegible or damaged email that results from any source. By entering, entrant agrees to abide by and be bound by the Official Rules. O'Reilly & Associates reserves the right to cancel the raffle if it becomes technically corrupted. 2. Eligibility: The O'Reilly Raffle is open to all who are 18 years of age or older, and reside in the U.S. or Canada, except employees of O'Reilly & Associates. Anyone else directly involved in this raffle is ineligible to participate. Raffle void where prohibited by law. All federal, state, and local laws apply. 3. Selection and Notification: The winners will be chosen at random from all eligible entries submitted by December 12, 2002. O'Reilly will notify winners by email or phone. A prize not claimed by January 27 will not be awarded. The odds of winning depend on the number of eligible entries received. 4. Other Rules: a) The prize is nontransferable and non-endorsable; no cash or other substitutions will be offered. 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All decisions by O'Reilly & Associates are final. c) By participating in this raffle, entrants agree to release and hold O'Reilly & Associates (and their employees, agents, representatives, or affiliated companies) harmless from any and all losses, damages, rights, claims, and actions of any kind in connection with the prize, including, without limitation, personal injuries, death or property damage, and claims based on publicity rights, defamation, or invasion of privacy. d) Entrant also agrees that in no event shall O'Reilly & Associates or its agents be liable to entrant or any other person for any damage, injuries or losses arising out of the introduction of any virus, bug or software malfunction resulting from participation in this raffle, or for any damage, injuries or losses arising in connection with the prize. e) O'Reilly & Associates reserves the right to modify the rules of the raffle in any way or at any time, as long as reasonable notice is given. f) To receive the name of the winner, or a copy of the Official Rules, send a self-addressed, stamped envelope to: O'Reilly Bioinformatics Technology Conference UG Raffle, c/o O'Reilly & Associates, 1005 GravensteinHighway North, Sebastopol, CA 95472, Attn: Marsee Henon, Post-marked prior to the close of the raffle (December 12, 2002). ----- End forwarded message ----- From DJaeggi at imim.es Thu Dec 5 06:17:40 2002 From: DJaeggi at imim.es (Jaeggi, Daniel M.) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Gentoo Linux port - disabling Tk test display References: <3DEB7416.7040102@imim.es> <20021202201133.GC46025@springfield.stanford.edu> Message-ID: <3DEF35D4.1010900@imim.es> Is there an easy way to disable the Tk test result display when running "python setup.py test"? Although my system has Tk, I just want to get the raw command line output. Thanks Dan Jeffrey Chang wrote: >On Mon, Dec 02, 2002 at 03:54:14PM +0100, Jaeggi, Daniel M. wrote: > > >>Is anyone else out there using Gentoo Linux? If so, have you written an >>ebuild (port) for it? If not, I'll probably be writing one in the next >>couple of days. >> >> > >Great! Let us know when it is finished. > >Also, be aware that we are working on putting out a new release of >Biopython. The build process won't change much, though. > >Jeff > > From clemens at came.sbg.ac.at Thu Dec 5 07:07:11 2002 From: clemens at came.sbg.ac.at (Clemens Zuzan) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] bug-request Message-ID: <02112816111701.23290@rita> Dear Coleagues! Trying to apply the PDB-Biopython-module with all PDB structures alvailable to me, I recognized that the job will sometimes be killed while processing a file, especially when processing large PDB files. The cause seems to be a lack of memory. Seemingly the problem files are read several times (-due to an error within the header reading routine?--> I came upon this, because the program is printing the same discontinuations several times to the screen.) Here is an example output for (pdb file) "1htq"> WARNING: Chain A is discontinuous at line 96431. WARNING: Chain B is discontinuous at line 96432. WARNING: Chain C is discontinuous at line 96433. WARNING: Chain D is discontinuous at line 96434. WARNING: Chain E is discontinuous at line 96435. WARNING: Chain F is discontinuous at line 96436. WARNING: Chain G is discontinuous at line 96437. WARNING: Chain H is discontinuous at line 96438. WARNING: Chain I is discontinuous at line 96439. WARNING: Chain J is discontinuous at line 96440. WARNING: Chain K is discontinuous at line 96441. WARNING: Chain L is discontinuous at line 96442. WARNING: Chain M is discontinuous at line 96443. WARNING: Chain N is discontinuous at line 96444. WARNING: Chain O is discontinuous at line 96445. WARNING: Chain P is discontinuous at line 96446. WARNING: Chain Q is discontinuous at line 96447. WARNING: Chain R is discontinuous at line 96448. WARNING: Chain S is discontinuous at line 96449. WARNING: Chain T is discontinuous at line 96450. WARNING: Chain U is discontinuous at line 96451. WARNING: Chain V is discontinuous at line 96452. WARNING: Chain W is discontinuous at line 96453. WARNING: Chain X is discontinuous at line 96454. WARNING: Chain A is discontinuous at line 194329. WARNING: Chain B is discontinuous at line 194330. WARNING: Chain C is discontinuous at line 194331. WARNING: Chain D is discontinuous at line 194332. WARNING: Chain E is discontinuous at line 194333. WARNING: Chain F is discontinuous at line 194334. WARNING: Chain G is discontinuous at line 194335. WARNING: Chain H is discontinuous at line 194336. WARNING: Chain I is discontinuous at line 194337. WARNING: Chain J is discontinuous at line 194338. WARNING: Chain K is discontinuous at line 194339. WARNING: Chain L is discontinuous at line 194340. WARNING: Chain M is discontinuous at line 194341. WARNING: Chain N is discontinuous at line 194342. WARNING: Chain O is discontinuous at line 194343. WARNING: Chain P is discontinuous at line 194344. WARNING: Chain Q is discontinuous at line 194345. WARNING: Chain R is discontinuous at line 194346. WARNING: Chain S is discontinuous at line 194347. WARNING: Chain T is discontinuous at line 194348. WARNING: Chain U is discontinuous at line 194349. WARNING: Chain V is discontinuous at line 194350. WARNING: Chain W is discontinuous at line 194351. WARNING: Chain X is discontinuous at line 194352. WARNING: Chain A is discontinuous at line 292227. WARNING: Chain B is discontinuous at line 292228. WARNING: Chain C is discontinuous at line 292229. WARNING: Chain D is discontinuous at line 292230. WARNING: Chain E is discontinuous at line 292231. WARNING: Chain F is discontinuous at line 292232. WARNING: Chain G is discontinuous at line 292233. WARNING: Chain H is discontinuous at line 292234. WARNING: Chain I is discontinuous at line 292235. WARNING: Chain J is discontinuous at line 292236. WARNING: Chain K is discontinuous at line 292237. WARNING: Chain L is discontinuous at line 292238. WARNING: Chain M is discontinuous at line 292239. WARNING: Chain N is discontinuous at line 292240. WARNING: Chain O is discontinuous at line 292241. WARNING: Chain P is discontinuous at line 292242. WARNING: Chain Q is discontinuous at line 292243. WARNING: Chain R is discontinuous at line 292244. WARNING: Chain S is discontinuous at line 292245. WARNING: Chain T is discontinuous at line 292246. WARNING: Chain U is discontinuous at line 292247. WARNING: Chain V is discontinuous at line 292248. WARNING: Chain W is discontinuous at line 292249. WARNING: Chain X is discontinuous at line 292250. WARNING: Chain A is discontinuous at line 390125. WARNING: Chain B is discontinuous at line 390126. WARNING: Chain C is discontinuous at line 390127. WARNING: Chain D is discontinuous at line 390128. WARNING: Chain E is discontinuous at line 390129. WARNING: Chain F is discontinuous at line 390130. WARNING: Chain G is discontinuous at line 390131. WARNING: Chain H is discontinuous at line 390132. WARNING: Chain I is discontinuous at line 390133. WARNING: Chain J is discontinuous at line 390134. WARNING: Chain K is discontinuous at line 390135. WARNING: Chain L is discontinuous at line 390136. WARNING: Chain M is discontinuous at line 390137. WARNING: Chain N is discontinuous at line 390138. WARNING: Chain O is discontinuous at line 390139. WARNING: Chain P is discontinuous at line 390140. WARNING: Chain Q is discontinuous at line 390141. WARNING: Chain R is discontinuous at line 390142. WARNING: Chain S is discontinuous at line 390143. WARNING: Chain T is discontinuous at line 390144. WARNING: Chain U is discontinuous at line 390145. WARNING: Chain V is discontinuous at line 390146. WARNING: Chain W is discontinuous at line 390147. WARNING: Chain X is discontinuous at line 390148. WARNING: Chain A is discontinuous at line 488023. WARNING: Chain B is discontinuous at line 488024. WARNING: Chain C is discontinuous at line 488025. WARNING: Chain D is discontinuous at line 488026. WARNING: Chain E is discontinuous at line 488027. WARNING: Chain F is discontinuous at line 488028. WARNING: Chain G is discontinuous at line 488029. WARNING: Chain H is discontinuous at line 488030. WARNING: Chain I is discontinuous at line 488031. WARNING: Chain J is discontinuous at line 488032. WARNING: Chain K is discontinuous at line 488033. WARNING: Chain L is discontinuous at line 488034. WARNING: Chain M is discontinuous at line 488035. WARNING: Chain N is discontinuous at line 488036. WARNING: Chain O is discontinuous at line 488037. WARNING: Chain P is discontinuous at line 488038. WARNING: Chain Q is discontinuous at line 488039. WARNING: Chain R is discontinuous at line 488040. WARNING: Chain S is discontinuous at line 488041. WARNING: Chain T is discontinuous at line 488042. WARNING: Chain U is discontinuous at line 488043. WARNING: Chain V is discontinuous at line 488044. WARNING: Chain W is discontinuous at line 488045. WARNING: Chain X is discontinuous at line 488046. WARNING: Chain A is discontinuous at line 585921. WARNING: Chain B is discontinuous at line 585922. WARNING: Chain C is discontinuous at line 585923. WARNING: Chain D is discontinuous at line 585924. WARNING: Chain E is discontinuous at line 585925. WARNING: Chain F is discontinuous at line 585926. WARNING: Chain G is discontinuous at line 585927. WARNING: Chain H is discontinuous at line 585928. WARNING: Chain I is discontinuous at line 585929. WARNING: Chain J is discontinuous at line 585930. WARNING: Chain K is discontinuous at line 585931. WARNING: Chain L is discontinuous at line 585932. WARNING: Chain M is discontinuous at line 585933. WARNING: Chain N is discontinuous at line 585934. WARNING: Chain O is discontinuous at line 585935. WARNING: Chain P is discontinuous at line 585936. WARNING: Chain Q is discontinuous at line 585937. WARNING: Chain R is discontinuous at line 585938. WARNING: Chain S is discontinuous at line 585939. WARNING: Chain T is discontinuous at line 585940. WARNING: Chain U is discontinuous at line 585941. WARNING: Chain V is discontinuous at line 585942. WARNING: Chain W is discontinuous at line 585943. WARNING: Chain X is discontinuous at line 585944. WARNING: Chain A is discontinuous at line 683819. WARNING: Chain B is discontinuous at line 683820. WARNING: Chain C is discontinuous at line 683821. WARNING: Chain D is discontinuous at line 683822. WARNING: Chain E is discontinuous at line 683823. WARNING: Chain F is discontinuous at line 683824. WARNING: Chain G is discontinuous at line 683825. WARNING: Chain H is discontinuous at line 683826. WARNING: Chain I is discontinuous at line 683827. WARNING: Chain J is discontinuous at line 683828. WARNING: Chain K is discontinuous at line 683829. WARNING: Chain L is discontinuous at line 683830. WARNING: Chain M is discontinuous at line 683831. WARNING: Chain N is discontinuous at line 683832. WARNING: Chain O is discontinuous at line 683833. WARNING: Chain P is discontinuous at line 683834. WARNING: Chain Q is discontinuous at line 683835. WARNING: Chain R is discontinuous at line 683836. WARNING: Chain S is discontinuous at line 683837. WARNING: Chain T is discontinuous at line 683838. WARNING: Chain U is discontinuous at line 683839. WARNING: Chain V is discontinuous at line 683840. WARNING: Chain W is discontinuous at line 683841. WARNING: Chain X is discontinuous at line 683842. WARNING: Chain A is discontinuous at line 781717. WARNING: Chain B is discontinuous at line 781718. WARNING: Chain C is discontinuous at line 781719. WARNING: Chain D is discontinuous at line 781720. WARNING: Chain E is discontinuous at line 781721. WARNING: Chain F is discontinuous at line 781722. WARNING: Chain G is discontinuous at line 781723. WARNING: Chain H is discontinuous at line 781724. WARNING: Chain I is discontinuous at line 781725. WARNING: Chain J is discontinuous at line 781726. WARNING: Chain K is discontinuous at line 781727. WARNING: Chain L is discontinuous at line 781728. WARNING: Chain M is discontinuous at line 781729. WARNING: Chain N is discontinuous at line 781730. WARNING: Chain O is discontinuous at line 781731. WARNING: Chain P is discontinuous at line 781732. WARNING: Chain Q is discontinuous at line 781733. WARNING: Chain R is discontinuous at line 781734. WARNING: Chain S is discontinuous at line 781735. WARNING: Chain T is discontinuous at line 781736. WARNING: Chain U is discontinuous at line 781737. WARNING: Chain V is discontinuous at line 781738. WARNING: Chain W is discontinuous at line 781739. WARNING: Chain X is discontinuous at line 781740. WARNING: Chain A is discontinuous at line 879615. WARNING: Chain B is discontinuous at line 879616. WARNING: Chain C is discontinuous at line 879617. WARNING: Chain D is discontinuous at line 879618. WARNING: Chain E is discontinuous at line 879619. WARNING: Chain F is discontinuous at line 879620. WARNING: Chain G is discontinuous at line 879621. WARNING: Chain H is discontinuous at line 879622. WARNING: Chain I is discontinuous at line 879623. WARNING: Chain J is discontinuous at line 879624. WARNING: Chain K is discontinuous at line 879625. WARNING: Chain L is discontinuous at line 879626. WARNING: Chain M is discontinuous at line 879627. WARNING: Chain N is discontinuous at line 879628. WARNING: Chain O is discontinuous at line 879629. WARNING: Chain P is discontinuous at line 879630. WARNING: Chain Q is discontinuous at line 879631. WARNING: Chain R is discontinuous at line 879632. WARNING: Chain S is discontinuous at line 879633. WARNING: Chain T is discontinuous at line 879634. WARNING: Chain U is discontinuous at line 879635. WARNING: Chain V is discontinuous at line 879636. WARNING: Chain W is discontinuous at line 879637. WARNING: Chain X is discontinuous at line 879638. Killed ----------------------------------------------------------------------------------------- The code for checking out what I experienced should be (I give you a python file here) > #!usr/bin/python2.0 import os, sys, string sys.path.append('/home/people/clemens/BIOPYTHON/BIO/PDB/') import PDBParser from PDBParser import * def main(): Testparser = PDBParser() self.Struktur = Testparser.get_structure('Stru','/usr/local/CAME/PDB/PDBFILES/pdb1htq') Testparser.file.close() if __name__ == "__main__" : main() ------------------------------------------------------------------------------------------ Again the core problem: Note that for example "1htq" and "1bxr" will not be processed correctly, but be killed after some time. Thank you for your help, Clemens (@CAME, Salzburg) From jchang at smi.stanford.edu Thu Dec 5 10:18:50 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Gentoo Linux port - disabling Tk test display In-Reply-To: <3DEF35D4.1010900@imim.es> References: <3DEB7416.7040102@imim.es> <20021202201133.GC46025@springfield.stanford.edu> <3DEF35D4.1010900@imim.es> Message-ID: <20021205151850.GB64337@springfield.stanford.edu> python setup.py test --no-gui On Thu, Dec 05, 2002 at 12:17:40PM +0100, Jaeggi, Daniel M. wrote: > Is there an easy way to disable the Tk test result display when running > "python setup.py test"? Although my system has Tk, I just want to get > the raw command line output. > > Thanks > > Dan > > Jeffrey Chang wrote: > > >On Mon, Dec 02, 2002 at 03:54:14PM +0100, Jaeggi, Daniel M. wrote: > > > > > >>Is anyone else out there using Gentoo Linux? If so, have you written an > >>ebuild (port) for it? If not, I'll probably be writing one in the next > >>couple of days. > >> > >> > > > >Great! Let us know when it is finished. > > > >Also, be aware that we are working on putting out a new release of > >Biopython. The build process won't change much, though. > > > >Jeff > > > > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From thamelry at vub.ac.be Thu Dec 5 10:37:47 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] bug-request In-Reply-To: <02112816111701.23290@rita> References: <02112816111701.23290@rita> Message-ID: <200212051532.gB5FWBm16660@vador.skynet.be> > Trying to apply the PDB-Biopython-module with all PDB structures alvailable > to me, I recognized that the job will sometimes be killed while processing > a file, especially when processing large PDB files. > The cause seems to be a lack of memory. Seemingly the problem files are > read several times (-due to an error within the header reading routine?--> > I came upon this, because the program is printing the same discontinuations > several times to the screen.) Thanks for the bug report. I'll look into this next week, I'm away for a couple of days. > Testparser = PDBParser() > self.Struktur = > Testparser.get_structure('Stru','/usr/local/CAME/PDB/PDBFILES/pdb1htq') > Testparser.file.close() I'm a bit puzzled by this last line.... What is it supposed to be doing? Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From jchang at smi.stanford.edu Fri Dec 6 15:09:27 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: [BioPython] bioperl with python In-Reply-To: <170350-22002124501538972@M2W064.mail2web.com> References: <170350-22002124501538972@M2W064.mail2web.com> Message-ID: <20021206200926.GB68407@springfield.stanford.edu> [moved to biopython-dev list] Has anyone else been experience problems? I don't think we're going to be able to diagnose this any time soon. Is there any other way you can get your fixes in? Do you have a local copy of the repository from which to make context diffs? Jeff On Wed, Dec 04, 2002 at 07:15:38PM -0500, katel@worldpath.net wrote: > > > Yes I referred to the documentation. First I tried renaming my current > biopython path and checking out the whole directory a second time. Then I > tried things like cvs, cvs-help, cvs --help. The message was cvs:not found. > > Cayte > > -------------------------------------------------------------------- > mail2web - Check your email from the web at > http://mail2web.com/ . > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From thamelry at vub.ac.be Tue Dec 10 08:22:24 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] bug-request In-Reply-To: <02112816111701.23290@rita> References: <02112816111701.23290@rita> Message-ID: <200212101316.gBADGe001745@durendal.skynet.be> > Trying to apply the PDB-Biopython-module with all PDB structures alvailable > to me, I recognized that the job will sometimes be killed while processing > a file, especially when processing large PDB files. > The cause seems to be a lack of memory. Well, yes. PDB file 1HTQ is a monster of 70 MB, containing almost a million atoms. If you want to use the PDB module for this you'll have to buy some more memory, I guess. :-) > Seemingly the problem files are > read several times (-due to an error within the header reading routine?--> > I came upon this, because the program is printing the same discontinuations > several times to the screen.) No, that is because the chains in the file are discontinuous. This is not the problem. > Again the core problem: Note that for example "1htq" and "1bxr" will not > be processed correctly, but be killed after some time. 1BXR contains an error. It has two residues with the same identifier. HETATM23384 K K 3985 -8.986 34.229 -48.036 1.00 54.69 K HETATM47621 K K 3985 -19.641 -25.353 -32.655 1.00 39.94 K Normally, this should be handled by using PDBParser(PERMISSIVE=1) which would leave out the duplicated atoms, but there was a bug in the error handling code (there was an old assert statement instead of a "raise PDBConstructionError" statement). That's been corrected now, you can try out the new version. 1BXR should parse OK now with PDBParser(PERMISSIVE=1). Cheers, -Thomas From biopython-bugs at bioperl.org Tue Dec 10 12:31:47 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/108 Message-ID: <200212101731.gBAHVlAW020429@pw600a.bioperl.org> JitterBug notification new message incoming/108 Message summary for PR#108 From: andreas.kuntzagk@mdc-berlin.de Subject: Bug in parsing GenBank-Files with Header Date: Tue, 10 Dec 2002 12:31:46 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From andreas.kuntzagk@mdc-berlin.de Tue Dec 10 12:31:46 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBAHVkAW020423 for ; Tue, 10 Dec 2002 12:31:46 -0500 Date: Tue, 10 Dec 2002 12:31:46 -0500 Message-Id: <200212101731.gBAHVkAW020423@pw600a.bioperl.org> From: andreas.kuntzagk@mdc-berlin.de To: biopython-bugs@bioperl.org Subject: Bug in parsing GenBank-Files with Header X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: Andreas Kuntzagk Module: Bio.GenBank.Iterator Version: OS: Submission from: (NULL) (141.80.80.40) While parsing the recent GenBank-Release, I got followin error: >>> from Bio import GenBank >>> f=file("gbest1.seq") >>> help(GenBank.Iterator) >>> GenBank.Iterator(f,has_header=1) Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 171, in __init__ self._reader = RecordReader.StartsWith(handle, "LOCUS") File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 133, in __init__ self.tagtable) File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 92, in _find_begin_positions raise ReaderError("invalid format starting with %s" % repr(text[:50])) Martel.RecordReader.ReaderError: invalid format starting with 'DEFINITION zd84h07.s1 Soares_fetal_heart_NbHH19W ' Problems seems, that in this file there is only one empty line after the "...reported sequences" instead of the expected two lines. From biopython-bugs at bioperl.org Thu Dec 12 08:44:34 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/109 Message-ID: <200212121344.gBCDiYSQ009955@pw600a.bioperl.org> JitterBug notification new message incoming/109 Message summary for PR#109 From: Andreas Kuntzagk Subject: Re: [Biopython-dev] Notification: incoming/108 Date: 12 Dec 2002 14:45:24 0100 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From andreas.kuntzagk@mdc-berlin.de Thu Dec 12 08:44:33 2002 Received: from guard.edv.mdc-berlin.de (guard.edv.mdc-berlin.de [141.80.8.30]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBCDiWSQ009950 for ; Thu, 12 Dec 2002 08:44:33 -0500 Received: from sulawesi.bioinf.mdc-berlin.de (sulawesi.bioinf.mdc-berlin.de [141.80.80.60]) by guard.edv.mdc-berlin.de (8.11.4/8.11.4) with ESMTP id gBCDiwh07148 for ; Thu, 12 Dec 2002 14:44:58 +0100 (MET) Subject: Re: [Biopython-dev] Notification: incoming/108 From: Andreas Kuntzagk To: biopython-bugs@bioperl.org In-Reply-To: <200212101731.gBAHVlAW020429@pw600a.bioperl.org> References: <200212101731.gBAHVlAW020429@pw600a.bioperl.org> Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.8 Date: 12 Dec 2002 14:45:24 +0100 Message-Id: <1039700724.20575.40.camel@sulawesi> Mime-Version: 1.0 X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > >From andreas.kuntzagk@mdc-berlin.de Tue Dec 10 12:31:46 2002 [...] > > While parsing the recent GenBank-Release, I got followin error: > > > >>> from Bio import GenBank > >>> f=file("gbest1.seq") > >>> help(GenBank.Iterator) > > >>> GenBank.Iterator(f,has_header=1) > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 171, in > __init__ > self._reader = RecordReader.StartsWith(handle, "LOCUS") > File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 133, in > __init__ > self.tagtable) > File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 92, in > _find_begin_positions > raise ReaderError("invalid format starting with %s" % repr(text[:50])) > Martel.RecordReader.ReaderError: invalid format starting with 'DEFINITION > zd84h07.s1 Soares_fetal_heart_NbHH19W ' > > Problems seems, that in this file there is only one empty line after the > "...reported sequences" instead of the expected two lines. > I would suggest the following patch. This reads all text from the handle into a string (which can consume quit some memory :-( ) and skips to the first LOCUS. All remaining text is the turned into a StrinIO (would cStringIO better?) --start patch-- RCS file: /home/repository/biopython/biopython/Bio/GenBank/__init__.py,v retrieving revision 1.34 diff -r1.34 __init__.py 154,156c154 < GenBank). If so, we'll iterate over the header to get past it, and < then the iterator will be set up to return the first record in < the file. --- > GenBank). If so, we'll skip to the next LOCUS. 159,170c157,161 < first_line = handle.readline() < assert first_line.find("Genetic Sequence Data Bank") >= 0, \ < "Doesn't seem to have a GenBank header." < while 1: < cur_line = handle.readline() < if cur_line.find("reported sequences") >= 0: < break < < # read off two more lines and we are ready to go < handle.readline() < handle.readline() < --- > re_locus = re.compile(r".*?(?=LOCUS)") > split_text = re_locus.split(handle.read(),1) > assert len(split_text)==2 > import StringIO > handle=StringIO.StringIO(split_text[1]) From jchang at SMI.Stanford.EDU Mon Dec 16 02:11:13 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do In-Reply-To: <20021203043643.GA47748@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> <20021203043643.GA47748@springfield.stanford.edu> Message-ID: <20021216071112.GA1762@springfield.stanford.edu> Alright, I think we're about ready to make the release. Please check in any last minute fixes tomorrow (Monday), so I can build the final version on Tuesday. Last minute fixes are things like: documentation fixes, critical bug fixes (shouldn't be any of those), regression testing updates, etc. No destabilizing changes, please! test_locuslink is still failing, which doesn't bode well for the package. Cayte, is this yours? If we can't get this fixed, we'll have to save locuslink for the next release. Jeff On Mon, Dec 02, 2002 at 08:36:43PM -0800, Jeffrey Chang wrote: > Hello everybody, > > Thanks for everybody who has been helping getting Biopython ready for > another release! Here's a check-list of stuff we still have left to > do, along with names of who is signed up to do it. Please send a > quick progress update on the status of the task, or at least an email > saying it's not getting done. > > Thanks, > Jeff > > > Biopython Release To-Do > ======================= > - dalke BUGZILLA: BerkeleyDB.py Problem? > - katel BUGZILLA: Tests/MetaTool/Meta9.out conflicts with meta9.out > - katel BUGZILLA: potential conflict between Bio/Rebase/Rebase.py and Bio/Rebase/__init__.py > - katel test_locuslink regression test fails > - gec BUGZILLA: Bio/SCOP/tests should be integrated with rest of regression tests > - chapmanb make sure tutorial is still current > - chapmanb make sure example scripts still work > - jchang update the NEWS file > - chapmanb DocSQL regression test fails > - grouse test_GFF regression test fails > - grouse test_easy regression test fails > - grouse move easy.py and GenericTools.py out of Bio namespace > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From thamelry at vub.ac.be Mon Dec 16 07:42:26 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do In-Reply-To: <20021216071112.GA1762@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> <20021203043643.GA47748@springfield.stanford.edu> <20021216071112.GA1762@springfield.stanford.edu> Message-ID: <200212161236.gBGCah911239@picard.skynet.be> > Alright, I think we're about ready to make the release. Please check > in any last minute fixes tomorrow (Monday), so I can build the final > version on Tuesday. Last minute fixes are things like: documentation > fixes, critical bug fixes (shouldn't be any of those), regression > testing updates, etc. No destabilizing changes, please! I added a Polypeptide object to the PDB module, so you can now extract polypeptides from PDB files. I added test code and documentation of this as well. As far as I can see the PDB module is tested, complete and ready to be shipped. Cheers, -Thomas From thamelry at vub.ac.be Mon Dec 16 16:26:53 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Tutorial In-Reply-To: <20021216071112.GA1762@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> <20021203043643.GA47748@springfield.stanford.edu> <20021216071112.GA1762@springfield.stanford.edu> Message-ID: <200212162121.gBGLLJI04221@riker.skynet.be> Hi, Compiling the LaTeX tutorial generates a lot of errors on my machine. At least some of these errors are due to missing LaTeX packages. What packages are presumed to be present? Would be useful to put that in a README file.... -Thomas --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From chapmanb at arches.uga.edu Mon Dec 16 17:42:42 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Tutorial In-Reply-To: <200212162121.gBGLLJI04221@riker.skynet.be> References: <20021121043244.GA7777@springfield.stanford.edu> <20021203043643.GA47748@springfield.stanford.edu> <20021216071112.GA1762@springfield.stanford.edu> <200212162121.gBGLLJI04221@riker.skynet.be> Message-ID: <20021216224242.GG23645@ci350185-a.athen1.ga.home.com> Hi Thomas; > Compiling the LaTeX tutorial generates a lot of errors on my machine. > At least some of these errors are due to missing LaTeX packages. > What packages are presumed to be present? Would be useful > to put that in a README file.... I've put most of the instructions of how I convert the LaTeX to pdf (and html) in the header of the Tutorial.tex file. I think the only non-standard package used in hevea (which I use to generate the html version of the docs) and the header has the information on where to get that. Please feel free to add additional information there; I definitely want to make it possible for people to edit/change/add/whatever to the Tutorial. It's a monster and needs work from lots of places. Brad From katel at worldpath.net Mon Dec 16 19:00:30 2002 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do Message-ID: <29950-22002122170030305@M2W036.mail2web.com> test_locuslink is still failing, which doesn't bode well for the package. Cayte, is this yours? If we can't get this fixed, we'll have to save locuslink for the next release. Jeff On Mon, Dec 02, 2002 at 08:36:43PM -0800, Jeffrey Chang wrote: > Hello everybody, > > Thanks for everybody who has been helping getting Biopython ready for > another release! Here's a check-list of stuff we still have left to > do, along with names of who is signed up to do it. Please send a > quick progress update on the status of the task, or at least an email > saying it's not getting done. > > Thanks, > Jeff I just tried to check it in but I continue to get cvs: command not found when I do anything with cvs on the new system. Cayte > > > Biopython Release To-Do > ======================= > - dalke BUGZILLA: BerkeleyDB.py Problem? > - katel BUGZILLA: Tests/MetaTool/Meta9.out conflicts with meta9.out > - katel BUGZILLA: potential conflict between Bio/Rebase/Rebase.py and Bio/Rebase/__init__.py > - katel test_locuslink regression test fails > - gec BUGZILLA: Bio/SCOP/tests should be integrated with rest of regression tests > - chapmanb make sure tutorial is still current > - chapmanb make sure example scripts still work > - jchang update the NEWS file > - chapmanb DocSQL regression test fails > - grouse test_GFF regression test fails > - grouse test_easy regression test fails > - grouse move easy.py and GenericTools.py out of Bio namespace > > _______________________________________________ > 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 -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From katel at worldpath.net Mon Dec 16 19:04:52 2002 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Biopython release To-Do Message-ID: <323910-2200212217045242@M2W036.mail2web.com> A possible solution to locuslink is I could copy it to a directory where others have access so someone could check it into Tests slash LocusLink. Cayte -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From idoerg at burnham.org Wed Dec 18 14:31:36 2002 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: [Biopython-announce] Biopython 1.10 Available References: <20021218064310.GA8656@springfield.stanford.edu> <3E007AA4.40909@asalup.org> <20021218185036.GB10608@springfield.stanford.edu> Message-ID: <3E00CD18.3080403@burnham.org> umm, sorry, AlignInfo is obviously not the right place. I guess a module in SeqUtils is a good choice, as the __init__.py file there seems pretty full already. I. Jeffrey Chang wrote: > No, it didn't make it into this release. We'll try to get it into the > next one. Iddo, did you decide on how to integrate the LCC code? > > Jeff > > > On Wed, Dec 18, 2002 at 10:39:48AM -0300, Sebastian Bassi wrote: > >>Jeffrey Chang wrote: >> >>>Hello Everybody, >>>I've just made Biopython 1.10 available at: >>>http://www.biopython.org/Download/ >>>This is a major release with lots of bug fixes and new features. >> >>Did the LCC function made into the new version? >> >> >> >>-- >>Best regards, >> >>//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ >>\=// IT Manager Advanta Seeds - Balcarce Research Center - \=// >>//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ >>\=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// >> >> Linux para todos: http://Linuxfacil.info > > > -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 From biopython-bugs at bioperl.org Wed Dec 18 21:54:26 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/110 Message-ID: <200212190254.gBJ2sQSQ021867@pw600a.bioperl.org> JitterBug notification new message incoming/110 Message summary for PR#110 From: a@bc.com Subject: distributions.py / vq.py Date: Wed, 18 Dec 2002 21:54:25 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From a@bc.com Wed Dec 18 21:54:26 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBJ2sPSQ021861 for ; Wed, 18 Dec 2002 21:54:25 -0500 Date: Wed, 18 Dec 2002 21:54:25 -0500 Message-Id: <200212190254.gBJ2sPSQ021861@pw600a.bioperl.org> From: a@bc.com To: biopython-bugs@bioperl.org Subject: distributions.py / vq.py X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: ......... Module: distributions.py Version: 1.10 distribution OS: W2K, SunOS 5.8 Submission from: cache.vic.csiro.au (138.194.15.102) File "C:\PROGRA~1\Python22\Lib\site-packages\scipy\cluster\vq.py", line 304, in kmeans guess = take(obs,randint(0,No,k),0) File "C:\PROGRA~1\Python22\lib\site-packages\scipy\stats\distributions.py", line 2727, in __call__ U = rv.random(size=self._size) AttributeError: 'module' object has no attribute 'random' Strangely, dir(rv) reveals no 'random' module! From jchang at smi.stanford.edu Wed Dec 18 23:24:14 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/110 In-Reply-To: <200212190254.gBJ2sQSQ021867@pw600a.bioperl.org> References: <200212190254.gBJ2sQSQ021867@pw600a.bioperl.org> Message-ID: <20021219042414.GA11508@springfield.stanford.edu> Are you sure this is from Biopython? We don't have a distributions module, and the traceback looks to be from scipy. > File "C:\PROGRA~1\Python22\lib\site-packages\scipy\stats\distributions.py", Jeff On Wed, Dec 18, 2002 at 09:54:26PM -0500, biopython-bugs@bioperl.org wrote: > JitterBug notification > > new message incoming/110 > > Message summary for PR#110 > From: a@bc.com > Subject: distributions.py / vq.py > Date: Wed, 18 Dec 2002 21:54:25 -0500 > 0 replies 0 followups > > ====> ORIGINAL MESSAGE FOLLOWS <==== > > >From a@bc.com Wed Dec 18 21:54:26 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBJ2sPSQ021861 > for ; Wed, 18 Dec 2002 21:54:25 -0500 > Date: Wed, 18 Dec 2002 21:54:25 -0500 > Message-Id: <200212190254.gBJ2sPSQ021861@pw600a.bioperl.org> > From: a@bc.com > To: biopython-bugs@bioperl.org > Subject: distributions.py / vq.py > X-Spam-Status: No > X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > > Full_Name: ......... > Module: distributions.py > Version: 1.10 distribution > OS: W2K, SunOS 5.8 > Submission from: cache.vic.csiro.au (138.194.15.102) > > > File "C:\PROGRA~1\Python22\Lib\site-packages\scipy\cluster\vq.py", line 304, > in kmeans > guess = take(obs,randint(0,No,k),0) > File "C:\PROGRA~1\Python22\lib\site-packages\scipy\stats\distributions.py", > line 2727, in __call__ > U = rv.random(size=self._size) > AttributeError: 'module' object has no attribute 'random' > > Strangely, dir(rv) reveals no 'random' module! > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From biopython-bugs at bioperl.org Wed Dec 18 23:24:54 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/111 Message-ID: <200212190424.gBJ4OsSQ022488@pw600a.bioperl.org> JitterBug notification new message incoming/111 Message summary for PR#111 From: Jeffrey Chang Subject: Re: [Biopython-dev] Notification: incoming/110 Date: Wed, 18 Dec 2002 20:24:14 -0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From jchang@springfield.stanford.edu Wed Dec 18 23:24:53 2002 Received: from springfield.stanford.edu ([128.12.147.41]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBJ4OqSQ022475 for ; Wed, 18 Dec 2002 23:24:52 -0500 Received: (from jchang@localhost) by springfield.stanford.edu (8.11.6/8.11.6) id gBJ4OE512028; Wed, 18 Dec 2002 20:24:14 -0800 (PST) (envelope-from jchang) Date: Wed, 18 Dec 2002 20:24:14 -0800 From: Jeffrey Chang To: biopython-bugs@bioperl.org Cc: biopython-dev@biopython.org Subject: Re: [Biopython-dev] Notification: incoming/110 Message-ID: <20021219042414.GA11508@springfield.stanford.edu> Mail-Followup-To: biopython-bugs@bioperl.org, biopython-dev@biopython.org References: <200212190254.gBJ2sQSQ021867@pw600a.bioperl.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <200212190254.gBJ2sQSQ021867@pw600a.bioperl.org> User-Agent: Mutt/1.4i X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Are you sure this is from Biopython? We don't have a distributions module, and the traceback looks to be from scipy. > File "C:\PROGRA~1\Python22\lib\site-packages\scipy\stats\distributions.py", Jeff On Wed, Dec 18, 2002 at 09:54:26PM -0500, biopython-bugs@bioperl.org wrote: > JitterBug notification > > new message incoming/110 > > Message summary for PR#110 > From: a@bc.com > Subject: distributions.py / vq.py > Date: Wed, 18 Dec 2002 21:54:25 -0500 > 0 replies 0 followups > > ====> ORIGINAL MESSAGE FOLLOWS <==== > > >From a@bc.com Wed Dec 18 21:54:26 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBJ2sPSQ021861 > for ; Wed, 18 Dec 2002 21:54:25 -0500 > Date: Wed, 18 Dec 2002 21:54:25 -0500 > Message-Id: <200212190254.gBJ2sPSQ021861@pw600a.bioperl.org> > From: a@bc.com > To: biopython-bugs@bioperl.org > Subject: distributions.py / vq.py > X-Spam-Status: No > X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > > Full_Name: ......... > Module: distributions.py > Version: 1.10 distribution > OS: W2K, SunOS 5.8 > Submission from: cache.vic.csiro.au (138.194.15.102) > > > File "C:\PROGRA~1\Python22\Lib\site-packages\scipy\cluster\vq.py", line 304, > in kmeans > guess = take(obs,randint(0,No,k),0) > File "C:\PROGRA~1\Python22\lib\site-packages\scipy\stats\distributions.py", > line 2727, in __call__ > U = rv.random(size=self._size) > AttributeError: 'module' object has no attribute 'random' > > Strangely, dir(rv) reveals no 'random' module! > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From jchang at SMI.Stanford.EDU Tue Dec 24 00:25:35 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: [Biopython-announce] Biopython 1.10 Available In-Reply-To: <3E00CD18.3080403@burnham.org> References: <20021218064310.GA8656@springfield.stanford.edu> <3E007AA4.40909@asalup.org> <20021218185036.GB10608@springfield.stanford.edu> <3E00CD18.3080403@burnham.org> Message-ID: <20021224052535.GA14656@springfield.stanford.edu> OK, SeqUtils sounds good. What's the deal with sequtils.py and SeqUtils/__init__.py? It looks like SeqUtils/__init__.py replaced sequtils.py. Will anybody object if I remove the latter? Jeff On Wed, Dec 18, 2002 at 11:31:36AM -0800, Iddo Friedberg wrote: > umm, sorry, AlignInfo is obviously not the right place. > > I guess a module in SeqUtils is a good choice, as the __init__.py file > there seems pretty full already. > > > I. > > > Jeffrey Chang wrote: > >No, it didn't make it into this release. We'll try to get it into the > >next one. Iddo, did you decide on how to integrate the LCC code? > > > >Jeff > > > > > >On Wed, Dec 18, 2002 at 10:39:48AM -0300, Sebastian Bassi wrote: > > > >>Jeffrey Chang wrote: > >> > >>>Hello Everybody, > >>>I've just made Biopython 1.10 available at: > >>>http://www.biopython.org/Download/ > >>>This is a major release with lots of bug fixes and new features. > >> > >>Did the LCC function made into the new version? > >> > >> > >> > >>-- > >>Best regards, > >> > >>//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ > >>\=// IT Manager Advanta Seeds - Balcarce Research Center - \=// > >>//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ > >>\=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// > >> > >> Linux para todos: http://Linuxfacil.info > > > > > > > > -- > Iddo Friedberg > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 From katel at worldpath.net Fri Dec 27 05:11:07 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] cvs Message-ID: <000701c2ad90$46a1cd20$c870bbd1@pcklindner> Hope everyone is enjoying a fantastic holiday! I'm still getting cvs: command not found messages in my ssh sessions on dev.open-bio.org. I won't get very far without resolving this issue! How do I contact the sysadmin? Cayte From biopython-bugs at bioperl.org Sat Dec 28 09:10:34 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/112 Message-ID: <200212281410.gBSEAYSQ016576@pw600a.bioperl.org> JitterBug notification new message incoming/112 Message summary for PR#112 From: oeed@online.no Subject: Problem: Documentation of PubMed Date: Sat, 28 Dec 2002 09:10:29 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From oeed@online.no Sat Dec 28 09:10:33 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBSEATSQ016570 for ; Sat, 28 Dec 2002 09:10:33 -0500 Date: Sat, 28 Dec 2002 09:10:29 -0500 Message-Id: <200212281410.gBSEATSQ016570@pw600a.bioperl.org> From: oeed@online.no To: biopython-bugs@bioperl.org Subject: Problem: Documentation of PubMed X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Full_Name: Øyvind Edvardsen Module: Medline/PubMed documentation Version: 1.10 OS: linux and winxp Submission from: kunde1936.tromso.alfanett.no (62.16.135.165) I was trying to exploit the PubMed stuff and followed the Cookbook available from the documentation page. No success! The problem is the import stuff: in all the docs I found it is shown as from Bio.Medline import PubMed from Bio import Medline but what really works is: from Bio import PubMed from Bio.PubMed import Medline After those imports a parser and dict can be set up just as in the example code in the Cookbook. And it works very good! Maybe the docs went out of sync with the code some time ago... Anyway, this stuff should be fixed in the docs so that other people can use biopython's Medline without having to figure out what's wrong first. OED. From biopython-bugs at bioperl.org Mon Dec 30 06:36:52 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Notification: incoming/87 Message-ID: <200212301136.gBUBaqSQ003585@pw600a.bioperl.org> JitterBug notification bienstam changed notes Message summary for PR#87 From: rickard.sandberg@mtc.ki.se Subject: genbank_format 2 added tags Date: Tue, 8 Oct 2002 07:46:53 -0400 0 replies 0 followups Notes: Included in 1.10. Closing bug report. ====> ORIGINAL MESSAGE FOLLOWS <==== >From rickard.sandberg@mtc.ki.se Tue Oct 8 07:46:57 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g98Bkr4P000656 for ; Tue, 8 Oct 2002 07:46:57 -0400 Date: Tue, 8 Oct 2002 07:46:53 -0400 Message-Id: <200210081146.g98Bkr4P000656@pw600a.bioperl.org> From: rickard.sandberg@mtc.ki.se To: biopython-bugs@bioperl.org Subject: genbank_format 2 added tags Full_Name: Rickard Sandberg Module: genbank_format.py Version: 1.00a4 OS: linux Submission from: generic2.mtc.ki.se (130.237.137.207) When parsing entries in GenBank (GID:9627127 and 14270686 for example). You get parser Error: Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1555, in __getitem__ return self.parser.parse(handle) File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 268, in parse self._scanner.feed(handle, self._consumer) File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1250, in feed self._parser.parseFile(handle) File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 230, in parseFile self.parseString(fileobj.read()) File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 258, in parseString self._err_handler.fatalError(result) File "/usr/lib/python2.2/xml/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 60674 However, I found that the reason being that the 2 documents contained Feature Tags not present in the genbank_format.py file. So, when I added "snoRNA" in feature_key_names and "isolation_source" in the feature_qualifier_names it works. Also, I added the possible use of "linear" in the residue_type in the LOCUS definition, which I think was the reason for parserError in some files I had couple of months ago. Bye From biopython-bugs at bioperl.org Mon Dec 30 06:36:52 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/87 Message-ID: <200212301136.gBUBaqSQ003589@pw600a.bioperl.org> JitterBug notification bienstam moved PR#87 from incoming to fixed-bugs Message summary for PR#87 From: rickard.sandberg@mtc.ki.se Subject: genbank_format 2 added tags Date: Tue, 8 Oct 2002 07:46:53 -0400 0 replies 0 followups Notes: Included in 1.10. Closing bug report. ====> ORIGINAL MESSAGE FOLLOWS <==== >From rickard.sandberg@mtc.ki.se Tue Oct 8 07:46:57 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g98Bkr4P000656 for ; Tue, 8 Oct 2002 07:46:57 -0400 Date: Tue, 8 Oct 2002 07:46:53 -0400 Message-Id: <200210081146.g98Bkr4P000656@pw600a.bioperl.org> From: rickard.sandberg@mtc.ki.se To: biopython-bugs@bioperl.org Subject: genbank_format 2 added tags Full_Name: Rickard Sandberg Module: genbank_format.py Version: 1.00a4 OS: linux Submission from: generic2.mtc.ki.se (130.237.137.207) When parsing entries in GenBank (GID:9627127 and 14270686 for example). You get parser Error: Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1555, in __getitem__ return self.parser.parse(handle) File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 268, in parse self._scanner.feed(handle, self._consumer) File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1250, in feed self._parser.parseFile(handle) File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 230, in parseFile self.parseString(fileobj.read()) File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 258, in parseString self._err_handler.fatalError(result) File "/usr/lib/python2.2/xml/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 60674 However, I found that the reason being that the 2 documents contained Feature Tags not present in the genbank_format.py file. So, when I added "snoRNA" in feature_key_names and "isolation_source" in the feature_qualifier_names it works. Also, I added the possible use of "linear" in the residue_type in the LOCUS definition, which I think was the reason for parserError in some files I had couple of months ago. Bye From biopython-bugs at bioperl.org Mon Dec 30 06:40:14 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/93 Message-ID: <200212301140.gBUBeESQ003657@pw600a.bioperl.org> JitterBug notification bienstam changed notes Message summary for PR#93 From: andreas.kuntzagk@mdc-berlin.de Subject: GenBank-Format (Feature-Qualifier /motif) Date: Thu, 7 Nov 2002 09:52:51 -0500 0 replies 0 followups Notes: Fix included in 1.10. Closing bug report. ====> ORIGINAL MESSAGE FOLLOWS <==== >From andreas.kuntzagk@mdc-berlin.de Thu Nov 7 09:52:52 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gA7Eqp6J025565 for ; Thu, 7 Nov 2002 09:52:52 -0500 Date: Thu, 7 Nov 2002 09:52:51 -0500 Message-Id: <200211071452.gA7Eqp6J025565@pw600a.bioperl.org> From: andreas.kuntzagk@mdc-berlin.de To: biopython-bugs@bioperl.org Subject: GenBank-Format (Feature-Qualifier /motif) Full_Name: Andreas Kuntzagk Module: genbank_format.py Version: OS: Submission from: sulawesi.bioinf.mdc-berlin.de (141.80.80.60) In Entry GI:4165449 (and others) there is a qualifier /motif in a CDS -Feature. Currently the genbank_format.py doesn't allow this. Fix: insert "motif" into the feature_qualifier_names diff -r1.20 genbank_format.py 528a529 > "motif", From biopython-bugs at bioperl.org Mon Dec 30 06:40:14 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/93 Message-ID: <200212301140.gBUBeESQ003661@pw600a.bioperl.org> JitterBug notification bienstam moved PR#93 from incoming to fixed-bugs Message summary for PR#93 From: andreas.kuntzagk@mdc-berlin.de Subject: GenBank-Format (Feature-Qualifier /motif) Date: Thu, 7 Nov 2002 09:52:51 -0500 0 replies 0 followups Notes: Fix included in 1.10. Closing bug report. ====> ORIGINAL MESSAGE FOLLOWS <==== >From andreas.kuntzagk@mdc-berlin.de Thu Nov 7 09:52:52 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gA7Eqp6J025565 for ; Thu, 7 Nov 2002 09:52:52 -0500 Date: Thu, 7 Nov 2002 09:52:51 -0500 Message-Id: <200211071452.gA7Eqp6J025565@pw600a.bioperl.org> From: andreas.kuntzagk@mdc-berlin.de To: biopython-bugs@bioperl.org Subject: GenBank-Format (Feature-Qualifier /motif) Full_Name: Andreas Kuntzagk Module: genbank_format.py Version: OS: Submission from: sulawesi.bioinf.mdc-berlin.de (141.80.80.60) In Entry GI:4165449 (and others) there is a qualifier /motif in a CDS -Feature. Currently the genbank_format.py doesn't allow this. Fix: insert "motif" into the feature_qualifier_names diff -r1.20 genbank_format.py 528a529 > "motif", From jchang at smi.stanford.edu Tue Dec 31 20:53:53 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/112 In-Reply-To: <200212281410.gBSEAYSQ016576@pw600a.bioperl.org> References: <200212281410.gBSEAYSQ016576@pw600a.bioperl.org> Message-ID: <20030101015353.GA77547@springfield.stanford.edu> Yep, the docs are a little behind the code. Thanks for letting us know. I have fixed these references. Jeff On Sat, Dec 28, 2002 at 09:10:34AM -0500, biopython-bugs@bioperl.org wrote: > JitterBug notification > > new message incoming/112 > > Message summary for PR#112 > From: oeed@online.no > Subject: Problem: Documentation of PubMed > Date: Sat, 28 Dec 2002 09:10:29 -0500 > 0 replies 0 followups > > ====> ORIGINAL MESSAGE FOLLOWS <==== > > >From oeed@online.no Sat Dec 28 09:10:33 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBSEATSQ016570 > for ; Sat, 28 Dec 2002 09:10:33 -0500 > Date: Sat, 28 Dec 2002 09:10:29 -0500 > Message-Id: <200212281410.gBSEATSQ016570@pw600a.bioperl.org> > From: oeed@online.no > To: biopython-bugs@bioperl.org > Subject: Problem: Documentation of PubMed > X-Spam-Status: No > X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > > Full_Name: ?yvind Edvardsen > Module: Medline/PubMed documentation > Version: 1.10 > OS: linux and winxp > Submission from: kunde1936.tromso.alfanett.no (62.16.135.165) > > > I was trying to exploit the PubMed stuff and > followed the Cookbook available from the documentation page. No success! > The problem is the import stuff: > in all the docs I found it is shown as > from Bio.Medline import PubMed > from Bio import Medline > but what really works is: > from Bio import PubMed > from Bio.PubMed import Medline > After those imports a parser and dict can > be set up just as in the example code in the Cookbook. And it works very good! > > Maybe the docs went out of sync with the code > some time ago... > > Anyway, this stuff should be fixed in the docs > so that other people can use biopython's Medline without having to figure out > what's wrong first. > > OED. > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From biopython-bugs at bioperl.org Tue Dec 31 20:53:44 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:20 2005 Subject: [Biopython-dev] Notification: incoming/113 Message-ID: <200301010153.h011riSQ021265@pw600a.bioperl.org> JitterBug notification new message incoming/113 Message summary for PR#113 From: Jeffrey Chang Subject: Re: [Biopython-dev] Notification: incoming/112 Date: Tue, 31 Dec 2002 17:53:53 -0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From jchang@springfield.stanford.edu Tue Dec 31 20:53:43 2002 Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h011rgSQ021258 for ; Tue, 31 Dec 2002 20:53:42 -0500 Received: (from jchang@localhost) by springfield.stanford.edu (8.11.6/8.11.6) id h011rrI77593; Tue, 31 Dec 2002 17:53:53 -0800 (PST) (envelope-from jchang) Date: Tue, 31 Dec 2002 17:53:53 -0800 From: Jeffrey Chang To: biopython-bugs@bioperl.org Cc: biopython-dev@biopython.org Subject: Re: [Biopython-dev] Notification: incoming/112 Message-ID: <20030101015353.GA77547@springfield.stanford.edu> Mail-Followup-To: biopython-bugs@bioperl.org, biopython-dev@biopython.org References: <200212281410.gBSEAYSQ016576@pw600a.bioperl.org> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <200212281410.gBSEAYSQ016576@pw600a.bioperl.org> User-Agent: Mutt/1.4i X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Yep, the docs are a little behind the code. Thanks for letting us know. I have fixed these references. Jeff On Sat, Dec 28, 2002 at 09:10:34AM -0500, biopython-bugs@bioperl.org wrote: > JitterBug notification > > new message incoming/112 > > Message summary for PR#112 > From: oeed@online.no > Subject: Problem: Documentation of PubMed > Date: Sat, 28 Dec 2002 09:10:29 -0500 > 0 replies 0 followups > > ====> ORIGINAL MESSAGE FOLLOWS <==== > > >From oeed@online.no Sat Dec 28 09:10:33 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBSEATSQ016570 > for ; Sat, 28 Dec 2002 09:10:33 -0500 > Date: Sat, 28 Dec 2002 09:10:29 -0500 > Message-Id: <200212281410.gBSEATSQ016570@pw600a.bioperl.org> > From: oeed@online.no > To: biopython-bugs@bioperl.org > Subject: Problem: Documentation of PubMed > X-Spam-Status: No > X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) > > Full_Name: Øyvind Edvardsen > Module: Medline/PubMed documentation > Version: 1.10 > OS: linux and winxp > Submission from: kunde1936.tromso.alfanett.no (62.16.135.165) > > > I was trying to exploit the PubMed stuff and > followed the Cookbook available from the documentation page. No success! > The problem is the import stuff: > in all the docs I found it is shown as > from Bio.Medline import PubMed > from Bio import Medline > but what really works is: > from Bio import PubMed > from Bio.PubMed import Medline > After those imports a parser and dict can > be set up just as in the example code in the Cookbook. And it works very good! > > Maybe the docs went out of sync with the code > some time ago... > > Anyway, this stuff should be fixed in the docs > so that other people can use biopython's Medline without having to figure out > what's wrong first. > > OED. > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev