From jonathan.taylor at utoronto.ca Thu Jan 13 02:36:59 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Application instances code Message-ID: <1105601819.18194.6.camel@localhost.localdomain> Hi, My last message got caught by the spam guard for some reason so excuse the odd subject line. I am doing quite a bit of infrastructure work using biopython. As I run into problems I will try to make the code available to the biopython project as appropriate. Here is a small patch: - allows you to easily figure out the return code of an application run through the Bio.Application framework - adds Fastacmd functionality to the Bio.Application framework Any problems, just respond to the list as I monitor it regularly. Regards, Jonathan Taylor. Botany Department, University of Toronto. From jonathan.taylor at utoronto.ca Thu Jan 13 03:17:58 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Application instances code In-Reply-To: <1105601819.18194.6.camel@localhost.localdomain> References: <1105601819.18194.6.camel@localhost.localdomain> Message-ID: <1105604278.18194.9.camel@localhost.localdomain> My mail client did not seem to attach the patch when I resent. Here, Jonathan Taylor. Botany Department, University of Toronto. On Thu, 2005-01-13 at 02:36 -0500, Jonathan Taylor wrote: > Hi, > > My last message got caught by the spam guard for some reason so excuse > the odd subject line. > > I am doing quite a bit of infrastructure work using biopython. As I run > into problems I will try to make the code available to the biopython > project as appropriate. > > Here is a small patch: > - allows you to easily figure out the return code of an application run > through the Bio.Application framework > - adds Fastacmd functionality to the Bio.Application framework > > Any problems, just respond to the list as I monitor it regularly. > > Regards, > Jonathan Taylor. > Botany Department, University of Toronto. > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From jonathan.taylor at utoronto.ca Thu Jan 13 07:50:20 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Application instances code In-Reply-To: <1105601819.18194.6.camel@localhost.localdomain> References: <1105601819.18194.6.camel@localhost.localdomain> Message-ID: <1105620620.18194.27.camel@localhost.localdomain> http://bbc.botany.utoronto.ca/~jtaylor/biopython-bio_application-return_code_and_fastacmd_support.diff.patch jon. On Thu, 2005-01-13 at 02:36 -0500, Jonathan Taylor wrote: > Hi, > > My last message got caught by the spam guard for some reason so excuse > the odd subject line. > > I am doing quite a bit of infrastructure work using biopython. As I run > into problems I will try to make the code available to the biopython > project as appropriate. > > Here is a small patch: > - allows you to easily figure out the return code of an application run > through the Bio.Application framework > - adds Fastacmd functionality to the Bio.Application framework > > Any problems, just respond to the list as I monitor it regularly. > > Regards, > Jonathan Taylor. > Botany Department, University of Toronto. > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From jonathan.taylor at utoronto.ca Thu Jan 13 07:52:24 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Can we turn off the spam filter? Message-ID: <1105620744.18194.30.camel@localhost.localdomain> I had a terrible time trying to post a patch. I think it would not accept anything with an attachment. In any case if the list is members only then do we really need a spam filter? Regards, Jonathan Taylor. From jonathan.taylor at utoronto.ca Thu Jan 13 07:38:19 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Application instances code In-Reply-To: <1105601819.18194.6.camel@localhost.localdomain> References: <1105601819.18194.6.camel@localhost.localdomain> Message-ID: <1105619899.18194.18.camel@localhost.localdomain> my apologies. On Thu, 2005-01-13 at 02:36 -0500, Jonathan Taylor wrote: > Hi, > > My last message got caught by the spam guard for some reason so excuse > the odd subject line. > > I am doing quite a bit of infrastructure work using biopython. As I run > into problems I will try to make the code available to the biopython > project as appropriate. > > Here is a small patch: > - allows you to easily figure out the return code of an application run > through the Bio.Application framework > - adds Fastacmd functionality to the Bio.Application framework > > Any problems, just respond to the list as I monitor it regularly. > > Regards, > Jonathan Taylor. > Botany Department, University of Toronto. > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython-bio_application-return_code_and_fastacmd_support.diff.patch Type: text/x-patch Size: 3149 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20050113/187dbd2c/biopython-bio_application-return_code_and_fastacmd_support.diff.bin From jonathan.taylor at utoronto.ca Thu Jan 13 07:45:15 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Application instances code for biopython In-Reply-To: <1105604278.18194.9.camel@localhost.localdomain> References: <1105601819.18194.6.camel@localhost.localdomain> <1105604278.18194.9.camel@localhost.localdomain> Message-ID: <1105620315.18194.21.camel@localhost.localdomain> my apologies. Jon. P.S. Can someone please turn down the spam filter. On Thu, 2005-01-13 at 03:17 -0500, Jonathan Taylor wrote: > My mail client did not seem to attach the patch when I resent. > > Here, > Jonathan Taylor. > Botany Department, University of Toronto. > > > On Thu, 2005-01-13 at 02:36 -0500, Jonathan Taylor wrote: > > Hi, > > > > My last message got caught by the spam guard for some reason so excuse > > the odd subject line. > > > > I am doing quite a bit of infrastructure work using biopython. As I run > > into problems I will try to make the code available to the biopython > > project as appropriate. > > > > Here is a small patch: > > - allows you to easily figure out the return code of an application run > > through the Bio.Application framework > > - adds Fastacmd functionality to the Bio.Application framework > > > > Any problems, just respond to the list as I monitor it regularly. > > > > Regards, > > Jonathan Taylor. > > Botany Department, University of Toronto. > > > > _______________________________________________ > > 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython-bio_application-return_code_and_fastacmd_support.diff.patch Type: text/x-patch Size: 3149 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20050113/d9b7b440/biopython-bio_application-return_code_and_fastacmd_support.diff.bin From jonathan.taylor at utoronto.ca Thu Jan 13 07:48:29 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Finished writing the update In-Reply-To: <1105601819.18194.6.camel@localhost.localdomain> References: <1105601819.18194.6.camel@localhost.localdomain> Message-ID: <1105620509.18194.24.camel@localhost.localdomain> Let's try this header. Jon. P.S. the spam filter is crazy for this list. If its invite only can we not turn it off? On Thu, 2005-01-13 at 02:36 -0500, Jonathan Taylor wrote: > Hi, > > My last message got caught by the spam guard for some reason so excuse > the odd subject line. > > I am doing quite a bit of infrastructure work using biopython. As I run > into problems I will try to make the code available to the biopython > project as appropriate. > > Here is a small patch: > - allows you to easily figure out the return code of an application run > through the Bio.Application framework > - adds Fastacmd functionality to the Bio.Application framework > > Any problems, just respond to the list as I monitor it regularly. > > Regards, > Jonathan Taylor. > Botany Department, University of Toronto. > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython-bio_application-return_code_and_fastacmd_support.diff.patch Type: text/x-patch Size: 3149 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20050113/415e83b6/biopython-bio_application-return_code_and_fastacmd_support.diff.bin From idoerg at burnham.org Thu Jan 13 12:15:11 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Can we turn off the spam filter? In-Reply-To: <1105620744.18194.30.camel@localhost.localdomain> References: <1105620744.18194.30.camel@localhost.localdomain> Message-ID: <41E6AC9F.4060809@burnham.org> Jonathan Taylor wrote: >I had a terrible time trying to post a patch. I think it would not >accept anything with an attachment. > >In any case if the list is members only then do we really need a spam >filter? > >Regards, >Jonathan Taylor. > >_______________________________________________ >Biopython-dev mailing list >Biopython-dev@biopython.org >http://biopython.org/mailman/listinfo/biopython-dev > > > > Jonathan, Thanks for the patch, and sorry for the frustration this caused you. I'll patch and commit this to CVS. 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) 713 9930 http://ffas.ljcrf.edu/~iddo From jonathan.taylor at utoronto.ca Thu Jan 13 12:31:36 2005 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] Can we turn off the spam filter? In-Reply-To: <41E6AC9F.4060809@burnham.org> References: <1105620744.18194.30.camel@localhost.localdomain> <41E6AC9F.4060809@burnham.org> Message-ID: <1105637496.18194.33.camel@localhost.localdomain> No problem. Sorry for all the posts. I thought those ones were not going to make it to the list since I got emails saying mailman thought they were spam. I'll prob have a few more patches coming in the next month or so. Cheers. Jon. On Thu, 2005-01-13 at 09:15 -0800, Iddo Friedberg wrote: > Jonathan Taylor wrote: > > >I had a terrible time trying to post a patch. I think it would not > >accept anything with an attachment. > > > >In any case if the list is members only then do we really need a spam > >filter? > > > >Regards, > >Jonathan Taylor. > > > >_______________________________________________ > >Biopython-dev mailing list > >Biopython-dev@biopython.org > >http://biopython.org/mailman/listinfo/biopython-dev > > > > > > > > > > Jonathan, > > Thanks for the patch, and sorry for the frustration this caused you. > I'll patch and commit this to CVS. > > Iddo > From bugzilla-daemon at portal.open-bio.org Mon Jan 17 09:52:02 2005 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 1733] compiler recognition in setup.py Message-ID: <200501171452.j0HEq2kc010627@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1733 ------- Additional Comments From MBatLE@gmx.de 2005-01-17 09:52 ------- The consequence in that the 'Bio.KDTree._CKDTree' extension cant get build. The relevant output of setup.py is: building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-i686-2.3/Bio/KDTree -I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o build/temp.linux-i686-2.3/Bio/KDTree/KDTree.swig.o unable to execute -I/usr/include/python2.3: No such file or directory error: command '-I/usr/include/python2.3' failed with exit status 1 ------- 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 Jan 17 09:47:39 2005 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 1733] New: compiler recognition in setup.py Message-ID: <200501171447.j0HElcDe010590@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1733 Summary: compiler recognition in setup.py Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: major Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: MBatLE@gmx.de in function build_extension (setup.py line 178) the c++ compiler cant get determined in my installation. My os.environ looks the following: {'SSH_ASKPASS': '/usr/bin/gtk2-ssh-askpass', 'LESS': '-R', 'LESSOPEN': '|lesspipe.sh %s', 'CVS_RSH': 'ssh', 'LOGNAME': 'root', 'USER': 'root', 'INPUTRC': '/etc/inputrc', 'QTDIR': '/usr/qt/3', 'PATH': '/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/3.3.5:/opt/ati/bin:/opt/Acrobat5:/usr/X11R6/bin:/opt/blackdown-jdk-1.4.2.01/bin:/opt/blackdown-jdk-1.4.2.01/jre/bin:/usr/qt/3/bin:/usr/kde/3.3/sbin:/usr/kde/3.3/bin', 'PS1': '\\[\\033[01;31m\\]\\h \\[\\033[01;34m\\]\\W \\$ \\[\\033[00m\\]', 'DISPLAY': ':0.0', 'KDEDIR': '/usr/kde/3.3', 'TERM': 'Eterm', 'SHELL': '/bin/bash', 'JDK_HOME': '/opt/blackdown-jdk-1.4.2.01', 'SHLVL': '1', 'CONFIG_PROTECT_MASK': '/etc/gconf /etc/terminfo', 'G_BROKEN_FILENAMES': '1', 'QMAKESPEC': 'linux-g++', 'EDITOR': '/bin/nano', 'MANPATH': '/usr/share/man:/usr/local/share/man:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/man:/usr/X11R6/man::/opt/blackdown-jdk-1.4.2.01/man:/usr/qt/3/doc/man', 'JAVA_HOME': '/opt/blackdown-jdk-1.4.2.01', 'HOME': '/root', 'KDE_MALLOC': '1', 'INFODIR': '/usr/share/info', 'INFOPATH': '/usr/share/info:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/info', 'GCCBITS': '', 'CLASSPATH': '.', 'PLAT': 'linux-i686', 'XINITRC': '/etc/X11/xinit/xinitrc', 'MOZILLA_FIVE_HOME': '/usr/lib/mozilla', 'XAUTHORITY': '/root/.xauth78ixrX', 'KDEDIRS': '/usr', '_': '/usr/bin/python', 'JAVAC': '/opt/blackdown-jdk-1.4.2.01/bin/javac', 'ANT_HOME': '/usr/share/ant-core', 'GDK_USE_XFT': '1', 'OLDPWD': '/root', 'HOSTNAME': 'gkws3', 'CONFIG_PROTECT': '/usr/lib/mozilla/defaults/pref /usr/X11R6/lib/X11/xkb /usr/kde/3.3/share/config /usr/kde/3.3/env /usr/kde/3.3/shutdown /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/xdvi/ /usr/share/config', 'PWD': '/tmp/biopython', 'SGML_CATALOG_FILES': '/etc/sgml/sgml-ent.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/openjade-1.3.2.cat:/etc/sgml/sgml-docbook-4.1.cat:/etc/sgml/sgml-docbook-4.0.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.0.cat:/etc/sgml/sgml-docbook-3.1.cat:/etc/sgml/sgml-lite.cat', 'MAIL': '/root/', 'PAGER': '/usr/bin/less', 'PYTHONDOCS': '/usr/share/doc/python-docs-2.3.4/html'} {'SSH_ASKPASS': '/usr/bin/gtk2-ssh-askpass', 'LESS': '-R', 'LESSOPEN': '|lesspipe.sh %s', 'CVS_RSH': 'ssh', 'LOGNAME': 'root', 'USER': 'root', 'INPUTRC': '/etc/inputrc', 'QTDIR': '/usr/qt/3', 'PATH': '/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/3.3.5:/opt/ati/bin:/opt/Acrobat5:/usr/X11R6/bin:/opt/blackdown-jdk-1.4.2.01/bin:/opt/blackdown-jdk-1.4.2.01/jre/bin:/usr/qt/3/bin:/usr/kde/3.3/sbin:/usr/kde/3.3/bin', 'PS1': '\\[\\033[01;31m\\]\\h \\[\\033[01;34m\\]\\W \\$ \\[\\033[00m\\]', 'DISPLAY': ':0.0', 'KDEDIR': '/usr/kde/3.3', 'TERM': 'Eterm', 'SHELL': '/bin/bash', 'JDK_HOME': '/opt/blackdown-jdk-1.4.2.01', 'SHLVL': '1', 'CONFIG_PROTECT_MASK': '/etc/gconf /etc/terminfo', 'G_BROKEN_FILENAMES': '1', 'QMAKESPEC': 'linux-g++', 'EDITOR': '/bin/nano', 'MANPATH': '/usr/share/man:/usr/local/share/man:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/man:/usr/X11R6/man::/opt/blackdown-jdk-1.4.2.01/man:/usr/qt/3/doc/man', 'JAVA_HOME': '/opt/blackdown-jdk-1.4.2.01', 'HOME': '/root', 'KDE_MALLOC': '1', 'INFODIR': '/usr/share/info', 'INFOPATH': '/usr/share/info:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/info', 'GCCBITS': '', 'CLASSPATH': '.', 'PLAT': 'linux-i686', 'XINITRC': '/etc/X11/xinit/xinitrc', 'MOZILLA_FIVE_HOME': '/usr/lib/mozilla', 'XAUTHORITY': '/root/.xauth78ixrX', 'KDEDIRS': '/usr', '_': '/usr/bin/python', 'JAVAC': '/opt/blackdown-jdk-1.4.2.01/bin/javac', 'ANT_HOME': '/usr/share/ant-core', 'GDK_USE_XFT': '1', 'OLDPWD': '/root', 'HOSTNAME': 'gkws3', 'CONFIG_PROTECT': '/usr/lib/mozilla/defaults/pref /usr/X11R6/lib/X11/xkb /usr/kde/3.3/share/config /usr/kde/3.3/env /usr/kde/3.3/shutdown /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/xdvi/ /usr/share/config', 'PWD': '/tmp/biopython', 'SGML_CATALOG_FILES': '/etc/sgml/sgml-ent.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/openjade-1.3.2.cat:/etc/sgml/sgml-docbook-4.1.cat:/etc/sgml/sgml-docbook-4.0.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.0.cat:/etc/sgml/sgml-docbook-3.1.cat:/etc/sgml/sgml-lite.cat', 'MAIL': '/root/', 'PAGER': '/usr/bin/less', 'PYTHONDOCS': '/usr/share/doc/python-docs-2.3.4/html'} and (the elif fallback) wont get g++ because : self.compiler.compiler_cxx = [] ------- 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 Tue Jan 18 03:27:07 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1733] compiler recognition in setup.py In-Reply-To: <200501171452.j0HEq2kc010627@portal.open-bio.org> References: <200501171452.j0HEq2kc010627@portal.open-bio.org> Message-ID: <41ECC85B.2010702@ims.u-tokyo.ac.jp> Compiling the two C++ modules Bio.KDTree and Bio.Affy has been a recurring problem for many Biopython users. From the KDTree source code, it seems that KDTree is implemented in C++ for the benefit of speed of the algorithms in KDTree.cpp. Can these routines be implemented in C or (better yet) using Numerical Python? Currently, Bio.KDTree is not included with the Windows installer either, because of compilation problems, and it would be nice to make this extension available to as many Biopython users as possible. On the other hand, compilation errors such as below may scare off new users, even if they are not planning to use Bio.KDTree and Bio.Affy, so it may be better to skip by default compilation of these extensions in setup.py. Thomas, any suggestions? --Michiel. bugzilla-daemon@portal.open-bio.org wrote: > http://bugzilla.open-bio.org/show_bug.cgi?id=1733 > > > > > > ------- Additional Comments From MBatLE@gmx.de 2005-01-17 09:52 ------- > The consequence in that the 'Bio.KDTree._CKDTree' extension cant get build. > The relevant output of setup.py is: > > building 'Bio.KDTree._CKDTree' extension > creating build/temp.linux-i686-2.3/Bio/KDTree > -I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o > build/temp.linux-i686-2.3/Bio/KDTree/KDTree.swig.o > unable to execute -I/usr/include/python2.3: No such file or directory > error: command '-I/usr/include/python2.3' failed with exit status 1 > > > > > ------- You are receiving this mail because: ------- > You are the assignee for the bug, or are watching the assignee. > _______________________________________________ > 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 thamelry at binf.ku.dk Tue Jan 18 02:38:16 2005 From: thamelry at binf.ku.dk (thamelry@binf.ku.dk) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1733] compiler recognition in setup.py In-Reply-To: <41ECC85B.2010702@ims.u-tokyo.ac.jp> References: <200501171452.j0HEq2kc010627@portal.open-bio.org> <41ECC85B.2010702@ims.u-tokyo.ac.jp> Message-ID: <33213.80.164.86.229.1106033896.squirrel@www.binf.ku.dk> > From the KDTree source code, it seems > that KDTree is implemented in C++ for the benefit of speed Correct. > Can these routines be implemented in C or (better yet) using > Numerical Python? An implementation in C is of course possible. A Numpy implementation is too slow (the KDTree prototype made use of Python/Numpy). But the problem really lies with Distutils: it does not deal well with C++ code. I don't think KDTree will be missed by many Biopython people, so it can be left out as far as I am concerned. It probably makes sense to make it available as an independent package (I know some astronomers are using it to study star maps for example :-). Best regards, -Thomas From mdehoon at ims.u-tokyo.ac.jp Wed Jan 19 08:54:58 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1733] compiler recognition in setup.py In-Reply-To: <33213.80.164.86.229.1106033896.squirrel@www.binf.ku.dk> References: <200501171452.j0HEq2kc010627@portal.open-bio.org> <41ECC85B.2010702@ims.u-tokyo.ac.jp> <33213.80.164.86.229.1106033896.squirrel@www.binf.ku.dk> Message-ID: <41EE66B2.3060209@ims.u-tokyo.ac.jp> Thanks, Thomas. Then unless somebody objects, I will switch off compilation of KDTree by default in setup.py, but still have it included with the Biopython source distribution. --Michiel. thamelry@binf.ku.dk wrote: >>From the KDTree source code, it seems >>that KDTree is implemented in C++ for the benefit of speed > > > Correct. > > >>Can these routines be implemented in C or (better yet) using >>Numerical Python? > > > An implementation in C is of course possible. A Numpy implementation is > too slow (the KDTree prototype made use of Python/Numpy). But the problem > really lies with Distutils: it does not deal well with C++ code. > > I don't think KDTree will be missed by many Biopython people, so it can be > left out as far as I am concerned. It probably makes sense to make it > available as an independent package (I know some astronomers are using it > to study star maps for example :-). > > Best regards, > > -Thomas > > > > > > > > -- 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 thamelry at binf.ku.dk Wed Jan 19 09:18:27 2005 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:56 2005 Subject: [Biopython-dev] [Bug 1733] compiler recognition in setup.py In-Reply-To: <41EE66B2.3060209@ims.u-tokyo.ac.jp> References: <200501171452.j0HEq2kc010627@portal.open-bio.org> <33213.80.164.86.229.1106033896.squirrel@www.binf.ku.dk> <41EE66B2.3060209@ims.u-tokyo.ac.jp> Message-ID: <200501191518.27328.thamelry@binf.ku.dk> On Wednesday 19 January 2005 14:54, Michiel Jan Laurens de Hoon wrote: > Thanks, Thomas. Then unless somebody objects, I will switch off compilation > of KDTree by default in setup.py, but still have it included with the > Biopython source distribution. That's fine by me. -Thomas From dlondon at ebi.ac.uk Thu Jan 20 12:58:59 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] BOSC 2005 Message-ID: <20050120175859.GA7254@parrot.ebi.ac.uk> {Please pass the word!} MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2006, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Email: bosc@open-bio.org FEES TO BE ANNOUNCED. Watch the bosc website for more information. SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2005. If you are interested in giving a software demonstration at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php SESSION CHAIRS WANTED If you would like to be involved BOSC 2005, we invite you to chair a session. This will not require much of your time. You will be given a schedule of presenters during your session. You simply introduce each speaker, and manage the time of their presentation (25 minutes for full presentations, 5-10 minutes for lightning talks/demos, depending on the number of entries). If you are interested in chairing a session, please send us your name and affiliation (if applicable). -- cheers, Darin London dlondon@ebi.ac.uk European Bioinformatics Institute, +44 (0)1223 49 2566 Wellcome Trust Genome Campus, Hinxton +44 (0)1223 49 4468 (fax) Cambridgeshire CB10 1SD, UK -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20050120/9bb1da79/attachment.bin From biopython-dev at maubp.freeserve.co.uk Thu Jan 20 13:35:47 2005 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] GenBank feature iterator Message-ID: <41EFFA03.7050202@maubp.freeserve.co.uk> Hello I'm trying to use BioPython to parse bacterial genomes from the NCBI:- ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ My initial impression is that all of the Bio.GenBank methods scale very badly with the size of the input file. For example, Nanoarchaeum equitans, file NC_005213.gbk is about 1.2 MB, and can be loaded in about one minute using either the FeatureParser or the RecordParser. ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk However, for larger files the parser seems to run out of system resources, or maybe requires more time than I have been prepared to give it. e.g. E. coli K12, file NC_000913.gbk (about 10MB):- ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K12/ See also related posts in November 2004, e.g. http://biopython.org/pipermail/biopython/2004-November/002470.html To avoid the memory issues, I would like to make a single pass though the file, iterating over the features (in particular, the CDS features) one by one into SeqFeature objects (not holding them all in memory at once). I have tried using the GenBank.Iterator, but as far as I can tell this reads in a file and each "step" is an entire plasmid/chromosome (the code looks for the LOCUS line). It would seem that I would need: A new "FeatureIterator", ideally using the existing Martel and mxTextTools 'regular expressions on steroids' framework (which does seem rather overwhelming!). and: A modified version of the FeatureParser to return (just) SeqFeature objects. Any thoughts? Thanks Peter -- PhD Student MOAC Doctoral Training Centre University of Warwick, UK From mdehoon at ims.u-tokyo.ac.jp Fri Jan 21 04:21:05 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] Re: [BioPython] build errors. "recompile with -fPIC" Biopython1.30 and CVS, Python2.3, SuSE 9.1, AMD64 . Solution Found In-Reply-To: References: Message-ID: <41F0C981.4050700@ims.u-tokyo.ac.jp> Thanks. I have updated setup.py in CVS. Metzidis Anthony wrote: > Hi, > Thanks for following up on the problem. > > Taking your advice, I started from the original setup.py from CVS, and > removed lines 201-202 as you instructed. The build completed > successfully. > > Best, > Tony > > -----Original Message----- > From: Michiel Jan Laurens de Hoon [mailto:mdehoon@ims.u-tokyo.ac.jp] > Sent: Friday, January 21, 2005 6:24 AM > To: Metzidis Anthony; Biopython mailing list > Subject: Re: [BioPython] build errors. "recompile with -fPIC" > Biopython1.30 and CVS, Python2.3, SuSE 9.1, AMD64 . Solution Found > > Hi Metzidis, > > Thanks for the patch. It seems though that removing the hacks completely > would > break compilation under Python 2.2, which is still supported by > Biopython. The > problem can be solved more easily by removing lines 201-202 in setup.py: > > elif build: # fix for 2.3, only if we are making C++ > modules > self.compiler.compiler_so = self.compiler.compiler_cxx > > Could you try and see if that fixes the compilation problem on your > machine? > > Compilation of KDTree is likely to be switched off by default in future > versions > of biopython because of recurring compilation problems on various > problems, but > it would be nice to fix setup.py as much as possible anyway for people > who want > to use it. > > --Michiel. > > > > Metzidis Anthony wrote: > > >>Hello everyone, >> >> >> >>My Biopython (both version 1.30 and CVS) build failed with the error >>"recompile with -fPIC" on the file Bio/KDTree/KDTree.o. >> >> >> >>I'm using BioPython CVS and 1.30, Python 2.3 on SuSE 9.1, AMD64. >> >> >> >>I discovered that the problem was caused by some old hacks in setup.py >>that altered the compilation of some c++ extensions. Those hacks were >>relevant to Python 2.2 (according to the documentation), but > > conflicted > >>with python 2.3 >> >> >> >>The solution was to remove those 'hacks'. After that, the build >>proceeded successfully. >> >> >> >>I've attached a patch to the current CVS version of setup.py. It > > seems > >>to apply to biopython 1.30 as well. >> >> >> >>Perhaps one of the developers could integrate the ideas in the patch >>into the code. >> >> >> >>Hope this helps someone! >> >> >> >>Have a great day! >> >> >> >>Best, >> >>Tony >> >> >> >> >> >> >> >> >> >> >> > > ------------------------------------------------------------------------ > >>_______________________________________________ >>BioPython mailing list - BioPython@biopython.org >>http://biopython.org/mailman/listinfo/biopython > > -- 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 Jan 21 03:29:39 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] [Bug 1735] Bio.Blast.NCBIStandalone.BlastParser crashs with unusual alignment fragments Message-ID: <200501210829.j0L8TdUG017823@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1735 ------- Additional Comments From gebauer-jung@ice.mpg.de 2005-01-21 03:29 ------- Created an attachment (id=191) --> (http://bugzilla.open-bio.org/attachment.cgi?id=191&action=view) blast output with unusual fragment ------- 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 Fri Jan 21 03:26:54 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] [Bug 1735] New: Bio.Blast.NCBIStandalone.BlastParser crashs with unusual alignment fragments Message-ID: <200501210826.j0L8Qski017798@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1735 Summary: Bio.Blast.NCBIStandalone.BlastParser crashs with unusual alignment fragments Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: gebauer-jung@ice.mpg.de This is possibly rather a problem of the blastall program than a bug of the parser, but maybe the parser should be able to handle it. I will attach the blast output which crashes the parser due to the crazy fragment within the last alignment. Following parameters were used for blastall: -p blastn -F F (filter off) -g (gapped blast) -G 1 (gap opening penalty) -E 1 (gap extension penalty) The parser crashes with the message: SyntaxError: I could not find the query in line Query: 0 -- Thanks ------- 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 Jan 26 17:39:04 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] [Bug 1740] New: change in GenBank.NCBIDictionary() Message-ID: <200501262239.j0QMd4XR001042@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1740 Summary: change in GenBank.NCBIDictionary() Product: Biopython Version: Not Applicable Platform: All URL: http://www.biopython.org/docs/tutorial/Tutorial004.html# toc13 OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Documentation AssignedTo: biopython-dev@biopython.org ReportedBy: andrea@salilab.org In the tutorial and cookbook the python statement >>> ncbi_dict = GenBank.NCBIDictionary() should be changed to something like >>> ncbi_dict = GenBank.NCBIDictionary(database='nucleotide', format = 'genbank') --- The current statement produce the following error message: Traceback (most recent call last): File "./parse_pfam.py", line 234, in ? main() File "./parse_pfam.py", line 228, in main example_genbank() File "./parse_pfam.py", line 150, in example_genbank ncbi_dict = GenBank.NCBIDictionary() TypeError: __init__() takes at least 3 arguments (1 given) --- This is my first bug I ever submitted. ;-) Hope the format is fine! ;-) Andrea ------- 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 Thu Jan 27 17:14:53 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] [Bug 1741] New: Bug in fasta consumer in Doc/tutorial.tex and Doc/examples/ Message-ID: <200501272214.j0RMErOG017867@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1741 Summary: Bug in fasta consumer in Doc/tutorial.tex and Doc/examples/ Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Documentation AssignedTo: biopython-dev@biopython.org ReportedBy: andrea@salilab.org Overview: --------- Script fasta_consumer.py in Doc/examples doesn't work Steps to Reproduce: ------------------- python fasta_consumer.py Actual Results: ------------- Traceback (most recent call last): File "fasta_consumer.py", line 35, in ? all_species = extract_organisms("ls_orchid.fasta", 94) File "fasta_consumer.py", line 21, in extract_organisms scanner = Fasta._Scanner() AttributeError: 'module' object has no attribute '_Scanner' Expected Results: ----------------- number of species: 92 species names: ['C.irapeanum', 'C.californicum', 'C.fasciculatum', 'C.margaritaceum', 'C.lichiangense', 'C.yatabeanum', 'C.guttatum', ... ------- 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 Jan 28 04:40:32 2005 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] Re: [BioPython] documentation issues In-Reply-To: <200501272056.j0RKuV5c026299@guitar.compbio.ucsf.edu> References: <200501272056.j0RKuV5c026299@guitar.compbio.ucsf.edu> Message-ID: <41FA0890.3090803@ims.u-tokyo.ac.jp> andrea rossi wrote: > from Bio import GenBank > > gi_list = GenBank.search_for("Opuntia AND rpl16") > print " gi_list[0] ", gi_list[0] > > I get the message: > > gi_list[0] Error: Sequence Viewer does not have any Presentations > for code='uilist_text' > > instead of: > > ['6273291', '6273290', '6273289', '6273287', '6273286', '6273285', > '6273284'] It seems that NCBI no longer accepts the "uilist" identifier. E.g. try the url http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&tool=EUtils_P ython_client&db=nucleotide&email=biopython-dev%40biopython.org&rettype=uilist&id =6273291 Does anybody know what this should be? -- 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 hoffman at ebi.ac.uk Fri Jan 28 09:37:30 2005 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] Re: documentation issues In-Reply-To: <41FA0890.3090803@ims.u-tokyo.ac.jp> References: <200501272056.j0RKuV5c026299@guitar.compbio.ucsf.edu> <41FA0890.3090803@ims.u-tokyo.ac.jp> Message-ID: On Fri, 28 Jan 2005, Michiel Jan Laurens de Hoon wrote: > It seems that NCBI no longer accepts the "uilist" identifier. E.g. try the > url > > http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&tool=EUtils_P > ython_client&db=nucleotide&email=biopython-dev%40biopython.org&rettype=uilist&id > =6273291 It works for PubMed, just not for nucleotide. -- Michael Hoffman European Bioinformatics Institute From biopython-dev at maubp.freeserve.co.uk Sun Jan 30 06:13:58 2005 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] GenBank feature iterator In-Reply-To: <41EFFA03.7050202@maubp.freeserve.co.uk> References: <41EFFA03.7050202@maubp.freeserve.co.uk> Message-ID: <41FCC176.9070203@maubp.freeserve.co.uk> I wrote: > I'm trying to use BioPython to parse bacterial genomes from the NCBI:- > > ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ > > My initial impression is that all of the Bio.GenBank methods scale very > badly with the size of the input file. More detailed testing would appear to confirm this. On the bright side, I haven't actually run into any errors parsing unknown formats. > For example, Nanoarchaeum equitans, file NC_005213.gbk is about 1.2 MB, > and can be loaded in about one minute using either the FeatureParser or > the RecordParser. > > ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk > > However, for larger files the parser seems to run out of system > resources, or maybe requires more time than I have been prepared to give > it. e.g. E. coli K12, file NC_000913.gbk (about 10MB):- > > ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K12/ While my laptop did not have sufficient RAM to deal with this file, my desktop could in about three minutes - see below. > See also related posts in November 2004, e.g. > > http://biopython.org/pipermail/biopython/2004-November/002470.html I have been doing some testing on this, and more memory makes a marked difference in the size of GenBank file that can be loaded (comparing my laptop and home desktop). The following times and memory usage figures are on Windows 2000, Python 2.3 running the attached script from idle. NC_003065.gbk 480 kb, 4 seconds, 28 MB RAM NC_003064.gbk 1,217 kb, 11 seconds, 56 MB RAM NC_000854.gbk 3,391 kb, 45 seconds, 165 MB RAM NC_003063.gbk 4,725 kb, 55 seconds, 195 MB RAM NC_003062.gbk 6,574 kb, 88 seconds, 268 MB RAM NC_005966.gbk 8,858 kb, 139 seconds, 372 MB RAM NC_000913.gbk 10,267 kb, 171 seconds, 409 MB RAM NC_000962.gbk 11,010 kb, 200 seconds, 486 MB RAM NC_003997.gbk 12,026 kb, 228 seconds, 496 MB RAM NC_002678.gbk 15,120 kb, 306 seconds, 586 MB RAM The computer was a 2.26 GHz Intel Pentium 4, with 735 MB RAM. For larger files (e.g. NC_005027.gbk at 18,211 kb) the system would run out of memory and begin paging to disk. For this particular example, the test eventually completed in half an hour. I have not performed this test under Linux, but a couple of examples suggests the behaviour is similar. In consuming these vast amounts of memory is the GenBank parser really running "as designed"? It is conceivable that as smaller genomes have tended to be sequenced first, that the parser was not originally expected to have to deal with such large genomes. Or is there a bug here? > To avoid the memory issues, I would like to make a single pass though > the file, iterating over the features (in particular, the CDS features) > one by one into SeqFeature objects (not holding them all in memory at > once). > > I have tried using the GenBank.Iterator, but as far as I can tell this > reads in a file and each step is an entire plasmid/chromosome (the > code looks for the LOCUS line). > > It would seem that I would need: > > A new FeatureIterator, ideally using the existing Martel and > mxTextTools 'regular expressions on steroids' framework (which does seem > rather overwhelming!). > > and: > > A modified version of the FeatureParser to return (just) SeqFeature > objects. I have tried (and so far failed) to understand how the Martel and mxTextTools parser, and thus modify it in the way I had hoped. Peter -- Here is the script, inline rather than as an attachment, which the mailing list didn't like: #Following is based on example code from #http://www.biopython.org/docs/tutorial/Tutorial.html #3.4.2 Parsing GenBank records #The example files are all from the NCBI's ftp site, #ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ import time from Bio import GenBank #The following times and memory usage figures are on Windows 2000, Python 2.3 running this script from idle. #The computer was a 2.26 GHz Intel Pentium 4, with 735 MB RAM. #The memory usage is at the end of the script, rather than the peak value which is slightly higher, as recorded #by the windows task manager's process watch. gb_file = "C:\\genomes\\Bacteria\\Agrobacterium_tumefaciens_C58_Cereon\\NC_003065.gbk" # 480 kb, 4 seconds, 28 MB RAM gb_file = "C:\\genomes\\Bacteria\\Agrobacterium_tumefaciens_C58_Cereon\\NC_003064.gbk" # 1,217 kb, 11 seconds, 56 MB RAM gb_file = "C:\\genomes\\Bacteria\\Aeropyrum_pernix\\NC_000854.gbk" # 3,391 kb, 45 seconds, 165 MB RAM gb_file = "C:\\genomes\\Bacteria\\Agrobacterium_tumefaciens_C58_Cereon\\NC_003063.gbk" # 4,725 kb, 55 seconds, 195 MB RAM gb_file = "C:\\genomes\\Bacteria\\Agrobacterium_tumefaciens_C58_Cereon\\NC_003062.gbk" # 6,574 kb, 88 seconds, 268 MB RAM gb_file = "C:\\genomes\\Bacteria\\Acinetobacter_sp_ADP1\\NC_005966.gbk" # 8,858 kb, 139 seconds, 372 MB RAM gb_file = "C:\\genomes\\Bacteria\\Escherichia_coli_K12\\NC_000913.gbk" # 10,267 kb, 171 seconds, 409 MB RAM gb_file = "C:\\genomes\\Bacteria\\Mycobacterium_tuberculosis_H37Rv\\NC_000962.gbk" # 11,010 kb, 200 seconds, 486 MB RAM gb_file = "C:\\genomes\\Bacteria\\Bacillus_anthracis_Ames\\NC_003997.gbk" # 12,026 kb, 228 seconds, 496 MB RAM gb_file = "C:\\genomes\\Bacteria\\Mesorhizobium_loti\\NC_002678.gbk" # 15,120 kb, 306 seconds, 586 MB RAM #During the following file, Windows ran out of RAM and was paging to the hard disk #almost continuously. After six minures, peak memory usage had been about 700MB and #I killed the process. Running this script from the command prompt rather than idle #took 30 minutes, however I do not have a memory usage figure on this: #gb_file = "C:\\genomes\\Bacteria\\Pirellula_sp\\NC_005027.gbk" # 18,211 kb #The following are even larger test examples, that I have not atempted: #gb_file = "C:\\genomes\\Bacteria\\Bradyrhizobium_japonicum\\NC_004463.gbk" # 19,500 kb #gb_file = "C:\\genomes\\Bacteria\\Streptomyces_coelicolor\\NC_003888.gbk" # 24,390 kb gb_handle = open(gb_file, 'r') feature_parser = GenBank.FeatureParser() start_time = time.time() gb_iterator = GenBank.Iterator(gb_handle, feature_parser) count = 0 while 1: print "Staring...", cur_record = gb_iterator.next() print "Done" if cur_record is None: break count = count + 1 # now do something with the record print count, cur_record.name, len(cur_record.features), len(cur_record.seq) job_time = time.time() - start_time print "Time elapsed %0.2f seconds" % job_time From biopython-dev at maubp.freeserve.co.uk Sun Jan 30 06:51:02 2005 From: biopython-dev at maubp.freeserve.co.uk (Peter) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] Can we turn off the spam filter? In-Reply-To: <1105620744.18194.30.camel@localhost.localdomain> References: <1105620744.18194.30.camel@localhost.localdomain> Message-ID: <41FCCA26.6010507@maubp.freeserve.co.uk> Jonathan Taylor wrote: > I had a terrible time trying to post a patch. I think it would not > accept anything with an attachment. > > In any case if the list is members only then do we really need a spam > filter? Its not just you it doesn't like, my message (sent 28 Jan 2004) with a Python script (plain text with a .py extension) was also held for moderator approval because: "Message has a suspicious header" (I cancelled it and sent the script in the body rather than as an attachment) Perhaps as a compromise, we should allow a few "harmless" attachment types like .txt, .py and .diff (and continue to block things like .exe and other windows executables). Peter From thamelry at binf.ku.dk Fri Jan 28 05:05:58 2005 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:57 2005 Subject: [Biopython-dev] New release? In-Reply-To: <41FA0890.3090803@ims.u-tokyo.ac.jp> References: <200501272056.j0RKuV5c026299@guitar.compbio.ucsf.edu> <41FA0890.3090803@ims.u-tokyo.ac.jp> Message-ID: <200501281105.58133.thamelry@binf.ku.dk> Hi everybody, Shouldn't we have a new release of Biopython soon? The last release dates from May 2004 (!). In the case of Bio.PDB for example, the CVS version contains a whole load of bugfixes and new features. I guess the same applies to other modules. Cheers, -- Thomas Hamelryck, Postdoctoral researcher Bioinformatics center University of Copenhagen Universitetsparken 15 Bygning 10 2100 Copenhagen, Denmark --- http://www.binf.ku.dk/users/thamelry/