From aloraine at gmail.com Sun May 6 09:40:43 2007 From: aloraine at gmail.com (Ann Loraine) Date: Sun, 6 May 2007 08:40:43 -0500 Subject: [BioPython] advice on structuring packages Message-ID: <83722dde0705060640t12799641q5b4454544e869325@mail.gmail.com> Dear friends, My group is getting ready to distribute some python modules and also to migrate some of our code to a publicly-accessible cvs repository. For the migration, we would like to restructure our cvs directory layout so as to be more compatible with community standards. We could really use some good ideas and suggestions on how to do this. Do you have any recommendations for books or other documentation we could read to bring ourselves up to speed on this topic? Looking at how the biopython code is organized has been very helpful, as well, of course! Thank you very much for your time, Ann Loraine -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From lucks at fas.harvard.edu Sun May 6 11:19:19 2007 From: lucks at fas.harvard.edu (Julius Lucks) Date: Sun, 6 May 2007 11:19:19 -0400 Subject: [BioPython] advice on structuring packages In-Reply-To: <83722dde0705060640t12799641q5b4454544e869325@mail.gmail.com> References: <83722dde0705060640t12799641q5b4454544e869325@mail.gmail.com> Message-ID: Hi Ann, If you are going to do a major restructuring, I HIGHLY recommend you switch from CVS to Subversion as well. Subversion works a lot like CVS but has many more nice features and is just structured better - it allows you to version binary files as well as text files, it has a better back end allowing the repository to be more space-efficient and speedy, and many more nice things. To that end, there is an EXCELLENT book called 'Pragmatic Version Control Using Subversion' http://www.pragmaticprogrammer.com/titles/svn/index.html I highly recommend this book - I went through the whole thing and it really taught be a lot about the best way to use subversion, as well as a whole chapter on how to structure the repository, manage tags and branches, etc. If you want to stick with CVS, Pragmatic Bookshelf also has the same book, but with CVS http://www.pragmaticprogrammer.com/starter_kit/vcc/index.html Hope this helps, Julius ----------------------------------------------------- http://openwetware.org/wiki/User:Lucks ----------------------------------------------------- On May 6, 2007, at 9:40 AM, Ann Loraine wrote: > Dear friends, > > My group is getting ready to distribute some python modules and > also to > migrate some of our code to a publicly-accessible cvs repository. > > For the migration, we would like to restructure our cvs directory > layout so > as to be more compatible with community standards. > > We could really use some good ideas and suggestions on how to do > this. Do > you have any recommendations for books or other documentation we > could read > to bring ourselves up to speed on this topic? > > Looking at how the biopython code is organized has been very > helpful, as > well, of course! > > Thank you very much for your time, > > Ann Loraine > > -- > Ann Loraine > Assistant Professor > University of Alabama at Birmingham > http://www.transvar.org > 205-996-4155 > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython From jean.lechner at gmail.com Wed May 9 04:14:51 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 10:14:51 +0200 Subject: [BioPython] bio.pdb.mmcif does not exist Message-ID: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> Hello I have installed Biopython without any problems but when I try tu use the mmcif parser or the mmcif2dict, I have a error saying the mmcif package does not exist. How can I install this package ? From biopython at maubp.freeserve.co.uk Wed May 9 06:59:01 2007 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 09 May 2007 11:59:01 +0100 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> Message-ID: <4641A975.4010901@maubp.freeserve.co.uk> (Forgot to reply to the mainling list last time, sending again) Jean Lechner wrote: > Hello > > > I have installed Biopython without any problems but when I try tu use > the mmcif parser or the mmcif2dict, I have a error saying the mmcif > package does not exist. > > How can I install this package ? Hi Jean, Are you using Windows, Linux, MacOS, other? How did you install Biopython? (and out of interest, which version?) As you can read on the download page, you will need flex (The Fast Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On Linux (and other Unix like systems) this is actually very straight forward. This may be the same issue here... Peter From jean.lechner at gmail.com Wed May 9 08:10:46 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 14:10:46 +0200 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <4641A935.9070700@maubp.freeserve.co.uk> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A935.9070700@maubp.freeserve.co.uk> Message-ID: <361281280705090510l1c7ea48fk87239ac39283274c@mail.gmail.com> Hi Peter Thank you for answering I m using MacOS X And I have installed BioPython(version 1,43) following the steps listed on biopython.org website I have installed flex and the directory has been created. But when I try tu use the MMCIF2Dict this error stay : "ImportError: No module named mmCIF.MMCIFlex" When I look in the Bio.PDB.mmCIF folder, MMCIFlex is here but it is a MMCIFlex.so and there is no __init__.py file So I don t know what to do now ... If you have any Idea please answer me Jean 2007/5/9, Peter : > Jean Lechner wrote: > > Hello > > > > > > I have installed Biopython without any problems but when I try tu use > > the mmcif parser or the mmcif2dict, I have a error saying the mmcif > > package does not exist. > > > > How can I install this package ? > > Hi Jean, > > Are you using Windows, Linux, MacOS, other? > How did you install Biopython? (and out of interest, which version?) > > As you can read on the download page, you will need flex (The Fast > Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On Linux > (and other Unix like systems) this is actually very straight forward. > This may be the same issue here... > > Peter > From alexl at users.sourceforge.net Wed May 9 08:20:49 2007 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Wed, 09 May 2007 05:20:49 -0700 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <4641A975.4010901@maubp.freeserve.co.uk> (Peter's message of "Wed\, 09 May 2007 11\:59\:01 +0100") References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> Message-ID: <9nirb22noe.fsf@delpy.biol.berkeley.edu> >>>>> "P" == Peter writes: >> I have installed Biopython without any problems but when I try tu >> use the mmcif parser or the mmcif2dict, I have a error saying the >> mmcif package does not exist. >> >> How can I install this package ? P> Hi Jean, P> Are you using Windows, Linux, MacOS, other? How did you install P> Biopython? (and out of interest, which version?) P> As you can read on the download page, you will need flex (The Fast P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On P> Linux (and other Unix like systems) this is actually very straight P> forward. This may be the same issue here... On this issue, it appears that in biopython 1.43 compilation of the mmCIF module is actually commented-out in the setup.py (which would account for the lack of the Bio.PDB.mmCIF module noted by Jean, even if flex was installed). It was removed in this commit: http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython with the somewhat confusing note: "Uncommented mmCIF module because of problems if GNU's Flex is missing" because it actually commented it out, not uncommented it! ;) It seems to me that the setup.py should test whether GNU Flex is there and then enable the module compilation if it is (as is done for reportlab), rather than force the user to uncomment sections in the setup.py. I would like to enable this functionality in my Fedora package, but as it currently stands it means that I now need to write a patch in my RPM to uncomment the stanzas. Alex From biopython at maubp.freeserve.co.uk Wed May 9 09:01:56 2007 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 09 May 2007 14:01:56 +0100 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <9nirb22noe.fsf@delpy.biol.berkeley.edu> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> Message-ID: <4641C644.8010304@maubp.freeserve.co.uk> Alex Lancaster wrote: > On this issue, it appears that in biopython 1.43 compilation of the > mmCIF module is actually commented-out in the setup.py (which would > account for the lack of the Bio.PDB.mmCIF module noted by Jean, even > if flex was installed). Well spotted - I had forgotten about that! > It was removed in this commit: > > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython > > with the somewhat confusing note: > > "Uncommented mmCIF module because of problems if GNU's Flex is > missing" > > because it actually commented it out, not uncommented it! ;) That does sound like a simple typing error given the change made. > It seems > to me that the setup.py should test whether GNU Flex is there and then > enable the module compilation if it is (as is done for reportlab), > rather than force the user to uncomment sections in the setup.py. That sounds reasonable - do you happen to know how to check for the flex headers cleanly? The way the setup.py script prompts the user about building Bio.KDTree with a simple yes/no prompt is a simple short term solution. I could certainly manage to make that change. ------------------------------------------------------------------------ Jean - this issue had slipped my mind (but I don't use this module). If you edit the setup.py file to uncomment the mmCIF extension lines, and retry the build/install that should fix your missing module problem: # Extension('Bio.PDB.mmCIF.MMCIFlex', # ['Bio/PDB/mmCIF/lex.yy.c', # 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], # include_dirs=["Bio"], # libraries=["fl"] # ), Should become: Extension('Bio.PDB.mmCIF.MMCIFlex', ['Bio/PDB/mmCIF/lex.yy.c', 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], include_dirs=["Bio"], libraries=["fl"] ), Please let us know if that works... Peter From alexl at users.sourceforge.net Wed May 9 09:13:05 2007 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Wed, 09 May 2007 06:13:05 -0700 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <4641C644.8010304@maubp.freeserve.co.uk> (Peter's message of "Wed\, 09 May 2007 14\:01\:56 +0100") References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <4641C644.8010304@maubp.freeserve.co.uk> Message-ID: >>>>> "P" == Peter writes: [...] >> It seems to me that the setup.py should test whether GNU Flex is >> there and then enable the module compilation if it is (as is done >> for reportlab), rather than force the user to uncomment sections in >> the setup.py. P> That sounds reasonable - do you happen to know how to check for the P> flex headers cleanly? You could just test for the flex binary, the headers should be there, but that's probably fragile. Have to dig into my fading knowledge of distutils... P> The way the setup.py script prompts the user about building P> Bio.KDTree with a simple yes/no prompt is a simple short term P> solution. I could certainly manage to make that change. I would prefer to that it also be a command-line options so that a biopython build can be automated by a build system, when making RPM packages. (Currently the Fedora package has to simulate the user typing "yes" to the Bio.KDTree question which is fragile). P> Jean - this issue had slipped my mind (but I don't use this P> module). If you edit the setup.py file to uncomment the mmCIF P> extension lines, and retry the build/install that should fix your P> missing module problem: P> # Extension('Bio.PDB.mmCIF.MMCIFlex', # ['Bio/PDB/mmCIF/lex.yy.c', P> # 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], # include_dirs=["Bio"], # P> libraries=["fl"] # ), P> Should become: P> Extension('Bio.PDB.mmCIF.MMCIFlex', ['Bio/PDB/mmCIF/lex.yy.c', P> 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], include_dirs=["Bio"], P> libraries=["fl"] ), There's one more change in addition to that, you need to also uncomment: # 'Bio.PDB.mmCIF', in the PACKAGES list in setup.py. Alex From jean.lechner at gmail.com Wed May 9 09:18:57 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 15:18:57 +0200 Subject: [BioPython] Fwd: bio.pdb.mmcif does not exist In-Reply-To: <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> Message-ID: <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> Hum I ve uncommented the lines and reinstalled all. But the problem stay the same. The directory Bio.PDB.mmCIF il here and there is a file named MMCIFlex.so into it But python can not load it... it is said that there is no module named mmCIF.MMCIFlex so i don t know what to do now ... If you know answer me please Jean 2007/5/9, Alex Lancaster : > >>>>> "P" == Peter writes: > >> I have installed Biopython without any problems but when I try tu > >> use the mmcif parser or the mmcif2dict, I have a error saying the > >> mmcif package does not exist. > >> > >> How can I install this package ? > > P> Hi Jean, > > P> Are you using Windows, Linux, MacOS, other? How did you install > P> Biopython? (and out of interest, which version?) > > P> As you can read on the download page, you will need flex (The Fast > P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On > P> Linux (and other Unix like systems) this is actually very straight > P> forward. This may be the same issue here... > > On this issue, it appears that in biopython 1.43 compilation of the > mmCIF module is actually commented-out in the setup.py (which would > account for the lack of the Bio.PDB.mmCIF module noted by Jean, even > if flex was installed). It was removed in this commit: > > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython > > with the somewhat confusing note: > > "Uncommented mmCIF module because of problems if GNU's Flex is > missing" > > because it actually commented it out, not uncommented it! ;) It seems > to me that the setup.py should test whether GNU Flex is there and then > enable the module compilation if it is (as is done for reportlab), > rather than force the user to uncomment sections in the setup.py. > > I would like to enable this functionality in my Fedora package, but as > it currently stands it means that I now need to write a patch in my > RPM to uncomment the stanzas. > > Alex > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > From mdehoon at c2b2.columbia.edu Wed May 9 09:54:04 2007 From: mdehoon at c2b2.columbia.edu (Michiel de Hoon) Date: Wed, 09 May 2007 22:54:04 +0900 Subject: [BioPython] Fwd: bio.pdb.mmcif does not exist In-Reply-To: <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> Message-ID: <4641D27C.9000803@c2b2.columbia.edu> Jean Lechner wrote: > Hum I ve uncommented the lines and reinstalled all. > But the problem stay the same. > The directory Bio.PDB.mmCIF il here and there is a file named > MMCIFlex.so into it > But python can not load it... it is said that there is no module named > mmCIF.MMCIFlex How exactly are you trying to import MMCIFlex (which command exactly do you type into Python)? On my Mac, I can import MMCIFlex with no problems. So it may be a path problem instead of a problem with MMCIFlex.so itself. Try going to the directory that contains MMCIFlex.so and try to import it there. --Michiel. From mdehoon at c2b2.columbia.edu Wed May 9 10:07:20 2007 From: mdehoon at c2b2.columbia.edu (Michiel de Hoon) Date: Wed, 09 May 2007 23:07:20 +0900 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <4641C644.8010304@maubp.freeserve.co.uk> Message-ID: <4641D598.4010702@c2b2.columbia.edu> Alex Lancaster wrote: > P> The way the setup.py script prompts the user about building > P> Bio.KDTree with a simple yes/no prompt is a simple short term > P> solution. I could certainly manage to make that change. > > I would prefer to that it also be a command-line options so that a > biopython build can be automated by a build system, when making RPM > packages. (Currently the Fedora package has to simulate the user > typing "yes" to the Bio.KDTree question which is fragile). I'm not too happy about adding a command-line option, so let me propose another solution. A little-known secret in Python is that you can do autoconf-like configuration from a setup.py script. All the machinery is already there in Python, but unfortunately it's not well documented. However, it's fairly simple to use in practice -- way easier than autoconf. What this amounts to is that before "python setup.py build", a user will also have to run "python setup.py config" to check if the flex library is present. If so, we can compile MMCIFlex during the build. If not, or if a user doesn't do the config step, assume that flex is not present and don't compile MMCIFlex. As far as I can see, this solves the problem for the Fedora packaging. Furthermore, the config lets us catch potential problems with flex before we start compiling stuff. A simple example of a configuration using setup.py can be found in a tiny statistics module I wrote a while ago. See: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/Statistics/ in case you want to try this approach. --Michiel. From jean.lechner at gmail.com Wed May 9 10:27:28 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 16:27:28 +0200 Subject: [BioPython] Fwd: bio.pdb.mmcif does not exist In-Reply-To: <4641D27C.9000803@c2b2.columbia.edu> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> <4641D27C.9000803@c2b2.columbia.edu> Message-ID: <361281280705090727o49e3cf50i64c5c23d030059e8@mail.gmail.com> OH damn I didn t think it can be a path problem ... In fact it search the file on the folder wich I have download to install biopython ... I tape in python from Bio.PDB import * You re rigth ... when I import the package into the mmCif folder it works ... Thank you very much ! How can I change the path ? Thank you all for our help ! Jean 2007/5/9, Michiel de Hoon : > Jean Lechner wrote: > > Hum I ve uncommented the lines and reinstalled all. > > But the problem stay the same. > > The directory Bio.PDB.mmCIF il here and there is a file named > > MMCIFlex.so into it > > But python can not load it... it is said that there is no module named > > mmCIF.MMCIFlex > > How exactly are you trying to import MMCIFlex (which command exactly do > you type into Python)? > On my Mac, I can import MMCIFlex with no problems. So it may be a path > problem instead of a problem with MMCIFlex.so itself. Try going to the > directory that contains MMCIFlex.so and try to import it there. > > --Michiel. > From biopython at maubp.freeserve.co.uk Wed May 9 13:13:23 2007 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 09 May 2007 18:13:23 +0100 Subject: [BioPython] Bio.SeqIO and Bio.AlignIO Message-ID: <46420133.5060700@maubp.freeserve.co.uk> Dear Biopython people, I hope most of you have tried, or at least looked at, the new Bio.SeqIO code introduced in Biopython 1.43. It is described in the cookbook/tutorial and on the website here: http://www.biopython.org/wiki/SeqIO Additional feedback would be welcome. For example - are we missing the ability to read or write your favourite file format? Or should I prioritise reading the annotation in Swiss-Prot files (Enhancement Bug 2235). Also, I have been thinking that perhaps we do need alignment specific handling code after all. The current Bio.SeqIO interface works fine for files containing a single alignment (made up of multiple sequences). However, some files can hold multiple alignments... Two examples that come to mind are (1) re-sampled alignments held as concatenated phylip files, produced by the seqboot tool in the PHYLIP suite, and (2) multiple pairwise alignments produced by the EMBOSS programs needle and water. What I have in mind is an extension of the Bio.SeqIO functions which work on SeqRecords, to a set of Bio.AlignIO functions which work on Alignment objects. i.e. The AlignIO.parse() function would be an iterator returning alignment objects, and the AlignIO.write() function would accept Alignment objects. This would allow code like this: from Bio import AlignIO for alignment in AlignIO.parse(open("many.phy"), "phylip") : print "Alignment with %i sequences of length %i" \ % (len(alignment.get_all_seqs()), alignment.get_alignment_length() Would anyone like to comment on the scheme? See also Bug 2285 http://bugzilla.open-bio.org/show_bug.cgi?id=2285 Note that this is also a good time to talk about enhancing the Alignment object itself - something Marc has raised on Bug 1944 http://bugzilla.open-bio.org/show_bug.cgi?id=1944 Peter From idoerg at gmail.com Thu May 10 13:18:23 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Thu, 10 May 2007 10:18:23 -0700 Subject: [BioPython] Biopython talk at BOSC 2007? Message-ID: <464353DF.6030700@burnham.org> Anybody giving a talk on Biopython? We can get a 20-30 minute slot in Vienna, but someone has to show up and talk. Personally, I will actually be there for the ISMB SIGs, but as I am running my own conference, it will be a bit of a strain to talk at BOSC. However, the main reason I do not want to speak is that there are people much more deserving here. So if anyone plans to be at ISMB 2007 in any case, and wishes to represent Biopython with serpentine honor, contact Darin. Best, Iddo -------- Original Message -------- Subject: BOSC 2007 Second Call For Papers Date: Thu, 10 May 2007 12:17:41 -0400 From: darin.london at duke.edu To: biopython-owner at lists.open-bio.org The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From idoerg at gmail.com Mon May 14 12:27:42 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 14 May 2007 09:27:42 -0700 Subject: [BioPython] Subject: BOSC 2007 2nd Call For Papers. Message-ID: <46488DFE.3070908@burnham.org> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From idoerg at gmail.com Mon May 14 12:28:36 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 14 May 2007 09:28:36 -0700 Subject: [BioPython] BOSC 2007 Abstract Submission Deadline Extension Message-ID: <46488E34.8000604@burnham.org> Subject: BOSC 2007 Abstract Submission Deadline Extension Due to technical difficulties in sending out the 2nd call for papers, the BOSC organizers are extending the deadline for abstract submissions to Monday May 21st. The announcement day will remain the same so that it remains before the Early Discount Date. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From jean.lechner at gmail.com Tue May 15 04:41:13 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Tue, 15 May 2007 10:41:13 +0200 Subject: [BioPython] MMCIF2Dict Key error Message-ID: <361281280705150141j3b559e97p70ecd4d43f2c457a@mail.gmail.com> Hello I havent seen any problems with the MMCIF2Dict in the archives... But I have a problem with ... If someone else can test it in order to say if it works by him ... I have download the 1BYL.CIF on the pdb and for some tag like a=mparse['_cell.length_a'] b=mparse['_cell.length_b'] c=mparse['_cell.length_c'] alpha=mparse['_cell.angle_alpha'] beta=mparse['_cell.angle_beta'] gamma=mparse['_cell.angle_gamma'] z=mparse['_cell.Z_PDB'] resolution=mparse['_reflns.d_resolution_high'] it works ... but for some else like title=mparse['_struct.title'] I have an error : title=mparse['_struct.title'] File "/Users/insilico/Desktop/biopython-1.43/build/lib.macosx-10.3-ppc-2.4/Bio/PDB/MMCIF2Dict.py", line 115, in __getitem__ KeyError: 'title=mparse['_struct.title']' It happened for a lot of fields ... I need to access them And I think I cannot acces them with teh structure parser... So if someone know what is the problem ... PS : I have checked if the fields for which it doesn t work are in the 1BYL file ... but they are all present From orlando.doehring at googlemail.com Fri May 18 13:03:17 2007 From: orlando.doehring at googlemail.com (=?ISO-8859-1?Q?Orlando_D=F6hring?=) Date: Fri, 18 May 2007 19:03:17 +0200 Subject: [BioPython] Biopython to parse not only .pdf--files but also NACCESS .asa files Message-ID: <8cc339d80705181003h461b6157xedff88ad329f1@mail.gmail.com> Dear community, I am applying the following tool: '*Naccess V2.1.1 - Atomic Solvent Accessible Area Calculations* ' to calculate two features which are not contained in standard .pdb-files. These two features are atomic accessiblity and van der Waal radius. As can be read in the readme file at http://wolf.bi.umist.ac.uk/naccess/nac_readme.html under 'example output files' and at the PDB-Format site at* * http://www.wwpdb.org/documentation/format23/sect9.html under 'Atom'. NACCESS does the following: 'The output format is PDB, with B-factors and occupancies removed, then atomic accessiblity in square Angstroms, followed by the assigned van der Waal radius.' Note that Occupancy gets replaced by atomic accessiblity and B-factor by the van der Waal radius. This 'new' .pdb-file has extension .asa. I chose a quite straight-forward approach: I wanted to use Biopython as before, e.g. calling the B-Factor method but yielding the atomic accessiblity instead. But Biopython seems to type-check the .asa-file and complains that the B-factor is not of type float. Here are some more technical details. As an example I chose the '1DHR' protein: ------------------------------------------------------------------------------ def *__init__*(*self*,structure_id=*"1DHR"*,indices=[0]): # which residues are part of the patch *self*.indices = indices # If 1 (DEFAULT), the exceptions are caught, but some residues or atoms will be missing. # THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE! *self*.p=PDBParser(PERMISSIVE=1) # which protein to analyse *self*.structure_id = structure_id *self*.fileName = *self*.structure_id + *'.asa' * *self*.structure = *self*.p.get_structure(*self*.structure_id, *self* .fileName) ------------------------------------------------------------------------------ Error message: Traceback (most recent call last): *File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 249, in * c = compact(indices=[0,1]) *File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 17, in __init__ * self.structure = self.p.get_structure(self.structure_id, self.fileName) *File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 65, in get_structure * self._parse(file.readlines()) *File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 85, in _parse * self.trailer=self._parse_coordinates(coords_trailer) *File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 159, in _parse_coordinates * bfactor=float(line[60:66]) ValueError: invalid literal for float(): 31 1. ------------------------------------------------------------------------------ What do you recommend for my situation. Many thanks! Yours, Orlando -- From O.Doehring at cs.ucl.ac.uk Mon May 21 15:45:36 2007 From: O.Doehring at cs.ucl.ac.uk (O.Doehring at cs.ucl.ac.uk) Date: 21 May 2007 20:45:36 +0100 Subject: [BioPython] Biopython to parse not only .pdb-files but also NACCESS .asa files Message-ID: Dear community, I am applying the following tool: 'Naccess V2.1.1 - Atomic Solvent Accessible Area Calculations ' to calculate two features which are not contained in standard .pdb-files. These two features are atomic accessiblity and van der Waal radius. As can be read in the readme file at http://wolf.bi.umist.ac.uk/naccess/nac_readme.html under 'example output files' and at the PDB-Format site at http://www.wwpdb.org/documentation/format23/sect9.html under 'Atom'. NACCESS does the following: 'The output format is PDB, with B-factors and occupancies removed, then atomic accessiblity in square Angstroms, followed by the assigned van der Waal radius.' Note that Occupancy gets replaced by atomic accessiblity and B-factor by the van der Waal radius. This 'new' .pdb-file has extension .asa. I chose a quite straight-forward approach: I wanted to use Biopython as before, e.g. calling the B-Factor method but yielding the atomic accessiblity instead. But Biopython seems to type-check the .asa-file and complains that the B-factor is not of type float. Is there a way to access the data of .asa-files programmatically via the Biopython library? The only other way then seems to write a parser for .asa-files and to figure out which atomic element in the .pdb-file corresponds to the respective one in the .asa-file and finally to retrieve the wanted values for atomic accessiblity and van der Waal radius. Here are some more technical details. As an example I chose the '1DHR' protein: ------------------------------------------------------------------------------ def __init__(self,structure_id="1DHR",indices=[ 0]): # which residues are part of the patch self.indices = indices # If 1 (DEFAULT), the exceptions are caught, but some residues or atoms will be missing. # THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE! self.p=PDBParser(PERMISSIVE= 1) # which protein to analyse self.structure_id = structure_id self.fileName = self.structure_id + '.asa' self.structure = self.p.get_structure(self.structure_id, self.fileName) ------------------------------------------------------------------------------ Error message: Traceback (most recent call last): File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 249, in c = compact(indices=[0,1]) File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 17, in __init__ self.structure = self.p.get_structure(self.structure_id, self.fileName) File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 65, in get_structure self._parse(file.readlines()) File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 85, in _parse self.trailer=self._parse_coordinates(coords_trailer) File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 159, in _parse_coordinates bfactor=float(line[60:66]) ValueError: invalid literal for float(): 31 1. ------------------------------------------------------------------------------ I hope this question above was not discussed before but neither the search engine at http://search.open-bio.org/cgi-bin/mail-search.cgi works nor could I find anything useful via a google search restricted to the archive using the 'site' attribute. What do you recommend for my situation. Many thanks! Yours, Orlando From edschofield at gmail.com Tue May 22 12:57:49 2007 From: edschofield at gmail.com (Ed Schofield) Date: Tue, 22 May 2007 17:57:49 +0100 Subject: [BioPython] Biopython to parse not only .pdb-files but also NACCESS .asa files In-Reply-To: References: Message-ID: <1b5a37350705220957o24f6a436k89d60764729695da@mail.gmail.com> On 21 May 2007 20:45:36 +0100, O.Doehring at cs.ucl.ac.uk wrote: > > ValueError: invalid literal for float(): 31 1. > > ... > > What do you recommend for my situation. Many thanks! Is that a space between 31 and 1? There's your problem. My advice is to insert import pdb pdb.set_trace() at line 159 in PDBParser.py and check out why the columns in your data are misaligned with what PDBParser.py expects. A quick scan of nac_readme.html implies that perhaps you need the -f argument to give you the full output format? But if you need to write your own parser for .asa files, you could use _parse_coordinates(self, coords_trailer) as a template. -- Ed From sbassi at gmail.com Wed May 30 23:37:52 2007 From: sbassi at gmail.com (Sebastian Bassi) Date: Thu, 31 May 2007 00:37:52 -0300 Subject: [BioPython] 454 sample file Message-ID: Hello, Does anyboy have a 454 sequence output sample file? It is XML so should be easy to write a parser. I don't have access to such machine (we are stuck with ABI 31xx series) so I would be glad to receive one file (you can scramble the sequence if it is private). Best, SB. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From chris.lasher at gmail.com Thu May 31 00:23:39 2007 From: chris.lasher at gmail.com (Chris Lasher) Date: Thu, 31 May 2007 00:23:39 -0400 Subject: [BioPython] 454 sample file In-Reply-To: References: Message-ID: <128a885f0705302123v68b8c246nb69d4d375f2eabcf@mail.gmail.com> 454 sent a FASTA format file that contained sequence data when I worked on a project last year. I don't suspect they provide the raw flowgrams; at least they didn't in our experiences with them. You can use Biopython's SeqIO to work with the FASTA file. Best, Chris On 5/30/07, Sebastian Bassi wrote: > Hello, > > Does anyboy have a 454 sequence output sample file? It is XML so > should be easy to write a parser. I don't have access to such machine > (we are stuck with ABI 31xx series) so I would be glad to receive one > file (you can scramble the sequence if it is private). > Best, > SB. > > -- > Bioinformatics news: http://www.bioinformatica.info > Lriser: http://www.linspire.com/lraiser_success.php?serial=318 > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > From sbassi at gmail.com Thu May 31 01:00:26 2007 From: sbassi at gmail.com (Sebastian Bassi) Date: Thu, 31 May 2007 02:00:26 -0300 Subject: [BioPython] 454 sample file In-Reply-To: <128a885f0705302123v68b8c246nb69d4d375f2eabcf@mail.gmail.com> References: <128a885f0705302123v68b8c246nb69d4d375f2eabcf@mail.gmail.com> Message-ID: On 5/31/07, Chris Lasher wrote: > 454 sent a FASTA format file that contained sequence data when I > worked on a project last year. I don't suspect they provide the raw > flowgrams; at least they didn't in our experiences with them. You can > use Biopython's SeqIO to work with the FASTA file. I thought that someone could be working in a lab with a 454 machine and could send me an output file. Just to make the parser for someone that could need it in the future. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From thamelry at binf.ku.dk Thu May 31 05:39:54 2007 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Thu, 31 May 2007 11:39:54 +0200 Subject: [BioPython] Jobs in protein structure prediction Message-ID: <2d7c25310705310239w51dd27e5l9f900e735bc1653b@mail.gmail.com> Hi all, There are two postdoc and two PhD positions available in my group (University of Copenhagen, Denmark, http://www.binf.ku.dk/) on the topic of protein structure prediction. For details, see: http://www.binf.ku.dk/Job4Apr17 http://www.binf.ku.dk/JobsNABIIT_0507 The applicants are expected to use (and probably extend) Biopython/Bio.PDB. Best regards, ---- Thomas Hamelryck Group leader Structural Bioinformatics Bioinformatics center Institute of Molecular Biology University of Copenhagen Ole Maaloes Vej 5 DK-2200 Copenhagen N Denmark http://www.binf.ku.dk/User:Thomas_Hamelryck http://www.binf.ku.dk/Protein_structure From arareko at campus.iztacala.unam.mx Thu May 31 11:37:49 2007 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 31 May 2007 10:37:49 -0500 Subject: [BioPython] FreeBSD port updated Message-ID: <465EEBCD.9060200@campus.iztacala.unam.mx> Folks, The FreeBSD port for BioPython has been upgraded from 1.42 to 1.43. Many thanks to Paulo Bandiera for taking the time to create the update. If you run into any issues with the new version please let me know. Regards, Mauricio. -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From aloraine at gmail.com Sun May 6 13:40:43 2007 From: aloraine at gmail.com (Ann Loraine) Date: Sun, 6 May 2007 08:40:43 -0500 Subject: [BioPython] advice on structuring packages Message-ID: <83722dde0705060640t12799641q5b4454544e869325@mail.gmail.com> Dear friends, My group is getting ready to distribute some python modules and also to migrate some of our code to a publicly-accessible cvs repository. For the migration, we would like to restructure our cvs directory layout so as to be more compatible with community standards. We could really use some good ideas and suggestions on how to do this. Do you have any recommendations for books or other documentation we could read to bring ourselves up to speed on this topic? Looking at how the biopython code is organized has been very helpful, as well, of course! Thank you very much for your time, Ann Loraine -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From lucks at fas.harvard.edu Sun May 6 15:19:19 2007 From: lucks at fas.harvard.edu (Julius Lucks) Date: Sun, 6 May 2007 11:19:19 -0400 Subject: [BioPython] advice on structuring packages In-Reply-To: <83722dde0705060640t12799641q5b4454544e869325@mail.gmail.com> References: <83722dde0705060640t12799641q5b4454544e869325@mail.gmail.com> Message-ID: Hi Ann, If you are going to do a major restructuring, I HIGHLY recommend you switch from CVS to Subversion as well. Subversion works a lot like CVS but has many more nice features and is just structured better - it allows you to version binary files as well as text files, it has a better back end allowing the repository to be more space-efficient and speedy, and many more nice things. To that end, there is an EXCELLENT book called 'Pragmatic Version Control Using Subversion' http://www.pragmaticprogrammer.com/titles/svn/index.html I highly recommend this book - I went through the whole thing and it really taught be a lot about the best way to use subversion, as well as a whole chapter on how to structure the repository, manage tags and branches, etc. If you want to stick with CVS, Pragmatic Bookshelf also has the same book, but with CVS http://www.pragmaticprogrammer.com/starter_kit/vcc/index.html Hope this helps, Julius ----------------------------------------------------- http://openwetware.org/wiki/User:Lucks ----------------------------------------------------- On May 6, 2007, at 9:40 AM, Ann Loraine wrote: > Dear friends, > > My group is getting ready to distribute some python modules and > also to > migrate some of our code to a publicly-accessible cvs repository. > > For the migration, we would like to restructure our cvs directory > layout so > as to be more compatible with community standards. > > We could really use some good ideas and suggestions on how to do > this. Do > you have any recommendations for books or other documentation we > could read > to bring ourselves up to speed on this topic? > > Looking at how the biopython code is organized has been very > helpful, as > well, of course! > > Thank you very much for your time, > > Ann Loraine > > -- > Ann Loraine > Assistant Professor > University of Alabama at Birmingham > http://www.transvar.org > 205-996-4155 > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython From jean.lechner at gmail.com Wed May 9 08:14:51 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 10:14:51 +0200 Subject: [BioPython] bio.pdb.mmcif does not exist Message-ID: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> Hello I have installed Biopython without any problems but when I try tu use the mmcif parser or the mmcif2dict, I have a error saying the mmcif package does not exist. How can I install this package ? From biopython at maubp.freeserve.co.uk Wed May 9 10:59:01 2007 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 09 May 2007 11:59:01 +0100 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> Message-ID: <4641A975.4010901@maubp.freeserve.co.uk> (Forgot to reply to the mainling list last time, sending again) Jean Lechner wrote: > Hello > > > I have installed Biopython without any problems but when I try tu use > the mmcif parser or the mmcif2dict, I have a error saying the mmcif > package does not exist. > > How can I install this package ? Hi Jean, Are you using Windows, Linux, MacOS, other? How did you install Biopython? (and out of interest, which version?) As you can read on the download page, you will need flex (The Fast Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On Linux (and other Unix like systems) this is actually very straight forward. This may be the same issue here... Peter From jean.lechner at gmail.com Wed May 9 12:10:46 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 14:10:46 +0200 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <4641A935.9070700@maubp.freeserve.co.uk> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A935.9070700@maubp.freeserve.co.uk> Message-ID: <361281280705090510l1c7ea48fk87239ac39283274c@mail.gmail.com> Hi Peter Thank you for answering I m using MacOS X And I have installed BioPython(version 1,43) following the steps listed on biopython.org website I have installed flex and the directory has been created. But when I try tu use the MMCIF2Dict this error stay : "ImportError: No module named mmCIF.MMCIFlex" When I look in the Bio.PDB.mmCIF folder, MMCIFlex is here but it is a MMCIFlex.so and there is no __init__.py file So I don t know what to do now ... If you have any Idea please answer me Jean 2007/5/9, Peter : > Jean Lechner wrote: > > Hello > > > > > > I have installed Biopython without any problems but when I try tu use > > the mmcif parser or the mmcif2dict, I have a error saying the mmcif > > package does not exist. > > > > How can I install this package ? > > Hi Jean, > > Are you using Windows, Linux, MacOS, other? > How did you install Biopython? (and out of interest, which version?) > > As you can read on the download page, you will need flex (The Fast > Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On Linux > (and other Unix like systems) this is actually very straight forward. > This may be the same issue here... > > Peter > From alexl at users.sourceforge.net Wed May 9 12:20:49 2007 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Wed, 09 May 2007 05:20:49 -0700 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <4641A975.4010901@maubp.freeserve.co.uk> (Peter's message of "Wed\, 09 May 2007 11\:59\:01 +0100") References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> Message-ID: <9nirb22noe.fsf@delpy.biol.berkeley.edu> >>>>> "P" == Peter writes: >> I have installed Biopython without any problems but when I try tu >> use the mmcif parser or the mmcif2dict, I have a error saying the >> mmcif package does not exist. >> >> How can I install this package ? P> Hi Jean, P> Are you using Windows, Linux, MacOS, other? How did you install P> Biopython? (and out of interest, which version?) P> As you can read on the download page, you will need flex (The Fast P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On P> Linux (and other Unix like systems) this is actually very straight P> forward. This may be the same issue here... On this issue, it appears that in biopython 1.43 compilation of the mmCIF module is actually commented-out in the setup.py (which would account for the lack of the Bio.PDB.mmCIF module noted by Jean, even if flex was installed). It was removed in this commit: http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython with the somewhat confusing note: "Uncommented mmCIF module because of problems if GNU's Flex is missing" because it actually commented it out, not uncommented it! ;) It seems to me that the setup.py should test whether GNU Flex is there and then enable the module compilation if it is (as is done for reportlab), rather than force the user to uncomment sections in the setup.py. I would like to enable this functionality in my Fedora package, but as it currently stands it means that I now need to write a patch in my RPM to uncomment the stanzas. Alex From biopython at maubp.freeserve.co.uk Wed May 9 13:01:56 2007 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 09 May 2007 14:01:56 +0100 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <9nirb22noe.fsf@delpy.biol.berkeley.edu> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> Message-ID: <4641C644.8010304@maubp.freeserve.co.uk> Alex Lancaster wrote: > On this issue, it appears that in biopython 1.43 compilation of the > mmCIF module is actually commented-out in the setup.py (which would > account for the lack of the Bio.PDB.mmCIF module noted by Jean, even > if flex was installed). Well spotted - I had forgotten about that! > It was removed in this commit: > > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython > > with the somewhat confusing note: > > "Uncommented mmCIF module because of problems if GNU's Flex is > missing" > > because it actually commented it out, not uncommented it! ;) That does sound like a simple typing error given the change made. > It seems > to me that the setup.py should test whether GNU Flex is there and then > enable the module compilation if it is (as is done for reportlab), > rather than force the user to uncomment sections in the setup.py. That sounds reasonable - do you happen to know how to check for the flex headers cleanly? The way the setup.py script prompts the user about building Bio.KDTree with a simple yes/no prompt is a simple short term solution. I could certainly manage to make that change. ------------------------------------------------------------------------ Jean - this issue had slipped my mind (but I don't use this module). If you edit the setup.py file to uncomment the mmCIF extension lines, and retry the build/install that should fix your missing module problem: # Extension('Bio.PDB.mmCIF.MMCIFlex', # ['Bio/PDB/mmCIF/lex.yy.c', # 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], # include_dirs=["Bio"], # libraries=["fl"] # ), Should become: Extension('Bio.PDB.mmCIF.MMCIFlex', ['Bio/PDB/mmCIF/lex.yy.c', 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], include_dirs=["Bio"], libraries=["fl"] ), Please let us know if that works... Peter From alexl at users.sourceforge.net Wed May 9 13:13:05 2007 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Wed, 09 May 2007 06:13:05 -0700 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: <4641C644.8010304@maubp.freeserve.co.uk> (Peter's message of "Wed\, 09 May 2007 14\:01\:56 +0100") References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <4641C644.8010304@maubp.freeserve.co.uk> Message-ID: >>>>> "P" == Peter writes: [...] >> It seems to me that the setup.py should test whether GNU Flex is >> there and then enable the module compilation if it is (as is done >> for reportlab), rather than force the user to uncomment sections in >> the setup.py. P> That sounds reasonable - do you happen to know how to check for the P> flex headers cleanly? You could just test for the flex binary, the headers should be there, but that's probably fragile. Have to dig into my fading knowledge of distutils... P> The way the setup.py script prompts the user about building P> Bio.KDTree with a simple yes/no prompt is a simple short term P> solution. I could certainly manage to make that change. I would prefer to that it also be a command-line options so that a biopython build can be automated by a build system, when making RPM packages. (Currently the Fedora package has to simulate the user typing "yes" to the Bio.KDTree question which is fragile). P> Jean - this issue had slipped my mind (but I don't use this P> module). If you edit the setup.py file to uncomment the mmCIF P> extension lines, and retry the build/install that should fix your P> missing module problem: P> # Extension('Bio.PDB.mmCIF.MMCIFlex', # ['Bio/PDB/mmCIF/lex.yy.c', P> # 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], # include_dirs=["Bio"], # P> libraries=["fl"] # ), P> Should become: P> Extension('Bio.PDB.mmCIF.MMCIFlex', ['Bio/PDB/mmCIF/lex.yy.c', P> 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], include_dirs=["Bio"], P> libraries=["fl"] ), There's one more change in addition to that, you need to also uncomment: # 'Bio.PDB.mmCIF', in the PACKAGES list in setup.py. Alex From jean.lechner at gmail.com Wed May 9 13:18:57 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 15:18:57 +0200 Subject: [BioPython] Fwd: bio.pdb.mmcif does not exist In-Reply-To: <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> Message-ID: <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> Hum I ve uncommented the lines and reinstalled all. But the problem stay the same. The directory Bio.PDB.mmCIF il here and there is a file named MMCIFlex.so into it But python can not load it... it is said that there is no module named mmCIF.MMCIFlex so i don t know what to do now ... If you know answer me please Jean 2007/5/9, Alex Lancaster : > >>>>> "P" == Peter writes: > >> I have installed Biopython without any problems but when I try tu > >> use the mmcif parser or the mmcif2dict, I have a error saying the > >> mmcif package does not exist. > >> > >> How can I install this package ? > > P> Hi Jean, > > P> Are you using Windows, Linux, MacOS, other? How did you install > P> Biopython? (and out of interest, which version?) > > P> As you can read on the download page, you will need flex (The Fast > P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On > P> Linux (and other Unix like systems) this is actually very straight > P> forward. This may be the same issue here... > > On this issue, it appears that in biopython 1.43 compilation of the > mmCIF module is actually commented-out in the setup.py (which would > account for the lack of the Bio.PDB.mmCIF module noted by Jean, even > if flex was installed). It was removed in this commit: > > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython > > with the somewhat confusing note: > > "Uncommented mmCIF module because of problems if GNU's Flex is > missing" > > because it actually commented it out, not uncommented it! ;) It seems > to me that the setup.py should test whether GNU Flex is there and then > enable the module compilation if it is (as is done for reportlab), > rather than force the user to uncomment sections in the setup.py. > > I would like to enable this functionality in my Fedora package, but as > it currently stands it means that I now need to write a patch in my > RPM to uncomment the stanzas. > > Alex > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > From mdehoon at c2b2.columbia.edu Wed May 9 13:54:04 2007 From: mdehoon at c2b2.columbia.edu (Michiel de Hoon) Date: Wed, 09 May 2007 22:54:04 +0900 Subject: [BioPython] Fwd: bio.pdb.mmcif does not exist In-Reply-To: <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> Message-ID: <4641D27C.9000803@c2b2.columbia.edu> Jean Lechner wrote: > Hum I ve uncommented the lines and reinstalled all. > But the problem stay the same. > The directory Bio.PDB.mmCIF il here and there is a file named > MMCIFlex.so into it > But python can not load it... it is said that there is no module named > mmCIF.MMCIFlex How exactly are you trying to import MMCIFlex (which command exactly do you type into Python)? On my Mac, I can import MMCIFlex with no problems. So it may be a path problem instead of a problem with MMCIFlex.so itself. Try going to the directory that contains MMCIFlex.so and try to import it there. --Michiel. From mdehoon at c2b2.columbia.edu Wed May 9 14:07:20 2007 From: mdehoon at c2b2.columbia.edu (Michiel de Hoon) Date: Wed, 09 May 2007 23:07:20 +0900 Subject: [BioPython] bio.pdb.mmcif does not exist In-Reply-To: References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <4641C644.8010304@maubp.freeserve.co.uk> Message-ID: <4641D598.4010702@c2b2.columbia.edu> Alex Lancaster wrote: > P> The way the setup.py script prompts the user about building > P> Bio.KDTree with a simple yes/no prompt is a simple short term > P> solution. I could certainly manage to make that change. > > I would prefer to that it also be a command-line options so that a > biopython build can be automated by a build system, when making RPM > packages. (Currently the Fedora package has to simulate the user > typing "yes" to the Bio.KDTree question which is fragile). I'm not too happy about adding a command-line option, so let me propose another solution. A little-known secret in Python is that you can do autoconf-like configuration from a setup.py script. All the machinery is already there in Python, but unfortunately it's not well documented. However, it's fairly simple to use in practice -- way easier than autoconf. What this amounts to is that before "python setup.py build", a user will also have to run "python setup.py config" to check if the flex library is present. If so, we can compile MMCIFlex during the build. If not, or if a user doesn't do the config step, assume that flex is not present and don't compile MMCIFlex. As far as I can see, this solves the problem for the Fedora packaging. Furthermore, the config lets us catch potential problems with flex before we start compiling stuff. A simple example of a configuration using setup.py can be found in a tiny statistics module I wrote a while ago. See: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/Statistics/ in case you want to try this approach. --Michiel. From jean.lechner at gmail.com Wed May 9 14:27:28 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Wed, 9 May 2007 16:27:28 +0200 Subject: [BioPython] Fwd: bio.pdb.mmcif does not exist In-Reply-To: <4641D27C.9000803@c2b2.columbia.edu> References: <361281280705090114y15a7956ftb7be06aabcafe393@mail.gmail.com> <4641A975.4010901@maubp.freeserve.co.uk> <9nirb22noe.fsf@delpy.biol.berkeley.edu> <361281280705090557s739b0846u6cc708b87db5b055@mail.gmail.com> <361281280705090618t7b1155a9qb6a17c7e677246bc@mail.gmail.com> <4641D27C.9000803@c2b2.columbia.edu> Message-ID: <361281280705090727o49e3cf50i64c5c23d030059e8@mail.gmail.com> OH damn I didn t think it can be a path problem ... In fact it search the file on the folder wich I have download to install biopython ... I tape in python from Bio.PDB import * You re rigth ... when I import the package into the mmCif folder it works ... Thank you very much ! How can I change the path ? Thank you all for our help ! Jean 2007/5/9, Michiel de Hoon : > Jean Lechner wrote: > > Hum I ve uncommented the lines and reinstalled all. > > But the problem stay the same. > > The directory Bio.PDB.mmCIF il here and there is a file named > > MMCIFlex.so into it > > But python can not load it... it is said that there is no module named > > mmCIF.MMCIFlex > > How exactly are you trying to import MMCIFlex (which command exactly do > you type into Python)? > On my Mac, I can import MMCIFlex with no problems. So it may be a path > problem instead of a problem with MMCIFlex.so itself. Try going to the > directory that contains MMCIFlex.so and try to import it there. > > --Michiel. > From biopython at maubp.freeserve.co.uk Wed May 9 17:13:23 2007 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 09 May 2007 18:13:23 +0100 Subject: [BioPython] Bio.SeqIO and Bio.AlignIO Message-ID: <46420133.5060700@maubp.freeserve.co.uk> Dear Biopython people, I hope most of you have tried, or at least looked at, the new Bio.SeqIO code introduced in Biopython 1.43. It is described in the cookbook/tutorial and on the website here: http://www.biopython.org/wiki/SeqIO Additional feedback would be welcome. For example - are we missing the ability to read or write your favourite file format? Or should I prioritise reading the annotation in Swiss-Prot files (Enhancement Bug 2235). Also, I have been thinking that perhaps we do need alignment specific handling code after all. The current Bio.SeqIO interface works fine for files containing a single alignment (made up of multiple sequences). However, some files can hold multiple alignments... Two examples that come to mind are (1) re-sampled alignments held as concatenated phylip files, produced by the seqboot tool in the PHYLIP suite, and (2) multiple pairwise alignments produced by the EMBOSS programs needle and water. What I have in mind is an extension of the Bio.SeqIO functions which work on SeqRecords, to a set of Bio.AlignIO functions which work on Alignment objects. i.e. The AlignIO.parse() function would be an iterator returning alignment objects, and the AlignIO.write() function would accept Alignment objects. This would allow code like this: from Bio import AlignIO for alignment in AlignIO.parse(open("many.phy"), "phylip") : print "Alignment with %i sequences of length %i" \ % (len(alignment.get_all_seqs()), alignment.get_alignment_length() Would anyone like to comment on the scheme? See also Bug 2285 http://bugzilla.open-bio.org/show_bug.cgi?id=2285 Note that this is also a good time to talk about enhancing the Alignment object itself - something Marc has raised on Bug 1944 http://bugzilla.open-bio.org/show_bug.cgi?id=1944 Peter From idoerg at gmail.com Thu May 10 17:18:23 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Thu, 10 May 2007 10:18:23 -0700 Subject: [BioPython] Biopython talk at BOSC 2007? Message-ID: <464353DF.6030700@burnham.org> Anybody giving a talk on Biopython? We can get a 20-30 minute slot in Vienna, but someone has to show up and talk. Personally, I will actually be there for the ISMB SIGs, but as I am running my own conference, it will be a bit of a strain to talk at BOSC. However, the main reason I do not want to speak is that there are people much more deserving here. So if anyone plans to be at ISMB 2007 in any case, and wishes to represent Biopython with serpentine honor, contact Darin. Best, Iddo -------- Original Message -------- Subject: BOSC 2007 Second Call For Papers Date: Thu, 10 May 2007 12:17:41 -0400 From: darin.london at duke.edu To: biopython-owner at lists.open-bio.org The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From idoerg at gmail.com Mon May 14 16:27:42 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 14 May 2007 09:27:42 -0700 Subject: [BioPython] Subject: BOSC 2007 2nd Call For Papers. Message-ID: <46488DFE.3070908@burnham.org> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From idoerg at gmail.com Mon May 14 16:28:36 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 14 May 2007 09:28:36 -0700 Subject: [BioPython] BOSC 2007 Abstract Submission Deadline Extension Message-ID: <46488E34.8000604@burnham.org> Subject: BOSC 2007 Abstract Submission Deadline Extension Due to technical difficulties in sending out the 2nd call for papers, the BOSC organizers are extending the deadline for abstract submissions to Monday May 21st. The announcement day will remain the same so that it remains before the Early Discount Date. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 wengophone: idoerg http://iddo-friedberg.org http://2007.BioFunctionPrediction.org From jean.lechner at gmail.com Tue May 15 08:41:13 2007 From: jean.lechner at gmail.com (Jean Lechner) Date: Tue, 15 May 2007 10:41:13 +0200 Subject: [BioPython] MMCIF2Dict Key error Message-ID: <361281280705150141j3b559e97p70ecd4d43f2c457a@mail.gmail.com> Hello I havent seen any problems with the MMCIF2Dict in the archives... But I have a problem with ... If someone else can test it in order to say if it works by him ... I have download the 1BYL.CIF on the pdb and for some tag like a=mparse['_cell.length_a'] b=mparse['_cell.length_b'] c=mparse['_cell.length_c'] alpha=mparse['_cell.angle_alpha'] beta=mparse['_cell.angle_beta'] gamma=mparse['_cell.angle_gamma'] z=mparse['_cell.Z_PDB'] resolution=mparse['_reflns.d_resolution_high'] it works ... but for some else like title=mparse['_struct.title'] I have an error : title=mparse['_struct.title'] File "/Users/insilico/Desktop/biopython-1.43/build/lib.macosx-10.3-ppc-2.4/Bio/PDB/MMCIF2Dict.py", line 115, in __getitem__ KeyError: 'title=mparse['_struct.title']' It happened for a lot of fields ... I need to access them And I think I cannot acces them with teh structure parser... So if someone know what is the problem ... PS : I have checked if the fields for which it doesn t work are in the 1BYL file ... but they are all present From orlando.doehring at googlemail.com Fri May 18 17:03:17 2007 From: orlando.doehring at googlemail.com (=?ISO-8859-1?Q?Orlando_D=F6hring?=) Date: Fri, 18 May 2007 19:03:17 +0200 Subject: [BioPython] Biopython to parse not only .pdf--files but also NACCESS .asa files Message-ID: <8cc339d80705181003h461b6157xedff88ad329f1@mail.gmail.com> Dear community, I am applying the following tool: '*Naccess V2.1.1 - Atomic Solvent Accessible Area Calculations* ' to calculate two features which are not contained in standard .pdb-files. These two features are atomic accessiblity and van der Waal radius. As can be read in the readme file at http://wolf.bi.umist.ac.uk/naccess/nac_readme.html under 'example output files' and at the PDB-Format site at* * http://www.wwpdb.org/documentation/format23/sect9.html under 'Atom'. NACCESS does the following: 'The output format is PDB, with B-factors and occupancies removed, then atomic accessiblity in square Angstroms, followed by the assigned van der Waal radius.' Note that Occupancy gets replaced by atomic accessiblity and B-factor by the van der Waal radius. This 'new' .pdb-file has extension .asa. I chose a quite straight-forward approach: I wanted to use Biopython as before, e.g. calling the B-Factor method but yielding the atomic accessiblity instead. But Biopython seems to type-check the .asa-file and complains that the B-factor is not of type float. Here are some more technical details. As an example I chose the '1DHR' protein: ------------------------------------------------------------------------------ def *__init__*(*self*,structure_id=*"1DHR"*,indices=[0]): # which residues are part of the patch *self*.indices = indices # If 1 (DEFAULT), the exceptions are caught, but some residues or atoms will be missing. # THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE! *self*.p=PDBParser(PERMISSIVE=1) # which protein to analyse *self*.structure_id = structure_id *self*.fileName = *self*.structure_id + *'.asa' * *self*.structure = *self*.p.get_structure(*self*.structure_id, *self* .fileName) ------------------------------------------------------------------------------ Error message: Traceback (most recent call last): *File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 249, in * c = compact(indices=[0,1]) *File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 17, in __init__ * self.structure = self.p.get_structure(self.structure_id, self.fileName) *File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 65, in get_structure * self._parse(file.readlines()) *File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 85, in _parse * self.trailer=self._parse_coordinates(coords_trailer) *File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 159, in _parse_coordinates * bfactor=float(line[60:66]) ValueError: invalid literal for float(): 31 1. ------------------------------------------------------------------------------ What do you recommend for my situation. Many thanks! Yours, Orlando -- From O.Doehring at cs.ucl.ac.uk Mon May 21 19:45:36 2007 From: O.Doehring at cs.ucl.ac.uk (O.Doehring at cs.ucl.ac.uk) Date: 21 May 2007 20:45:36 +0100 Subject: [BioPython] Biopython to parse not only .pdb-files but also NACCESS .asa files Message-ID: Dear community, I am applying the following tool: 'Naccess V2.1.1 - Atomic Solvent Accessible Area Calculations ' to calculate two features which are not contained in standard .pdb-files. These two features are atomic accessiblity and van der Waal radius. As can be read in the readme file at http://wolf.bi.umist.ac.uk/naccess/nac_readme.html under 'example output files' and at the PDB-Format site at http://www.wwpdb.org/documentation/format23/sect9.html under 'Atom'. NACCESS does the following: 'The output format is PDB, with B-factors and occupancies removed, then atomic accessiblity in square Angstroms, followed by the assigned van der Waal radius.' Note that Occupancy gets replaced by atomic accessiblity and B-factor by the van der Waal radius. This 'new' .pdb-file has extension .asa. I chose a quite straight-forward approach: I wanted to use Biopython as before, e.g. calling the B-Factor method but yielding the atomic accessiblity instead. But Biopython seems to type-check the .asa-file and complains that the B-factor is not of type float. Is there a way to access the data of .asa-files programmatically via the Biopython library? The only other way then seems to write a parser for .asa-files and to figure out which atomic element in the .pdb-file corresponds to the respective one in the .asa-file and finally to retrieve the wanted values for atomic accessiblity and van der Waal radius. Here are some more technical details. As an example I chose the '1DHR' protein: ------------------------------------------------------------------------------ def __init__(self,structure_id="1DHR",indices=[ 0]): # which residues are part of the patch self.indices = indices # If 1 (DEFAULT), the exceptions are caught, but some residues or atoms will be missing. # THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE! self.p=PDBParser(PERMISSIVE= 1) # which protein to analyse self.structure_id = structure_id self.fileName = self.structure_id + '.asa' self.structure = self.p.get_structure(self.structure_id, self.fileName) ------------------------------------------------------------------------------ Error message: Traceback (most recent call last): File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 249, in c = compact(indices=[0,1]) File "C:\Dokumente und Einstellungen\Renate D?hring\workspace\test\src\root\nested\compactness.py", line 17, in __init__ self.structure = self.p.get_structure(self.structure_id, self.fileName) File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 65, in get_structure self._parse(file.readlines()) File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 85, in _parse self.trailer=self._parse_coordinates(coords_trailer) File "C:\Python25\Lib\site-packages\Bio\PDB\PDBParser.py", line 159, in _parse_coordinates bfactor=float(line[60:66]) ValueError: invalid literal for float(): 31 1. ------------------------------------------------------------------------------ I hope this question above was not discussed before but neither the search engine at http://search.open-bio.org/cgi-bin/mail-search.cgi works nor could I find anything useful via a google search restricted to the archive using the 'site' attribute. What do you recommend for my situation. Many thanks! Yours, Orlando From edschofield at gmail.com Tue May 22 16:57:49 2007 From: edschofield at gmail.com (Ed Schofield) Date: Tue, 22 May 2007 17:57:49 +0100 Subject: [BioPython] Biopython to parse not only .pdb-files but also NACCESS .asa files In-Reply-To: References: Message-ID: <1b5a37350705220957o24f6a436k89d60764729695da@mail.gmail.com> On 21 May 2007 20:45:36 +0100, O.Doehring at cs.ucl.ac.uk wrote: > > ValueError: invalid literal for float(): 31 1. > > ... > > What do you recommend for my situation. Many thanks! Is that a space between 31 and 1? There's your problem. My advice is to insert import pdb pdb.set_trace() at line 159 in PDBParser.py and check out why the columns in your data are misaligned with what PDBParser.py expects. A quick scan of nac_readme.html implies that perhaps you need the -f argument to give you the full output format? But if you need to write your own parser for .asa files, you could use _parse_coordinates(self, coords_trailer) as a template. -- Ed From sbassi at gmail.com Thu May 31 03:37:52 2007 From: sbassi at gmail.com (Sebastian Bassi) Date: Thu, 31 May 2007 00:37:52 -0300 Subject: [BioPython] 454 sample file Message-ID: Hello, Does anyboy have a 454 sequence output sample file? It is XML so should be easy to write a parser. I don't have access to such machine (we are stuck with ABI 31xx series) so I would be glad to receive one file (you can scramble the sequence if it is private). Best, SB. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From chris.lasher at gmail.com Thu May 31 04:23:39 2007 From: chris.lasher at gmail.com (Chris Lasher) Date: Thu, 31 May 2007 00:23:39 -0400 Subject: [BioPython] 454 sample file In-Reply-To: References: Message-ID: <128a885f0705302123v68b8c246nb69d4d375f2eabcf@mail.gmail.com> 454 sent a FASTA format file that contained sequence data when I worked on a project last year. I don't suspect they provide the raw flowgrams; at least they didn't in our experiences with them. You can use Biopython's SeqIO to work with the FASTA file. Best, Chris On 5/30/07, Sebastian Bassi wrote: > Hello, > > Does anyboy have a 454 sequence output sample file? It is XML so > should be easy to write a parser. I don't have access to such machine > (we are stuck with ABI 31xx series) so I would be glad to receive one > file (you can scramble the sequence if it is private). > Best, > SB. > > -- > Bioinformatics news: http://www.bioinformatica.info > Lriser: http://www.linspire.com/lraiser_success.php?serial=318 > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > From sbassi at gmail.com Thu May 31 05:00:26 2007 From: sbassi at gmail.com (Sebastian Bassi) Date: Thu, 31 May 2007 02:00:26 -0300 Subject: [BioPython] 454 sample file In-Reply-To: <128a885f0705302123v68b8c246nb69d4d375f2eabcf@mail.gmail.com> References: <128a885f0705302123v68b8c246nb69d4d375f2eabcf@mail.gmail.com> Message-ID: On 5/31/07, Chris Lasher wrote: > 454 sent a FASTA format file that contained sequence data when I > worked on a project last year. I don't suspect they provide the raw > flowgrams; at least they didn't in our experiences with them. You can > use Biopython's SeqIO to work with the FASTA file. I thought that someone could be working in a lab with a 454 machine and could send me an output file. Just to make the parser for someone that could need it in the future. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From thamelry at binf.ku.dk Thu May 31 09:39:54 2007 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Thu, 31 May 2007 11:39:54 +0200 Subject: [BioPython] Jobs in protein structure prediction Message-ID: <2d7c25310705310239w51dd27e5l9f900e735bc1653b@mail.gmail.com> Hi all, There are two postdoc and two PhD positions available in my group (University of Copenhagen, Denmark, http://www.binf.ku.dk/) on the topic of protein structure prediction. For details, see: http://www.binf.ku.dk/Job4Apr17 http://www.binf.ku.dk/JobsNABIIT_0507 The applicants are expected to use (and probably extend) Biopython/Bio.PDB. Best regards, ---- Thomas Hamelryck Group leader Structural Bioinformatics Bioinformatics center Institute of Molecular Biology University of Copenhagen Ole Maaloes Vej 5 DK-2200 Copenhagen N Denmark http://www.binf.ku.dk/User:Thomas_Hamelryck http://www.binf.ku.dk/Protein_structure From arareko at campus.iztacala.unam.mx Thu May 31 15:37:49 2007 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 31 May 2007 10:37:49 -0500 Subject: [BioPython] FreeBSD port updated Message-ID: <465EEBCD.9060200@campus.iztacala.unam.mx> Folks, The FreeBSD port for BioPython has been upgraded from 1.42 to 1.43. Many thanks to Paulo Bandiera for taking the time to create the update. If you run into any issues with the new version please let me know. Regards, Mauricio. -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM