From idoerg at burnham.org Tue Nov 7 12:48:05 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 07 Nov 2006 09:48:05 -0800 Subject: [BioPython] InterProScan parser? Message-ID: <4550C6D5.10606@burnham.org> Hi, Does anybody have an interproscan parser, by any chance? Preferably for the XML or EBIXML output. Thanks, Iddo -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From srini_iyyer_bio at yahoo.com Wed Nov 8 20:49:38 2006 From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer) Date: Wed, 8 Nov 2006 17:49:38 -0800 (PST) Subject: [BioPython] EUtils module Message-ID: <20061109014938.11961.qmail@web38113.mail.mud.yahoo.com> Dear Group, I downloaded EUtils module. I am trying to reproduce the code given in : http://www.dalkescientific.com/writings/diary/archive/2005/09/30/using_eutils.html I am getting Errors. I want to know which databases in Entrez are supported by EUtils. Could any one please help me whats the problem. Are not many people using EUtils. Thanks >>> import EUtils >>> dbs = EUtils.dblist() Traceback (most recent call last): File "", line 1, in -toplevel- dbs = EUtils.dblist() AttributeError: 'module' object has no attribute 'dblist' >>> dbinfo = EUtils.dbinfo("pubmed") Traceback (most recent call last): File "", line 1, in -toplevel- dbinfo = EUtils.dbinfo("pubmed") AttributeError: 'module' object has no attribute 'dbinfo' ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From srini_iyyer_bio at yahoo.com Wed Nov 8 21:03:45 2006 From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer) Date: Wed, 8 Nov 2006 18:03:45 -0800 (PST) Subject: [BioPython] Querying Entrez Gene - Use EUtils In-Reply-To: <200610101401.59622.luca.beltrame@unimi.it> Message-ID: <20061109020346.29413.qmail@web38114.mail.mud.yahoo.com> Hello, Previously, I used to download those flat files from NCBI ftp site. In fact, the most powerful 'nukes' created by NCBI staff to query Entrez named 'eUtils' are under utilized. I suggest you to take a look at : http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html I tried Dalke's Eutils module. There appears to be some (problem) with the modules, although some of the other examples worked. I wish Andrew Dalke or other elders of BioPython help us more by making it more clear. Andrew himself wrote that he does not have time to make it better. I wish I am a better programmer to help him. If not try using SOAP to query Entrez. --- Luca Beltrame wrote: > Hello. > I'm currently in need of querying the Entrez Gene > database using a list of IDs > I have. After searching in the Biopython > documentation, I have found no > indication of whether that is possible or not. > Is there a way to query NCBI's Entrez Gene database? > > Thanks in advance. > _______________________________________________ > BioPython mailing list - > BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > ____________________________________________________________________________________ Sponsored Link Degrees online in as fast as 1 Yr - MBA, Bachelor's, Master's, Associate Click now to apply http://yahoo.degrees.info From idoerg at burnham.org Wed Nov 8 21:39:23 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 08 Nov 2006 18:39:23 -0800 Subject: [BioPython] EUtils module In-Reply-To: <20061109014938.11961.qmail@web38113.mail.mud.yahoo.com> References: <20061109014938.11961.qmail@web38113.mail.mud.yahoo.com> Message-ID: <455294DB.6000105@burnham.org> Srinivas Iyyer wrote: > Dear Group, > > I downloaded EUtils module. > > I am trying to reproduce the code given in : > > http://www.dalkescientific.com/writings/diary/archive/2005/09/30/using_eutils.html > > I am getting Errors. This is code from an alpha version of EUtils used at a presentation. I don't think it was meant to be reproducible, or even made it into the final module. You might want to look under the hood. There is a README file in the EUtils installation, which has some examples. But NCBI change the EUtils specifications quite frequently, so chances are, if no one used EUtils ofr a while, that it might be broken. > > I want to know which databases in Entrez are supported > by EUtils. > > Could any one please help me whats the problem. > > Are not many people using EUtils. > > Thanks > >>>> import EUtils >>>> dbs = EUtils.dblist() > > Traceback (most recent call last): > File "", line 1, in -toplevel- > dbs = EUtils.dblist() > AttributeError: 'module' object has no attribute > 'dblist' >>>> dbinfo = EUtils.dbinfo("pubmed") > > Traceback (most recent call last): > File "", line 1, in -toplevel- > dbinfo = EUtils.dbinfo("pubmed") > AttributeError: 'module' object has no attribute > 'dbinfo' > > > > > > > > ____________________________________________________________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. > http://music.yahoo.com/unlimited > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From cariel at citic.es Tue Nov 14 06:56:17 2006 From: cariel at citic.es (Christian) Date: Tue, 14 Nov 2006 12:56:17 +0100 Subject: [BioPython] Blast implementation Message-ID: <00f601c707e3$eae89470$6901a8c0@christian> Hi, Anyone can help me where to find information in depth about NCBI C Implementation of Blast algorithm? I've read the book "BLAST by Joseph Bedell" and I understand the method but when I analyze the c code of ncbi there are many things that i don't understand Thaks in advance Christian From km at mrna.tn.nic.in Wed Nov 15 07:27:36 2006 From: km at mrna.tn.nic.in (km) Date: Wed, 15 Nov 2006 17:57:36 +0530 Subject: [BioPython] SProt module Message-ID: <20061115122736.GA10639@mrna.tn.nic.in> Hi all, SProt module no longer seems to work with current version of Uniprot KB database. do anyone have work around for this module ? regards, KM -- From cjfields at uiuc.edu Wed Nov 15 09:16:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:16:30 -0600 Subject: [BioPython] SProt module In-Reply-To: <20061115122736.GA10639@mrna.tn.nic.in> Message-ID: <000901c708c0$a8787c80$15327e82@pyrimidine> > -----Original Message----- > From: biopython-bounces at lists.open-bio.org > [mailto:biopython-bounces at lists.open-bio.org] On Behalf Of km > Sent: Wednesday, November 15, 2006 6:28 AM > To: BioPython at lists.open-bio.org > Subject: [BioPython] SProt module > > Hi all, > > SProt module no longer seems to work with current version of > Uniprot KB database. do anyone have work around for this module ? > > regards, > KM There have been recent changes in the format for the ID line in UniProt/SwisProt files, which could be part of the problem. We just fixed this in BioPerl; not sure how it would be handled in BioPython. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From biopython at maubp.freeserve.co.uk Thu Nov 16 07:48:34 2006 From: biopython at maubp.freeserve.co.uk (Peter (BioPython List)) Date: Thu, 16 Nov 2006 12:48:34 +0000 Subject: [BioPython] SProt module In-Reply-To: <000901c708c0$a8787c80$15327e82@pyrimidine> References: <000901c708c0$a8787c80$15327e82@pyrimidine> Message-ID: <455C5E22.1020102@maubp.freeserve.co.uk> Chris Fields wrote: >> Hi all, >> >> SProt module no longer seems to work with current version of >> Uniprot KB database. do anyone have work around for this module ? >> >> regards, >> KM > > There have been recent changes in the format for the ID line in > UniProt/SwisProt files, which could be part of the problem. We just fixed > this in BioPerl; not sure how it would be handled in BioPython. Hi KM As Chris points out, there have been a few format changes. I'm pretty sure that BioPython has been updated to cope: Bug 2131 - SProt.py fails to parse the current Swiss-Prot version 51.0 http://bugzilla.open-bio.org/show_bug.cgi?id=2131 Fixed Bug 2043 - SProt.py fails to parse the current Swiss-Prot version (RX and OH lines are broken) http://bugzilla.open-bio.org/show_bug.cgi?id=2043 Fixed These changes where made after BioPython 1.42 was released. I'm pretty sure that all you need to do is update the file Bio/SwissProt/SProt.py in your python site-library with the version from CVS, available here: http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SwissProt/SProt.py?cvsroot=biopython (Or, if you would rather, get the entire latest source code from CVS, and build and install that). If you find a problem with that code, then please let us know (ideally by logging a new bug). Peter From km at mrna.tn.nic.in Fri Nov 17 14:25:55 2006 From: km at mrna.tn.nic.in (km) Date: Sat, 18 Nov 2006 00:55:55 +0530 Subject: [BioPython] SProt module In-Reply-To: <455C5E22.1020102@maubp.freeserve.co.uk> References: <000901c708c0$a8787c80$15327e82@pyrimidine> <455C5E22.1020102@maubp.freeserve.co.uk> Message-ID: <20061117192555.GB30167@mrna.tn.nic.in> Hi, Oh! - too late to know that. I have fixed it myself but defining method for 'OH'- organism host apart from other changes. anyway will check out the official version from cvs too. thank you :) regards KM ------------------------------------------------------------------- > Hi KM > > As Chris points out, there have been a few format changes. I'm pretty > sure that BioPython has been updated to cope: > > Bug 2131 - SProt.py fails to parse the current Swiss-Prot version 51.0 > http://bugzilla.open-bio.org/show_bug.cgi?id=2131 > Fixed > > Bug 2043 - SProt.py fails to parse the current Swiss-Prot version (RX > and OH lines are broken) > http://bugzilla.open-bio.org/show_bug.cgi?id=2043 > Fixed > > These changes where made after BioPython 1.42 was released. > > I'm pretty sure that all you need to do is update the file > Bio/SwissProt/SProt.py in your python site-library with the version from > CVS, available here: > > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SwissProt/SProt.py?cvsroot=biopython > > (Or, if you would rather, get the entire latest source code from CVS, > and build and install that). > > If you find a problem with that code, then please let us know (ideally > by logging a new bug). > > Peter > From sbassi at gmail.com Sun Nov 26 19:20:52 2006 From: sbassi at gmail.com (Sebastian Bassi) Date: Sun, 26 Nov 2006 21:20:52 -0300 Subject: [BioPython] Report of blast 2.2.15 parsing error. Message-ID: I think I found a bug. I am using Biopython 1.42 and Blast 2.2.15. I got my blast output be running blastall like this: sbassi at hp:~/bioinfo/blast-2.2.15/bin$ ./blastall -p blastn -d ../data/patnt -i ../data/intest.faa -o ../data/BlastLocal The output is located here is you need to see it: http://www.bioinformatica.info/download/BlastLocal Here is my code: from Bio.Blast import NCBIStandalone bout=open('BlastLocal') b_parser=NCBIStandalone.BlastParser() b_record=b_parser.parse(bout) for alig in b_record.alignments: for hsp in alig.hsps: hitsequence=hsp.sbjct.replace("-","") if "Patent WO" in alig.title and len(hitsequence)>80: print alig.title+";"+hitsequence and this is the error I get: >>> Traceback (most recent call last): File "/home/sbassi/bioinfo/blastparser.py", line 4, in -toplevel- b_record=b_parser.parse(bout) File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", line 624, in parse self._scanner.feed(handle, self._consumer) File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", line 99, in feed self._scan_parameters(uhandle, consumer) File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", line 570, in _scan_parameters has_re=re.compile(r"[Ll]ength of \s*[Dd]atabase")) File "/usr/lib/python2.4/site-packages/Bio/ParserSupport.py", line 300, in read_and_call raise SyntaxError, errmsg SyntaxError: Line does not match regex '[Ll]ength of \s*[Dd]atabase': Number of HSP's gapped: 118145 This error is not a problem for me since I can use the xml output and it works fine (with the xml parser), but I was writting a tutorial and I found this error. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From meesters at uni-mainz.de Mon Nov 27 02:44:08 2006 From: meesters at uni-mainz.de (Christian Meesters) Date: Mon, 27 Nov 2006 08:44:08 +0100 Subject: [BioPython] "centering" pdb files Message-ID: <200611270844.08421.meesters@uni-mainz.de> Hi, I'm new to the list and just installed BioPython (wanted to do that, anyway - apart from the question I have). Many proteins have internal rotational symmetry. Is it possible to read in a PDB file and center in a way that the axis of the rotational symmetry and one axis of the coordinates aligns / is superimposed? Has anyone done that using BioPython or knows a different Python module which allows this? TIA Christian From thamelry at binf.ku.dk Mon Nov 27 03:28:30 2006 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Mon, 27 Nov 2006 09:28:30 +0100 Subject: [BioPython] "centering" pdb files In-Reply-To: <200611270844.08421.meesters@uni-mainz.de> References: <200611270844.08421.meesters@uni-mainz.de> Message-ID: <2d7c25310611270028s26f13508j824e14d0dd395626@mail.gmail.com> Hi, > Many proteins have internal rotational symmetry. Is it possible to read in a > PDB file and center in a way that the axis of the rotational symmetry and one > axis of the coordinates aligns / is superimposed? Has anyone done that using > BioPython or knows a different Python module which allows this? Take a look at Bio.PDB and the functions in the Vector module. That exact functionality is not there (not sure what you mean actually), but it would be fairly easy to implement. Hint: you can apply tranlstions/rotations to atoms using the transform method of the Atom class. Best, -Thomas From s9heweis at stud.uni-saarland.de Mon Nov 27 22:18:59 2006 From: s9heweis at stud.uni-saarland.de (Hendrik Weisser) Date: Tue, 28 Nov 2006 04:18:59 +0100 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree Message-ID: <005301c7129b$f3222300$b400a8c0@Sirius> Hi, I'm new to BioPython and although I can already see how greatly helpful the package could be for me, I have some problems using it on Windows, with Python 2.5 (specifically, the Bio.PDB module, which is what I need at the moment). 1. issue: BioPython requires the package Numeric, which is no longer supported and - what's worse - *not available* for Python 2.5. I could fix this by manually changing the code to import numpy instead, so that "from Bio.PDB import *" would work. But I don't think it's a good idea to put an installer for use with Python 2.5 on the website, if the requirements cannot be met directly... 2. issue: I want to use the NeighborSearch class in Bio.PDB, but the required KDTree module doesn't get made during install. I already found out that the corresponding section in setup.py in the sources is commented out ("Disabled by default to avoid C++ compilation errors"), but uncommenting this and trying to build from the source doesn't work for me. Therefore, a new Windows installer that includes KDTree would be very much appreciated (according to the mailing list archives, this solved the same problem when it occurred with Python 2.4). 3. issue (bug?): In the Entity class in Bio.PDB, the method "get_full_id()" fails because (typically) at the structure level, get_parent() throws an exception (which is not handled later) instead of returning "None". The main question for me is whether these issues (the 2nd, mostly) can be adressed quickly, or whether it is recommended to use the "old" Python 2.4 and corresponding packages for the time being. Can anyone help me with that? Thanks in advance Hendrik Weisser From thamelry at binf.ku.dk Tue Nov 28 03:15:37 2006 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Tue, 28 Nov 2006 09:15:37 +0100 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree In-Reply-To: <005301c7129b$f3222300$b400a8c0@Sirius> References: <005301c7129b$f3222300$b400a8c0@Sirius> Message-ID: <2d7c25310611280015i5c40760h94a6085cb90929@mail.gmail.com> Hi Hendrik, 3. issue (bug?): > In the Entity class in Bio.PDB, the method "get_full_id()" fails because > (typically) at the structure level, get_parent() throws an exception > (which > is not handled later) instead of returning "None". This is already fixed in CVS. About numpy: biopython should indeed move to numpy now. The numpy toolkit has matured and Numeric is definitely obsolete now. About KDTree: I know next to nothing about Windows but maybe Cygwin compilation is a solution? Best, -Thomas ---- Thomas Hamelryck, Marie Curie EU-Research fellow Bioinformatics center Institute of Molecular Biology University of Copenhagen Universitetsparken 15 - Building 10 DK-2100 Copenhagen ? Denmark Homepage: http://www.binf.ku.dk/Protein_structure From mdehoon at c2b2.columbia.edu Tue Nov 28 11:24:15 2006 From: mdehoon at c2b2.columbia.edu (Michiel Jan Laurens de Hoon) Date: Tue, 28 Nov 2006 11:24:15 -0500 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree In-Reply-To: <005301c7129b$f3222300$b400a8c0@Sirius> References: <005301c7129b$f3222300$b400a8c0@Sirius> Message-ID: <456C62AF.5020201@c2b2.columbia.edu> Hendrik Weisser wrote: > 1. issue: > BioPython requires the package Numeric, which is no longer supported and - > what's worse - *not available* for Python 2.5. > I could fix this by manually changing the code to import numpy instead, so > that "from Bio.PDB import *" would work. But I don't think it's a good idea > to put an installer for use with Python 2.5 on the website, if the > requirements cannot be met directly... > As a temporary solution, I've put a Windows installer for Numeric for Python 2.5 on the Biopython website. See the download page under Required Software. --Michiel. -- Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1130 St Nicholas Avenue New York, NY 10032 From mdehoon at c2b2.columbia.edu Tue Nov 28 11:15:00 2006 From: mdehoon at c2b2.columbia.edu (Michiel Jan Laurens de Hoon) Date: Tue, 28 Nov 2006 11:15:00 -0500 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree In-Reply-To: <005301c7129b$f3222300$b400a8c0@Sirius> References: <005301c7129b$f3222300$b400a8c0@Sirius> Message-ID: <456C6084.7050504@c2b2.columbia.edu> Hendrik Weisser wrote: > 2. issue: > I want to use the NeighborSearch class in Bio.PDB, but the required KDTree > module doesn't get made during install. > I already found out that the corresponding section in setup.py in the > sources is commented out ("Disabled by default to avoid C++ compilation > errors"), but uncommenting this and trying to build from the source doesn't > work for me. Therefore, a new Windows installer that includes KDTree would > be very much appreciated (according to the mailing list archives, this > solved the same problem when it occurred with Python 2.4). I have replaced the Windows installers for Python 2.3 and 2.5 with new ones that include KDTree. The Windows installer for Python 2.4 already included KDTree. --Michiel. -- Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1130 St Nicholas Avenue New York, NY 10032 From sdavis2 at mail.nih.gov Wed Nov 29 14:30:01 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 29 Nov 2006 14:30:01 -0500 Subject: [BioPython] Graphics similar to bioperl Bio::Graphics Message-ID: <200611291430.01627.sdavis2@mail.nih.gov> I have some data that I would like to display in a genome browser-type view. I've looked around and haven't found anything quite akin to Bio::Graphics (from Lincoln Stein) in python. Does such a thing exist? If not, what are folks using for graphics work? Thanks, Sean From s9heweis at stud.uni-saarland.de Wed Nov 29 18:23:01 2006 From: s9heweis at stud.uni-saarland.de (Hendrik Weisser) Date: Thu, 30 Nov 2006 00:23:01 +0100 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree References: <005301c7129b$f3222300$b400a8c0@Sirius> <456C6084.7050504@c2b2.columbia.edu> Message-ID: <001b01c7140d$508d0ce0$b400a8c0@Sirius> Hi! I've tried the new installers and everything works like a charm now. :-) Just wanted to let you know and say thank you for helping me out on such short notice. (I hope this is not considered spamming...) Regards Hendrik From lpritc at scri.ac.uk Thu Nov 30 05:09:05 2006 From: lpritc at scri.ac.uk (Leighton Pritchard) Date: Thu, 30 Nov 2006 10:09:05 +0000 Subject: [BioPython] Graphics similar to bioperl Bio::Graphics In-Reply-To: <200611291430.01627.sdavis2@mail.nih.gov> References: <200611291430.01627.sdavis2@mail.nih.gov> Message-ID: <1164881345.20253.0.camel@lplinuxdev.scri.sari.ac.uk> Hi Sean, There isn't anything directly comparable to Bio::Graphics as far as I am aware, but I think there are a couple of graphics packages in BioPython. I have written scripts, using the Python Imaging Library, to generate graphical summaries of BLAST output similar to Bio::Graphics output, and you're welcome to those, if you like (they are *very* ad hoc, though, and I'm not proud of them). Also, and possibly more suited to what you want, there is GenomeDiagram, which uses BioPython and ReportLab to generate images of genome-scale data. You can find that at http://bioinf.scri.ac.uk/lp/programs.html#genomediagram - I have plans to change the structure significantly, and use a different backend for browsing interactively (ATM you have to open up the images in something like Acrobat Reader), but there's no motion on that, yet. I wrote it mostly because there wasn't a Bio::Graphics equivalent module. As an aside, I'm happy to contribute the GenomeDiagram code to BioPython, if people are interested. L. On Wed, 2006-11-29 at 14:30 -0500, Sean Davis wrote: > I have some data that I would like to display in a genome browser-type view. > I've looked around and haven't found anything quite akin to Bio::Graphics > (from Lincoln Stein) in python. Does such a thing exist? If not, what are > folks using for graphics work? > > Thanks, > Sean > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > -- Dr Leighton Pritchard AMRSC D131, Plant Pathology, Scottish Crop Research Institute W: http://bioinf.scri.ac.uk/lp E: lpritc at scri.ac.uk GPG: 0xE58BA41B _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.sari.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). From Leighton.Pritchard at scri.ac.uk Thu Nov 30 04:49:50 2006 From: Leighton.Pritchard at scri.ac.uk (Leighton Pritchard) Date: Thu, 30 Nov 2006 09:49:50 -0000 Subject: [BioPython] Graphics similar to bioperl Bio::Graphics In-Reply-To: <200611291430.01627.sdavis2@mail.nih.gov> References: <200611291430.01627.sdavis2@mail.nih.gov> Message-ID: <1164880190.6758.60.camel@lplinuxdev.scri.sari.ac.uk> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://lists.open-bio.org/pipermail/biopython/attachments/20061130/197e6e3e/attachment.ksh -------------- next part -------------- An embedded message was scrubbed... From: "Leighton Pritchard" Subject: Re: [BioPython] Graphics similar to bioperl Bio::Graphics Date: Thu, 30 Nov 2006 09:49:50 -0000 Size: 3533 Url: http://lists.open-bio.org/pipermail/biopython/attachments/20061130/197e6e3e/attachment.mht From idoerg at burnham.org Tue Nov 7 17:48:05 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 07 Nov 2006 09:48:05 -0800 Subject: [BioPython] InterProScan parser? Message-ID: <4550C6D5.10606@burnham.org> Hi, Does anybody have an interproscan parser, by any chance? Preferably for the XML or EBIXML output. Thanks, Iddo -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From srini_iyyer_bio at yahoo.com Thu Nov 9 01:49:38 2006 From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer) Date: Wed, 8 Nov 2006 17:49:38 -0800 (PST) Subject: [BioPython] EUtils module Message-ID: <20061109014938.11961.qmail@web38113.mail.mud.yahoo.com> Dear Group, I downloaded EUtils module. I am trying to reproduce the code given in : http://www.dalkescientific.com/writings/diary/archive/2005/09/30/using_eutils.html I am getting Errors. I want to know which databases in Entrez are supported by EUtils. Could any one please help me whats the problem. Are not many people using EUtils. Thanks >>> import EUtils >>> dbs = EUtils.dblist() Traceback (most recent call last): File "", line 1, in -toplevel- dbs = EUtils.dblist() AttributeError: 'module' object has no attribute 'dblist' >>> dbinfo = EUtils.dbinfo("pubmed") Traceback (most recent call last): File "", line 1, in -toplevel- dbinfo = EUtils.dbinfo("pubmed") AttributeError: 'module' object has no attribute 'dbinfo' ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From srini_iyyer_bio at yahoo.com Thu Nov 9 02:03:45 2006 From: srini_iyyer_bio at yahoo.com (Srinivas Iyyer) Date: Wed, 8 Nov 2006 18:03:45 -0800 (PST) Subject: [BioPython] Querying Entrez Gene - Use EUtils In-Reply-To: <200610101401.59622.luca.beltrame@unimi.it> Message-ID: <20061109020346.29413.qmail@web38114.mail.mud.yahoo.com> Hello, Previously, I used to download those flat files from NCBI ftp site. In fact, the most powerful 'nukes' created by NCBI staff to query Entrez named 'eUtils' are under utilized. I suggest you to take a look at : http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html I tried Dalke's Eutils module. There appears to be some (problem) with the modules, although some of the other examples worked. I wish Andrew Dalke or other elders of BioPython help us more by making it more clear. Andrew himself wrote that he does not have time to make it better. I wish I am a better programmer to help him. If not try using SOAP to query Entrez. --- Luca Beltrame wrote: > Hello. > I'm currently in need of querying the Entrez Gene > database using a list of IDs > I have. After searching in the Biopython > documentation, I have found no > indication of whether that is possible or not. > Is there a way to query NCBI's Entrez Gene database? > > Thanks in advance. > _______________________________________________ > BioPython mailing list - > BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > ____________________________________________________________________________________ Sponsored Link Degrees online in as fast as 1 Yr - MBA, Bachelor's, Master's, Associate Click now to apply http://yahoo.degrees.info From idoerg at burnham.org Thu Nov 9 02:39:23 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 08 Nov 2006 18:39:23 -0800 Subject: [BioPython] EUtils module In-Reply-To: <20061109014938.11961.qmail@web38113.mail.mud.yahoo.com> References: <20061109014938.11961.qmail@web38113.mail.mud.yahoo.com> Message-ID: <455294DB.6000105@burnham.org> Srinivas Iyyer wrote: > Dear Group, > > I downloaded EUtils module. > > I am trying to reproduce the code given in : > > http://www.dalkescientific.com/writings/diary/archive/2005/09/30/using_eutils.html > > I am getting Errors. This is code from an alpha version of EUtils used at a presentation. I don't think it was meant to be reproducible, or even made it into the final module. You might want to look under the hood. There is a README file in the EUtils installation, which has some examples. But NCBI change the EUtils specifications quite frequently, so chances are, if no one used EUtils ofr a while, that it might be broken. > > I want to know which databases in Entrez are supported > by EUtils. > > Could any one please help me whats the problem. > > Are not many people using EUtils. > > Thanks > >>>> import EUtils >>>> dbs = EUtils.dblist() > > Traceback (most recent call last): > File "", line 1, in -toplevel- > dbs = EUtils.dblist() > AttributeError: 'module' object has no attribute > 'dblist' >>>> dbinfo = EUtils.dbinfo("pubmed") > > Traceback (most recent call last): > File "", line 1, in -toplevel- > dbinfo = EUtils.dbinfo("pubmed") > AttributeError: 'module' object has no attribute > 'dbinfo' > > > > > > > > ____________________________________________________________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. > http://music.yahoo.com/unlimited > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From cariel at citic.es Tue Nov 14 11:56:17 2006 From: cariel at citic.es (Christian) Date: Tue, 14 Nov 2006 12:56:17 +0100 Subject: [BioPython] Blast implementation Message-ID: <00f601c707e3$eae89470$6901a8c0@christian> Hi, Anyone can help me where to find information in depth about NCBI C Implementation of Blast algorithm? I've read the book "BLAST by Joseph Bedell" and I understand the method but when I analyze the c code of ncbi there are many things that i don't understand Thaks in advance Christian From km at mrna.tn.nic.in Wed Nov 15 12:27:36 2006 From: km at mrna.tn.nic.in (km) Date: Wed, 15 Nov 2006 17:57:36 +0530 Subject: [BioPython] SProt module Message-ID: <20061115122736.GA10639@mrna.tn.nic.in> Hi all, SProt module no longer seems to work with current version of Uniprot KB database. do anyone have work around for this module ? regards, KM -- From cjfields at uiuc.edu Wed Nov 15 14:16:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:16:30 -0600 Subject: [BioPython] SProt module In-Reply-To: <20061115122736.GA10639@mrna.tn.nic.in> Message-ID: <000901c708c0$a8787c80$15327e82@pyrimidine> > -----Original Message----- > From: biopython-bounces at lists.open-bio.org > [mailto:biopython-bounces at lists.open-bio.org] On Behalf Of km > Sent: Wednesday, November 15, 2006 6:28 AM > To: BioPython at lists.open-bio.org > Subject: [BioPython] SProt module > > Hi all, > > SProt module no longer seems to work with current version of > Uniprot KB database. do anyone have work around for this module ? > > regards, > KM There have been recent changes in the format for the ID line in UniProt/SwisProt files, which could be part of the problem. We just fixed this in BioPerl; not sure how it would be handled in BioPython. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From biopython at maubp.freeserve.co.uk Thu Nov 16 12:48:34 2006 From: biopython at maubp.freeserve.co.uk (Peter (BioPython List)) Date: Thu, 16 Nov 2006 12:48:34 +0000 Subject: [BioPython] SProt module In-Reply-To: <000901c708c0$a8787c80$15327e82@pyrimidine> References: <000901c708c0$a8787c80$15327e82@pyrimidine> Message-ID: <455C5E22.1020102@maubp.freeserve.co.uk> Chris Fields wrote: >> Hi all, >> >> SProt module no longer seems to work with current version of >> Uniprot KB database. do anyone have work around for this module ? >> >> regards, >> KM > > There have been recent changes in the format for the ID line in > UniProt/SwisProt files, which could be part of the problem. We just fixed > this in BioPerl; not sure how it would be handled in BioPython. Hi KM As Chris points out, there have been a few format changes. I'm pretty sure that BioPython has been updated to cope: Bug 2131 - SProt.py fails to parse the current Swiss-Prot version 51.0 http://bugzilla.open-bio.org/show_bug.cgi?id=2131 Fixed Bug 2043 - SProt.py fails to parse the current Swiss-Prot version (RX and OH lines are broken) http://bugzilla.open-bio.org/show_bug.cgi?id=2043 Fixed These changes where made after BioPython 1.42 was released. I'm pretty sure that all you need to do is update the file Bio/SwissProt/SProt.py in your python site-library with the version from CVS, available here: http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SwissProt/SProt.py?cvsroot=biopython (Or, if you would rather, get the entire latest source code from CVS, and build and install that). If you find a problem with that code, then please let us know (ideally by logging a new bug). Peter From km at mrna.tn.nic.in Fri Nov 17 19:25:55 2006 From: km at mrna.tn.nic.in (km) Date: Sat, 18 Nov 2006 00:55:55 +0530 Subject: [BioPython] SProt module In-Reply-To: <455C5E22.1020102@maubp.freeserve.co.uk> References: <000901c708c0$a8787c80$15327e82@pyrimidine> <455C5E22.1020102@maubp.freeserve.co.uk> Message-ID: <20061117192555.GB30167@mrna.tn.nic.in> Hi, Oh! - too late to know that. I have fixed it myself but defining method for 'OH'- organism host apart from other changes. anyway will check out the official version from cvs too. thank you :) regards KM ------------------------------------------------------------------- > Hi KM > > As Chris points out, there have been a few format changes. I'm pretty > sure that BioPython has been updated to cope: > > Bug 2131 - SProt.py fails to parse the current Swiss-Prot version 51.0 > http://bugzilla.open-bio.org/show_bug.cgi?id=2131 > Fixed > > Bug 2043 - SProt.py fails to parse the current Swiss-Prot version (RX > and OH lines are broken) > http://bugzilla.open-bio.org/show_bug.cgi?id=2043 > Fixed > > These changes where made after BioPython 1.42 was released. > > I'm pretty sure that all you need to do is update the file > Bio/SwissProt/SProt.py in your python site-library with the version from > CVS, available here: > > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SwissProt/SProt.py?cvsroot=biopython > > (Or, if you would rather, get the entire latest source code from CVS, > and build and install that). > > If you find a problem with that code, then please let us know (ideally > by logging a new bug). > > Peter > From sbassi at gmail.com Mon Nov 27 00:20:52 2006 From: sbassi at gmail.com (Sebastian Bassi) Date: Sun, 26 Nov 2006 21:20:52 -0300 Subject: [BioPython] Report of blast 2.2.15 parsing error. Message-ID: I think I found a bug. I am using Biopython 1.42 and Blast 2.2.15. I got my blast output be running blastall like this: sbassi at hp:~/bioinfo/blast-2.2.15/bin$ ./blastall -p blastn -d ../data/patnt -i ../data/intest.faa -o ../data/BlastLocal The output is located here is you need to see it: http://www.bioinformatica.info/download/BlastLocal Here is my code: from Bio.Blast import NCBIStandalone bout=open('BlastLocal') b_parser=NCBIStandalone.BlastParser() b_record=b_parser.parse(bout) for alig in b_record.alignments: for hsp in alig.hsps: hitsequence=hsp.sbjct.replace("-","") if "Patent WO" in alig.title and len(hitsequence)>80: print alig.title+";"+hitsequence and this is the error I get: >>> Traceback (most recent call last): File "/home/sbassi/bioinfo/blastparser.py", line 4, in -toplevel- b_record=b_parser.parse(bout) File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", line 624, in parse self._scanner.feed(handle, self._consumer) File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", line 99, in feed self._scan_parameters(uhandle, consumer) File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", line 570, in _scan_parameters has_re=re.compile(r"[Ll]ength of \s*[Dd]atabase")) File "/usr/lib/python2.4/site-packages/Bio/ParserSupport.py", line 300, in read_and_call raise SyntaxError, errmsg SyntaxError: Line does not match regex '[Ll]ength of \s*[Dd]atabase': Number of HSP's gapped: 118145 This error is not a problem for me since I can use the xml output and it works fine (with the xml parser), but I was writting a tutorial and I found this error. -- Bioinformatics news: http://www.bioinformatica.info Lriser: http://www.linspire.com/lraiser_success.php?serial=318 From meesters at uni-mainz.de Mon Nov 27 07:44:08 2006 From: meesters at uni-mainz.de (Christian Meesters) Date: Mon, 27 Nov 2006 08:44:08 +0100 Subject: [BioPython] "centering" pdb files Message-ID: <200611270844.08421.meesters@uni-mainz.de> Hi, I'm new to the list and just installed BioPython (wanted to do that, anyway - apart from the question I have). Many proteins have internal rotational symmetry. Is it possible to read in a PDB file and center in a way that the axis of the rotational symmetry and one axis of the coordinates aligns / is superimposed? Has anyone done that using BioPython or knows a different Python module which allows this? TIA Christian From thamelry at binf.ku.dk Mon Nov 27 08:28:30 2006 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Mon, 27 Nov 2006 09:28:30 +0100 Subject: [BioPython] "centering" pdb files In-Reply-To: <200611270844.08421.meesters@uni-mainz.de> References: <200611270844.08421.meesters@uni-mainz.de> Message-ID: <2d7c25310611270028s26f13508j824e14d0dd395626@mail.gmail.com> Hi, > Many proteins have internal rotational symmetry. Is it possible to read in a > PDB file and center in a way that the axis of the rotational symmetry and one > axis of the coordinates aligns / is superimposed? Has anyone done that using > BioPython or knows a different Python module which allows this? Take a look at Bio.PDB and the functions in the Vector module. That exact functionality is not there (not sure what you mean actually), but it would be fairly easy to implement. Hint: you can apply tranlstions/rotations to atoms using the transform method of the Atom class. Best, -Thomas From s9heweis at stud.uni-saarland.de Tue Nov 28 03:18:59 2006 From: s9heweis at stud.uni-saarland.de (Hendrik Weisser) Date: Tue, 28 Nov 2006 04:18:59 +0100 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree Message-ID: <005301c7129b$f3222300$b400a8c0@Sirius> Hi, I'm new to BioPython and although I can already see how greatly helpful the package could be for me, I have some problems using it on Windows, with Python 2.5 (specifically, the Bio.PDB module, which is what I need at the moment). 1. issue: BioPython requires the package Numeric, which is no longer supported and - what's worse - *not available* for Python 2.5. I could fix this by manually changing the code to import numpy instead, so that "from Bio.PDB import *" would work. But I don't think it's a good idea to put an installer for use with Python 2.5 on the website, if the requirements cannot be met directly... 2. issue: I want to use the NeighborSearch class in Bio.PDB, but the required KDTree module doesn't get made during install. I already found out that the corresponding section in setup.py in the sources is commented out ("Disabled by default to avoid C++ compilation errors"), but uncommenting this and trying to build from the source doesn't work for me. Therefore, a new Windows installer that includes KDTree would be very much appreciated (according to the mailing list archives, this solved the same problem when it occurred with Python 2.4). 3. issue (bug?): In the Entity class in Bio.PDB, the method "get_full_id()" fails because (typically) at the structure level, get_parent() throws an exception (which is not handled later) instead of returning "None". The main question for me is whether these issues (the 2nd, mostly) can be adressed quickly, or whether it is recommended to use the "old" Python 2.4 and corresponding packages for the time being. Can anyone help me with that? Thanks in advance Hendrik Weisser From thamelry at binf.ku.dk Tue Nov 28 08:15:37 2006 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Tue, 28 Nov 2006 09:15:37 +0100 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree In-Reply-To: <005301c7129b$f3222300$b400a8c0@Sirius> References: <005301c7129b$f3222300$b400a8c0@Sirius> Message-ID: <2d7c25310611280015i5c40760h94a6085cb90929@mail.gmail.com> Hi Hendrik, 3. issue (bug?): > In the Entity class in Bio.PDB, the method "get_full_id()" fails because > (typically) at the structure level, get_parent() throws an exception > (which > is not handled later) instead of returning "None". This is already fixed in CVS. About numpy: biopython should indeed move to numpy now. The numpy toolkit has matured and Numeric is definitely obsolete now. About KDTree: I know next to nothing about Windows but maybe Cygwin compilation is a solution? Best, -Thomas ---- Thomas Hamelryck, Marie Curie EU-Research fellow Bioinformatics center Institute of Molecular Biology University of Copenhagen Universitetsparken 15 - Building 10 DK-2100 Copenhagen ? Denmark Homepage: http://www.binf.ku.dk/Protein_structure From mdehoon at c2b2.columbia.edu Tue Nov 28 16:24:15 2006 From: mdehoon at c2b2.columbia.edu (Michiel Jan Laurens de Hoon) Date: Tue, 28 Nov 2006 11:24:15 -0500 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree In-Reply-To: <005301c7129b$f3222300$b400a8c0@Sirius> References: <005301c7129b$f3222300$b400a8c0@Sirius> Message-ID: <456C62AF.5020201@c2b2.columbia.edu> Hendrik Weisser wrote: > 1. issue: > BioPython requires the package Numeric, which is no longer supported and - > what's worse - *not available* for Python 2.5. > I could fix this by manually changing the code to import numpy instead, so > that "from Bio.PDB import *" would work. But I don't think it's a good idea > to put an installer for use with Python 2.5 on the website, if the > requirements cannot be met directly... > As a temporary solution, I've put a Windows installer for Numeric for Python 2.5 on the Biopython website. See the download page under Required Software. --Michiel. -- Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1130 St Nicholas Avenue New York, NY 10032 From mdehoon at c2b2.columbia.edu Tue Nov 28 16:15:00 2006 From: mdehoon at c2b2.columbia.edu (Michiel Jan Laurens de Hoon) Date: Tue, 28 Nov 2006 11:15:00 -0500 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree In-Reply-To: <005301c7129b$f3222300$b400a8c0@Sirius> References: <005301c7129b$f3222300$b400a8c0@Sirius> Message-ID: <456C6084.7050504@c2b2.columbia.edu> Hendrik Weisser wrote: > 2. issue: > I want to use the NeighborSearch class in Bio.PDB, but the required KDTree > module doesn't get made during install. > I already found out that the corresponding section in setup.py in the > sources is commented out ("Disabled by default to avoid C++ compilation > errors"), but uncommenting this and trying to build from the source doesn't > work for me. Therefore, a new Windows installer that includes KDTree would > be very much appreciated (according to the mailing list archives, this > solved the same problem when it occurred with Python 2.4). I have replaced the Windows installers for Python 2.3 and 2.5 with new ones that include KDTree. The Windows installer for Python 2.4 already included KDTree. --Michiel. -- Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1130 St Nicholas Avenue New York, NY 10032 From sdavis2 at mail.nih.gov Wed Nov 29 19:30:01 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 29 Nov 2006 14:30:01 -0500 Subject: [BioPython] Graphics similar to bioperl Bio::Graphics Message-ID: <200611291430.01627.sdavis2@mail.nih.gov> I have some data that I would like to display in a genome browser-type view. I've looked around and haven't found anything quite akin to Bio::Graphics (from Lincoln Stein) in python. Does such a thing exist? If not, what are folks using for graphics work? Thanks, Sean From s9heweis at stud.uni-saarland.de Wed Nov 29 23:23:01 2006 From: s9heweis at stud.uni-saarland.de (Hendrik Weisser) Date: Thu, 30 Nov 2006 00:23:01 +0100 Subject: [BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree References: <005301c7129b$f3222300$b400a8c0@Sirius> <456C6084.7050504@c2b2.columbia.edu> Message-ID: <001b01c7140d$508d0ce0$b400a8c0@Sirius> Hi! I've tried the new installers and everything works like a charm now. :-) Just wanted to let you know and say thank you for helping me out on such short notice. (I hope this is not considered spamming...) Regards Hendrik From lpritc at scri.ac.uk Thu Nov 30 10:09:05 2006 From: lpritc at scri.ac.uk (Leighton Pritchard) Date: Thu, 30 Nov 2006 10:09:05 +0000 Subject: [BioPython] Graphics similar to bioperl Bio::Graphics In-Reply-To: <200611291430.01627.sdavis2@mail.nih.gov> References: <200611291430.01627.sdavis2@mail.nih.gov> Message-ID: <1164881345.20253.0.camel@lplinuxdev.scri.sari.ac.uk> Hi Sean, There isn't anything directly comparable to Bio::Graphics as far as I am aware, but I think there are a couple of graphics packages in BioPython. I have written scripts, using the Python Imaging Library, to generate graphical summaries of BLAST output similar to Bio::Graphics output, and you're welcome to those, if you like (they are *very* ad hoc, though, and I'm not proud of them). Also, and possibly more suited to what you want, there is GenomeDiagram, which uses BioPython and ReportLab to generate images of genome-scale data. You can find that at http://bioinf.scri.ac.uk/lp/programs.html#genomediagram - I have plans to change the structure significantly, and use a different backend for browsing interactively (ATM you have to open up the images in something like Acrobat Reader), but there's no motion on that, yet. I wrote it mostly because there wasn't a Bio::Graphics equivalent module. As an aside, I'm happy to contribute the GenomeDiagram code to BioPython, if people are interested. L. On Wed, 2006-11-29 at 14:30 -0500, Sean Davis wrote: > I have some data that I would like to display in a genome browser-type view. > I've looked around and haven't found anything quite akin to Bio::Graphics > (from Lincoln Stein) in python. Does such a thing exist? If not, what are > folks using for graphics work? > > Thanks, > Sean > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > -- Dr Leighton Pritchard AMRSC D131, Plant Pathology, Scottish Crop Research Institute W: http://bioinf.scri.ac.uk/lp E: lpritc at scri.ac.uk GPG: 0xE58BA41B _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.sari.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). From Leighton.Pritchard at scri.ac.uk Thu Nov 30 09:49:50 2006 From: Leighton.Pritchard at scri.ac.uk (Leighton Pritchard) Date: Thu, 30 Nov 2006 09:49:50 -0000 Subject: [BioPython] Graphics similar to bioperl Bio::Graphics In-Reply-To: <200611291430.01627.sdavis2@mail.nih.gov> References: <200611291430.01627.sdavis2@mail.nih.gov> Message-ID: <1164880190.6758.60.camel@lplinuxdev.scri.sari.ac.uk> An embedded and charset-unspecified text was scrubbed... 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