5 Aug 2004 05:06
6 Aug 2004 00:36
[Bug 1675] New: complement() returns string instead of Seq object
<bugzilla-daemon <at> portal.open-bio.org>
2004-08-05 22:36:54 GMT
2004-08-05 22:36:54 GMT
http://bugzilla.open-bio.org/show_bug.cgi?id=1675 Summary: complement() returns string instead of Seq object Product: Biopython Version: Not Applicable Platform: Macintosh OS/Version: MacOS X Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev <at> biopython.org ReportedBy: martin.ligr <at> rockefeller.edu complement in SeqUtils (and therefore also antiparallel) return string, but a Seq object would be more logical, IMHO. The way it is now one has to type additional code to get a Seq obj. back. (Ideal would be complement, reverse, and reverse_complement as MutableSeq methods, though.) ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.
10 Aug 2004 04:16
biopython-dev <at> biopython.org Press release
info <lfinancing <at> runbox.com>
2004-08-10 02:16:27 GMT
2004-08-10 02:16:27 GMT
biopython-dev <at> biopython.org Canadian Subsidy Directory 4865 Hwy 138,R.R 1 Saint-Andrews West Ontario, KOC 2A0 PRESS RELEASE CANADIAN SUBSIDY DIRECTORY 2004 EDITION Legal Deposit-National Library of Canada: ISBN 2-922870-05-7 The newly revised Canadian Subsidy Directory 2004 edition is now available. A guide containing information to more than 2000 direct and indirect subsidies, grants, and loans offered by various levels of Government; Foundation; Association; and other similar Organizations. Over 20 000 copies sold. The Canadian Subsidy Directory is a most comprehensive and a much needed tool to create or enrich any business. A true valuable resource required to improve your cost efficiency with crucial information held by professionals. Agriculture; Transport; Communication; Education; Import-Export; Labor; Research & Development; Arts, Theater, Music & Entertainment; Hospitality & Culinary Services; Notably the(Continue reading)
13 Aug 2004 00:22
Re: Blast invent his own sequence
Brad Chapman <chapmanb <at> 50mail.com>
2004-08-12 22:22:46 GMT
2004-08-12 22:22:46 GMT
Hi Sylvain; > I tried to parse a blast result using the code above. It was > working quite well till I tried a specific file. For all the > previous Blast I've done, everything were working, the parsing > of blast result very good. > But for one file I've a problem. > > The file (see enc.) look totally normal, like a Fasta file > with thousand entries. But when I use it in a blast (with blast > library from BioPython, of course), in the ouput file a new entry > appears, always at the same place. First, please do not send large files like this as attachments to the mailing list. Your problem is more likely to have someone look at it if you can distill your problem down to a use case that we can examine. If you feel it is impossible for you to narrow the problem down to a smaller file, then please either put the file on a web page to be downloaded, or file a bug in our bug tracker and attach it there. Okay, but on to the problem. This does not have anything to do with Biopython, but is a problem with your input file. The input file is not FASTA format. Fasta looks like: > Title GAGAGAGA Your file has additional '//' lines for some reason.(Continue reading)
13 Aug 2004 13:19
Restriction analysis package.
fsms <at> users.sourceforge.net <fsms <at> users.sourceforge.net>
2004-08-13 11:19:59 GMT
2004-08-13 11:19:59 GMT
Hi, I would like to know where do we stand for the Restriction analysis package. I posted a message on the biopython-dev list but got no response. As previously said, I am ready to maintain the package in Biopython. Just tell me if you still are interested. best regards Fred.
13 Aug 2004 14:41
[Bug 1678] New: NCBIXML error in 1.30
<bugzilla-daemon <at> portal.open-bio.org>
2004-08-13 12:41:25 GMT
2004-08-13 12:41:25 GMT
http://bugzilla.open-bio.org/show_bug.cgi?id=1678 Summary: NCBIXML error in 1.30 Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: blocker Priority: P2 Component: Main Distribution AssignedTo: biopython-dev <at> biopython.org ReportedBy: d.lapointe <at> comcast.net Running Betrtands script generates an error at line 111 of NCBIXML.py that filename is not defined globally. 'filename' should be changed to 'handler' ... def parse(self, handler): """Parses the XML data handler -- file handler or StringIO ''' self._parser.parse(filename) <=== line 111 return self._blast should read self._parser.parse(handler) I changed this in my source and it worked fine.(Continue reading)
13 Aug 2004 20:19
Re: Restriction analysis package.
Brad Chapman <chapmanb <at> 50mail.com>
2004-08-13 18:19:16 GMT
2004-08-13 18:19:16 GMT
Hi Fred; > I would like to know where do we stand for the Restriction analysis package. > I posted a message on the biopython-dev list but got no response. > As previously said, I am ready to maintain the package in Biopython. > Just tell me if you still are interested. Sorry for the delay in getting back with you. We are definitely still interested in the code, and I've went and integrated into Biopython CVS. Please let me know if I didn't get anything into CVS correctly. For those who are interested in checking it out, here is what is included: Bio/Restriction -- very nice set of modules for dealing with Restriction Enzymes, including searching for enzymes within sequences and performing cuts with them Doc/cookbook/Restriction -- documentation on using the modules (also included on the website) Scripts/Restriction -- scripts for updating the enzyme classes from Rebase The only modification I made was to add a catalyze function (which just calls the catalyse function). I was having a bit of trouble getting used to the British spelling(Continue reading). I also added some basic tests in Tests/test_Restriction.py -- please do feel free to add to these, they are pretty basic right now. Thanks much for this contribution -- everything looks very well
14 Aug 2004 10:10
complement, reverse_complement in Bio.Seq
Michiel Jan Laurens de Hoon <mdehoon <at> ims.u-tokyo.ac.jp>
2004-08-14 08:10:34 GMT
2004-08-14 08:10:34 GMT
Dear Biopythoneers (especially Dr. Chapman), I have added the functions 'complement' and 'reverse_complement' to Bio.Seq's Seq and MutableSeq objects, which we discussed some weeks ago. Similar functions previously existed in various locations in BioPython: - forward_complement, reverse_complement in Bio.GFF.easy - complement, antiparallel in Bio.SeqUtils These functions have now been deprecated, and will generate a DeprecationWarning when used. The functions complement and reverse_complement, when applied to a Seq object, will return a new Seq object. The same function applied to a MutableSeq object will modify the MutableSeq object itself, and don't return anything. By the way, do we still need separate Seq and MutableSeq classes? As far as I understand, Seq is needed so that we can use strings, but since strings are immutable in Python we also need a MutableSeq. Wouldn't it be possible to implement this class in C, so that we can have mutable sequences that are still fast? --Michiel. -- -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon(Continue reading)
17 Aug 2004 11:35
[BioPython] Re: Restriction analysis package.
<f.sohm <at> whsmithnet.co.uk>
2004-08-17 09:35:37 GMT
2004-08-17 09:35:37 GMT
Hi Brad Felicitation for your PhD and thank you for uploading the code into the CVS. For the catalyse method, you are right and I should have made the change earlier. There is a simpler way to add a catalyze method though : in the classes : Unknown, Blunt, Ov5 and Ov3 at the end of the definition of the catalyse method, you need to replace : catalyse = classmethod(catalyse) by catalyze = catalyse = classmethod(catalyse) This suppress the need for a new class and avoid to add a function call. I have made the modif but how do you want me to send them ? a bug report against Restriction and the module as an attachement ? Bye Fred _______________________________________________ BioPython mailing list - BioPython <at> biopython.org http://biopython.org/mailman/listinfo/biopython
17 Aug 2004 15:02
interface/SQL development policies
James Casbon <j.a.casbon <at> qmul.ac.uk>
2004-08-17 13:02:34 GMT
2004-08-17 13:02:34 GMT
Hi, Say I have a module X, which depends heavily on flat file databases. I wish to decompose into two classes XFile and XDatabase, where XFile uses the files and XDatabase use and SQL backend. This raises a number of questions: * the two classes imply a common interface X, what is the best way of handling this in python? An abstract base class? * How are regression tests managed for SQL based classes (ie how do you provide a dummy database, given there might not be an sql server on a particular client)? These questions might be best answered with an example, so if there are any examples covering this kind of stuff already in biopython, please point them out. Thanks, James -- -- James Casbon PhD Student Centre for Infectious Disease Institute of Cell and Molecular Science Barts and The London http://compbio.mds.qmw.ac.uk(Continue reading)
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