From chapmanb at 50mail.com Fri Apr 1 06:37:26 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 1 Apr 2011 06:37:26 -0400 Subject: [Biopython-dev] GSoC: "Variant representation, parser, generator, and coordinate converter" In-Reply-To: References: <4D953DA3.7010408@cornell.edu> Message-ID: <20110401103726.GB2330@kunkel> Maximiliano; Thanks for the introduction and interest in the project. I'm cc'ing in the mailing list and Reece, who is the primary mentor. > >> My name is Maximiliano David Bustos, I am from La Rioja, Argentina. I am > >> 20 years old, and currently studying Computer Science at "Facultad de > >> Matem?tica Astronom?a y F?sica" (Fa.M.A.F - UNC). > >> > >> I have read about your organization, in I like the projects that you are > >> developing. I am really interested in contributing in the project > >> "Variant representation, parser, generator, and coordinate converter", > >> taken from your wiki. > >> > >> I want to read more about the topic before writing to the corresponding > >> mailing list. Great to hear. Could you provide some more background and details about why you are interested in the project and what areas you would like to read more on? It would be really helpful to understand how comfortable you are with Python programming, with the Biopython project, and with the biological concepts (variations, genes, proteins). Thanks again, Brad From p.j.a.cock at googlemail.com Fri Apr 1 06:48:21 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 1 Apr 2011 11:48:21 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> Message-ID: On Tue, Mar 29, 2011 at 1:26 PM, Peter Cock wrote: > On Tue, Mar 29, 2011 at 1:05 PM, Brad Chapman wrote: >> Peter; >> >>> > What is our timeline for 1.57? >> >>> I was hoping for some more comments on the tutorial, and ideally fix >>> http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html >>> but other than that we're good to go. Do you want to do the honours? >> >> For your fastq file examples, we could use the EBI short read >> archive, which is staying around for a while longer: >> >> ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/ > > Good plan - why didn't I think of that the other night when I was > looking at this? I may even be able to find the equivalent files to > the ones we used to use from the NCBI SRA. I'll try and sort > that today or tomorrow... Good news - the tutorial update is nearly done now. Bad news - I updated to NCBI BLAST 2.2.25+ and the unit test is complaining about some new switches like -db_hard_mask which we'll need to add and then white-list in test_NCBI_BLAST_tools.py (or just turn off this bit of the tests) Peter From p.j.a.cock at googlemail.com Fri Apr 1 12:35:58 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 1 Apr 2011 17:35:58 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> Message-ID: On Fri, Apr 1, 2011 at 11:48 AM, Peter Cock wrote: > > Good news - the tutorial update is nearly done now. > > Bad news - I updated to NCBI BLAST 2.2.25+ and the unit test is > complaining about some new switches like -db_hard_mask which > we'll need to add and then white-list in test_NCBI_BLAST_tools.py > (or just turn off this bit of the tests) > OK, I think both the SRA links in the Tutorial and the new arguments added to the BLAST+ tools are done. We are also all green on the buildbot (I just forced a set of builds after making those commits): http://testing.open-bio.org/biopython/grid Ready when you are Brad, and if you'd like to wait until after April 1st is over to avoid any jokes, that's OK with me ;) Peter From chapmanb at 50mail.com Fri Apr 1 14:50:42 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 1 Apr 2011 14:50:42 -0400 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> Message-ID: <20110401185042.GG2330@kunkel> Peter; Thanks for fixing the BLAST+ issue and the tutorial. We'll plan for a release later this evening or tomorrow morning, so everyone please hold off commits until it's finished. Below are the release notes and contributors list for the release. Please let me know anything or anyone is missing; additionally if anyone wants to clean up the text or add more flourishes of brilliance, that would be very welcome. Thanks everyone for all the hard work for the release, Brad In progress: Biopython 1.57 (not yet released). Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary. Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the ability to run the BLAST tools and save the output as ASN.1 format, and then convert this to any other supported BLAST ouput format (plain text, tabular, XML, or HTML) with the blast_formatter tool. The wrappers were also updated to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask. The SeqRecord object now has a reverse_complement method (similar to that of the Seq object). This is most useful to reversing per-letter-annotation (such as quality scores from FASTQ) or features (such as annotation from GenBank). Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now uses an optimised routine for FASTQ to QUAL making this much faster. Biopython can now be installed with pip. Thanks to David Koppstein and James Casbon for reporting the problem. Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and IMGT output. The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary (previously it was a list of key,value tuples) to better match the standard. (At least) 14 people have contributed to this release, including 5 new people: Brad Chapman Eric Talevich Erick Matsen (first contribution) Hongbo Zhu Jeffrey Finkelstein (first contribution) Joanna & Dominik Kasprzak (first contribution) Joao Rodrigues Kristian Rother Leighton Pritchard Michiel de Hoon Peter Cock Phillip Garland Walter Gillett (first contribution) From eric.talevich at gmail.com Fri Apr 1 18:08:14 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Fri, 1 Apr 2011 18:08:14 -0400 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: <20110401185042.GG2330@kunkel> References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: On Fri, Apr 1, 2011 at 2:50 PM, Brad Chapman wrote: > > Below are the release notes and contributors list for the release. > Please let me know anything or anyone is missing; additionally if > anyone wants to clean up the text or add more flourishes of > brilliance, that would be very welcome. > > Thanks everyone for all the hard work for the release, > Brad > > > In progress: Biopython 1.57 (not yet released). > > Bio.SeqIO now includes an index_db() function which extends the existing > indexing functionality to allow indexing many files, and more importantly > this keeps the index on disk in a simple SQLite3 database rather than in > memory in a Python dictionary. > > Bio.Blast.Applications now includes a wrapper for the BLAST+ > blast_formatter > tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the > ability to run the BLAST tools and save the output as ASN.1 format, and > then > convert this to any other supported BLAST ouput format (plain text, > tabular, > XML, or HTML) with the blast_formatter tool. The wrappers were also updated > to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask. > > The SeqRecord object now has a reverse_complement method (similar to that > of > the Seq object). This is most useful to reversing per-letter-annotation > (such > as quality scores from FASTQ) or features (such as annotation from > GenBank). > > Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now > uses an optimised routine for FASTQ to QUAL making this much faster. > > Biopython can now be installed with pip. Thanks to David Koppstein and > James Casbon for reporting the problem. > > Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and > IMGT output. > > The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary > (previously it was a list of key,value tuples) to better match the > standard. > > The Bio.PDB module received several fixes and improvements. We've started merging Jo?o's work from GSoC 2010, and consequently Atom objects now know their element type and IUPAC mass. (The new features that use these attributes won't be included in Biopython until the next release, though, so stay tuned.) -E From updates at feedmyinbox.com Sat Apr 2 04:09:17 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Sat, 2 Apr 2011 04:09:17 -0400 Subject: [Biopython-dev] 4/2 active questions tagged biopython - Stack Overflow Message-ID: <11b208e29a7233e2df1e3969f1afc4b9@74.63.51.88> // Bio.IUPAC problem in Biopython // April 1, 2011 at 5:28 PM http://stackoverflow.com/questions/5519081/bio-iupac-problem-in-biopython i was testing this simple code from Bio.Alphabet import IUPAC from Bio import Seq my_prot=Seq("AGTACACTGGT",IUPAC.protein) and it gives me this error TypeError: 'module' object is not callable can anyone explain why this is happening? PS: this is an Example from the BioPython's Cookbook -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From weichen302 at aol.com Sat Apr 2 04:49:13 2011 From: weichen302 at aol.com (Chen Wei) Date: Sat, 2 Apr 2011 16:49:13 +0800 Subject: [Biopython-dev] 4/2 active questions tagged biopython - Stack Overflow In-Reply-To: <11b208e29a7233e2df1e3969f1afc4b9@74.63.51.88> References: <11b208e29a7233e2df1e3969f1afc4b9@74.63.51.88> Message-ID: <20110402084913.GA9993@Tungsten.DarkStar> On Sat, Apr 02, 2011 at 04:09:17AM -0400, Feed My Inbox wrote: > from Bio.Alphabet import IUPAC > from Bio import Seq > my_prot=Seq("AGTACACTGGT",IUPAC.protein) > > and it gives me this error > > TypeError: 'module' object is not callable > it is a namespace problem, Seq is a class lives inside module Seq. Take a look at Bio/Seq.py. u can either change the code to: my_prot=Seq.Seq("AGTACACTGGT",IUPAC.protein) or use: from Bio.Seq import Seq -- Chen Wei From p.j.a.cock at googlemail.com Sat Apr 2 09:43:30 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Apr 2011 14:43:30 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: Thanks Brad :) http://news.open-bio.org/news/2011/04/biopython-1-57-released/ I'll get the Windows installers done on Monday. Peter From redmine at redmine.open-bio.org Sat Apr 2 10:25:57 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Sat, 2 Apr 2011 14:25:57 +0000 Subject: [Biopython-dev] [Biopython - Feature #3193] (New) Bio.Phylo.Applications support for MrBayes Message-ID: Issue #3193 has been reported by Eric Talevich. ---------------------------------------- Feature #3193: Bio.Phylo.Applications support for MrBayes https://redmine.open-bio.org/issues/3193 Author: Eric Talevich Status: New Priority: Normal Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: MrBayes is a popular tool for inferring phylogenies, reasonably best-practice, open-source, and packaged for Debian. Let's create a wrapper for it in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Sat Apr 2 10:59:29 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Sat, 2 Apr 2011 14:59:29 +0000 Subject: [Biopython-dev] [Biopython - Feature #3194] (New) Bio.Phylo export to 'ape' via Rpy2 Message-ID: Issue #3194 has been reported by Eric Talevich. ---------------------------------------- Feature #3194: Bio.Phylo export to 'ape' via Rpy2 https://redmine.open-bio.org/issues/3194 Author: Eric Talevich Status: New Priority: Low Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: There are many more packages for working with phylogenetic data in R, and most of these operate on the basic tree object defined in the ape package. Let's support interoperability through Rpy2. The trivial way to do this is serialize a tree to a Newick string, then feed that to the read.tree() function. Maybe we can build the tree object in R directly and retain the tree annotations that Newick doesn't handle. See: http://ape.mpl.ird.fr/ http://rpy.sourceforge.net/rpy2.html ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From eric.talevich at gmail.com Sat Apr 2 15:16:32 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Sat, 2 Apr 2011 15:16:32 -0400 Subject: [Biopython-dev] New functions in Bio.PDB: renumber_residues(), remove_disordered_atoms() In-Reply-To: References: Message-ID: Hi Jo?o, Now that Biopython 1.57 is out, I'd like to try merging some more features into the trunk. I'm looking at this branch: https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements Can I pull and merge the whole branch, or should I cherry-pick certain commits? And, have you already squashed the history to your own satisfaction? Thanks, Eric On Thu, Feb 17, 2011 at 7:59 AM, Jo?o Rodrigues wrote: > Hey Kristian, > > To Tests/test_pdb.py ? Just to make sure that the renumbering acts on both > accordingly? I agree. > > Jo?o > > On Thu, Feb 17, 2011 at 7:54 AM, Kristian Rother wrote: > > Hi Joao, > > I think we should add a simple test function that ensures consistency of > child_dict and child_list upon renumbering. Let me know if you'd prefer me > to explain in Python what I mean. > > Kristian > > > > > Dear All, > > > > I've been working on the above-mentioned functions following really great > > feedback from Eric, Kristian, and Peter. I've been also using them > > routinely > > and I've had no problems yet so they should be stable enough. Therefore I > > think they can be cherry-picked from my pdb_enhancements branch and added > > to > > the main branch. Let me know what you think. > > > > Cheers, > > > > Jo??o > > > > _______________________________________________ > From p.j.a.cock at googlemail.com Mon Apr 4 04:57:51 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Apr 2011 09:57:51 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: On Sat, Apr 2, 2011 at 2:43 PM, Peter Cock wrote: > Thanks Brad :) > > http://news.open-bio.org/news/2011/04/biopython-1-57-released/ > > I'll get the Windows installers done on Monday. > > Peter They're up. I included one for Python 2.4 put stuck 'unsupported' at the end of its filename. I'm wondering if we should make a couple for Python 3.1 and 3.2 but clearly mark them as alpha quality? Perhaps a little branch on github just to change the version to 1.57a and edit the setup.py description? Speaking of which, I found our first bug: I didn't add do2to3.py to the manifest, so it isn't included in the tar ball or zip. This means you can't install from a source release under Python 3. Not a big issue as we haven't claimed to support Python 3 yet: https://github.com/biopython/biopython/commit/4b1cc1e501a136188c41c1345c1d22ceb11cdb0c Peter From chapmanb at 50mail.com Mon Apr 4 08:51:49 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Mon, 4 Apr 2011 08:51:49 -0400 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: <20110404125149.GB17045@sobchak> Peter; [Windows installers] > They're up. I included one for Python 2.4 put stuck 'unsupported' > at the end of its filename. Awesome, thanks much. > I'm wondering if we should make a couple for Python 3.1 and 3.2 > but clearly mark them as alpha quality? Perhaps a little branch > on github just to change the version to 1.57a and edit the setup.py > description? This is a good idea and could help us get a sense of if people are using Python 3 yet. > Speaking of which, I found our first bug: I didn't add do2to3.py > to the manifest, so it isn't included in the tar ball or zip. This > means you can't install from a source release under Python 3. > Not a big issue as we haven't claimed to support Python 3 yet: > https://github.com/biopython/biopython/commit/4b1cc1e501a136188c41c1345c1d22ceb11cdb0c Whoops. Should we freshen up the tarballs with this or wait until the next release? For your manifest fix, we should add do2to3.py to the MANIFEST.in instead of checking in the MANIFEST directly, since the MANIFEST is generated during building the release. Brad From p.j.a.cock at googlemail.com Mon Apr 4 09:10:19 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Apr 2011 14:10:19 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: <20110404125149.GB17045@sobchak> References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> <20110404125149.GB17045@sobchak> Message-ID: On Mon, Apr 4, 2011 at 1:51 PM, Brad Chapman wrote: > Peter; > > [Windows installers] >> They're up. I included one for Python 2.4 put stuck 'unsupported' >> at the end of its filename. > > Awesome, thanks much. > >> I'm wondering if we should make a couple for Python 3.1 and 3.2 >> but clearly mark them as alpha quality? Perhaps a little branch >> on github just to change the version to 1.57a and edit the setup.py >> description? > > This is a good idea and could help us get a sense of if people are > using Python 3 yet. > >> Speaking of which, I found our first bug: I didn't add do2to3.py >> to the manifest, so it isn't included in the tar ball or zip. This >> means you can't install from a source release under Python 3. >> Not a big issue as we haven't claimed to support Python 3 yet: >> https://github.com/biopython/biopython/commit/4b1cc1e501a136188c41c1345c1d22ceb11cdb0c > > Whoops. Should we freshen up the tarballs with this or wait until > the next release? I'm tempted to leave it as is. Anyone keen to use Biopython from source under Python 3 can try from git. > For your manifest fix, we should add do2to3.py to the MANIFEST.in > instead of checking in the MANIFEST directly, since the MANIFEST is > generated during building the release. Good catch - that's what I meant to do, I guess I missed the extension in my git add command (over reliant on tab auto completion). Fixed now. Peter From bjclavijo at gmail.com Mon Apr 4 12:28:50 2011 From: bjclavijo at gmail.com (Bernardo Clavijo) Date: Mon, 4 Apr 2011 13:28:50 -0300 Subject: [Biopython-dev] DAS implementation Message-ID: Hello everyone, new subscriber here, hopefully lending a hand around from now on (Python fan working on bioinformatics, so this is the place). I've been searching for a DAS server/client but found none written in python. Since I'm writting some Chado+Gbrowse+tools web glue in python, don't want to attach a perl implementation or such. Have anyone some code for this? Maybe it's just that my googling skills aren't so good. If not, wouldn't it be nice to have such a module in biopython? I'm not the best developer in the world, but maybe I could code something that serves us all and then it could be included in biopython. Well, that all for now... hope to hear some answers, and if you think that impelmenting DAS would be a nice idea, I'm sure you could provide me with a hint in how I could design it (a module interacting with Seq? Is there some webserver capabilities, or just write functions and let the code ready to glue into a webserver?, etc). Greets bj From p.j.a.cock at googlemail.com Mon Apr 4 12:35:02 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Apr 2011 17:35:02 +0100 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo wrote: > Hello everyone, new subscriber here, hopefully lending a hand around > from now on (Python fan working on bioinformatics, so this is the > place). > I've been searching for a DAS server/client but found none written in > python. Since I'm writting some Chado+Gbrowse+tools web glue in > python, don't want to attach a perl implementation or such. > Have anyone some code for this? Maybe it's just that my googling > skills aren't so good. If not, wouldn't it be nice to have such a > module in biopython? > I'm not the best developer in the world, but maybe I could code > something that serves us all and then it could be included in > biopython. > Well, that all for now... hope to hear some answers, and if you think > that impelmenting DAS would be a nice idea, I'm sure you could provide > me with a hint in how I could design it (a module interacting with > Seq? Is there some webserver capabilities, or just write functions and > let the code ready to glue into a webserver?, etc). > > Greets > > bj Hi Bernardo, Andrea Pierleoni started looking at a DAS client last year: http://github.com/apierleoni/biopython/tree/das-client http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html More eyes on this code would be good :) Peter From bjclavijo at gmail.com Mon Apr 4 12:44:41 2011 From: bjclavijo at gmail.com (Bernardo Clavijo) Date: Mon, 4 Apr 2011 13:44:41 -0300 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: On Mon, Apr 4, 2011 at 1:35 PM, Peter Cock wrote: > On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo wrote: >> Hello everyone, new subscriber here, hopefully lending a hand around >> from now on (Python fan working on bioinformatics, so this is the >> place). >> I've been searching for a DAS server/client but found none written in >> python. Since I'm writting some Chado+Gbrowse+tools web glue in >> python, don't want to attach a perl implementation or such. >> Have anyone some code for this? Maybe it's just that my googling >> skills aren't so good. If not, wouldn't it be nice to have such a >> module in biopython? >> I'm not the best developer in the world, but maybe I could code >> something that serves us all and then it could be included in >> biopython. >> Well, that all for now... hope to hear some answers, and if you think >> that impelmenting DAS would be a nice idea, I'm sure you could provide >> me with a hint in how I could design it (a module interacting with >> Seq? Is there some webserver capabilities, or just write functions and >> let the code ready to glue into a webserver?, etc). >> >> Greets >> >> bj > > Hi Bernardo, > > Andrea Pierleoni started looking at a DAS client last year: > http://github.com/apierleoni/biopython/tree/das-client > http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html > > More eyes on this code would be good :) > > Peter > Great! a starting point for the client part... i'll check it out that for a starting point, I see there are some "TODO" parts... i'll try to handle those. Anyone having something similar as for the server part? Greets bj From bpederse at gmail.com Mon Apr 4 15:31:51 2011 From: bpederse at gmail.com (Brent Pedersen) Date: Mon, 4 Apr 2011 13:31:51 -0600 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: On Mon, Apr 4, 2011 at 10:44 AM, Bernardo Clavijo wrote: > On Mon, Apr 4, 2011 at 1:35 PM, Peter Cock wrote: >> On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo wrote: >>> Hello everyone, new subscriber here, hopefully lending a hand around >>> from now on (Python fan working on bioinformatics, so this is the >>> place). >>> I've been searching for a DAS server/client but found none written in >>> python. Since I'm writting some Chado+Gbrowse+tools web glue in >>> python, don't want to attach a perl implementation or such. >>> Have anyone some code for this? Maybe it's just that my googling >>> skills aren't so good. If not, wouldn't it be nice to have such a >>> module in biopython? >>> I'm not the best developer in the world, but maybe I could code >>> something that serves us all and then it could be included in >>> biopython. >>> Well, that all for now... hope to hear some answers, and if you think >>> that impelmenting DAS would be a nice idea, I'm sure you could provide >>> me with a hint in how I could design it (a module interacting with >>> Seq? Is there some webserver capabilities, or just write functions and >>> let the code ready to glue into a webserver?, etc). >>> >>> Greets >>> >>> bj >> >> Hi Bernardo, >> >> Andrea Pierleoni started looking at a DAS client last year: >> http://github.com/apierleoni/biopython/tree/das-client >> http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html >> >> More eyes on this code would be good :) >> >> Peter >> > > Great! a starting point for the client part... i'll check it out that > for a starting point, I see there are some "TODO" parts... i'll try to > handle those. > Anyone having something similar as for the server part? > > Greets > > bj > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > if you fork this on github (and especially if you start the server stuff) and link back here, perhaps you'll get some help. i'd be very interested in server and client for biodas in biopython. -brentp From jblanca at upv.es Tue Apr 5 02:58:41 2011 From: jblanca at upv.es (Jose Blanca) Date: Tue, 05 Apr 2011 08:58:41 +0200 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: <4D9ABDA1.7090505@btc.upv.es> El 04/04/11 18:28, Bernardo Clavijo escribi?: > Hello everyone, new subscriber here, hopefully lending a hand around > from now on (Python fan working on bioinformatics, so this is the > place). > I've been searching for a DAS server/client but found none written in > python. Since I'm writting some Chado+Gbrowse+tools web glue in > python, don't want to attach a perl implementation or such. Hi: I've no idea about the DAS server, but I'm very interested in the Chado stuff. We're building a django application to browse a Chado database. It is still not completely ready, but you can take a look at: http://bioinf.comav.upv.es/git//?p=gene_web.git;a=summary We were thinking about showing this code in the Chado mailing list once completed in case anyone could be interested in using it and improving it. But here it is. If anyone could be interested, it is free software, we like AGPL, but we're open about other free software licences. Regards, Jose Blanca > Have anyone some code for this? Maybe it's just that my googling > skills aren't so good. If not, wouldn't it be nice to have such a > module in biopython? > I'm not the best developer in the world, but maybe I could code > something that serves us all and then it could be included in > biopython. > Well, that all for now... hope to hear some answers, and if you think > that impelmenting DAS would be a nice idea, I'm sure you could provide > me with a hint in how I could design it (a module interacting with > Seq? Is there some webserver capabilities, or just write functions and > let the code ready to glue into a webserver?, etc). > > Greets > > bj > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > -- Jose M. Blanca Postigo Instituto Universitario de Conservacion y Mejora de la Agrodiversidad Valenciana (COMAV) Universidad Politecnica de Valencia (UPV) Edificio CPI (Ciudad Politecnica de la Innovacion), 8E 46022 Valencia (SPAIN) Tlf.:+34-96-3877000 (ext 88473) From anaryin at gmail.com Tue Apr 5 11:50:34 2011 From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=) Date: Tue, 5 Apr 2011 17:50:34 +0200 Subject: [Biopython-dev] New functions in Bio.PDB: renumber_residues(), remove_disordered_atoms() In-Reply-To: References: Message-ID: Hey Eric, Let me write the Tests Kristian proposed. I haven't had time to do it yet and those are quite important :) I'll update the branch with the current version, correct some bugs that might show up with the merging, write the tests, clean the history, and let you know. I think merging should be good, but cherry-picking is safer I guess! Cheers, J From andrea at biocomp.unibo.it Tue Apr 5 12:08:21 2011 From: andrea at biocomp.unibo.it (Andrea Pierleoni) Date: Tue, 5 Apr 2011 18:08:21 +0200 (CEST) Subject: [Biopython-dev] DAS implementation (Bernardo Clavijo) In-Reply-To: References: Message-ID: <3b5245fb50ceea358894429e89dc1464.squirrel@lipid.biocomp.unibo.it> Bernardo if you want I can grant you access to the DAS repository in my github profile. so we can work on the same version. Regarding the DAS server implementation, how could this be included in Biopython? A DAS server will require a webserver. Andrea From bjclavijo at gmail.com Tue Apr 5 14:28:42 2011 From: bjclavijo at gmail.com (Bernardo Clavijo) Date: Tue, 5 Apr 2011 15:28:42 -0300 Subject: [Biopython-dev] DAS implementation (Bernardo Clavijo) In-Reply-To: <3b5245fb50ceea358894429e89dc1464.squirrel@lipid.biocomp.unibo.it> References: <3b5245fb50ceea358894429e89dc1464.squirrel@lipid.biocomp.unibo.it> Message-ID: That would be great (the client access) i'll send you a private mail later. As for the server, I'll try to create a class that handles all the back functions (generating the responses from the Bio.Seq module, for example, maybe it's not the best design). As for the web server, we could just let it open for anyone to glue it on (it's just a matter of passing the requests), or use one of the simple http modules already in python (I didn't know if some module is already used in another point in biopython). Greets bj On Tue, Apr 5, 2011 at 1:08 PM, Andrea Pierleoni wrote: > Bernardo if you want I can grant you access to the DAS repository in my > github profile. so we can work on the same version. > Regarding the DAS server implementation, how could this be included in > Biopython? > A DAS server will require a webserver. > > Andrea > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > From redmine at redmine.open-bio.org Wed Apr 6 19:26:08 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 6 Apr 2011 23:26:08 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] (New) SeqIO parse error with some genbank files Message-ID: Issue #3197 has been reported by Cedar McKay. ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Category: Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 6 19:42:54 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 6 Apr 2011 23:42:54 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Peter Cock. Assignee set to Biopython Dev Mailing List ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 6 21:01:11 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 7 Apr 2011 01:01:11 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Cedar McKay. I did a little more poking, and it really seems like a common mistake. I'm working with this file: ftp://ftp.ncbi.nih.gov/refseq/release/plastid/plastid1.genomic.gbff.gz which is a file containing all plastid genomes in genbank. It has 208 records, and of those, 124 have an illegal location containing the string 'order(join(' One thing that I noticed is that all but two examples of 'order(join(' that appear across those 124 records are describing the location of a ycf3 feature! Strange! I'll send them an email about it, but I'm not really sure what is going on. I followed your suggestion for my test file, and changed the the location of that misc_feature. It got hung up on yet another ycf3 gene: 
     misc_feature    complement(order(42643..42645,42652..42654,42664..42666,
                     43470..43472,43515..43517,43524..43526,43536..43538,
                     43572..43574,43626..43628,43635..43637,43647..43649,
                     join(43683..43684,44430)))
                     /gene="ycf3"
I got rid of the join there too, and finally it could be parsed. Thanks for looking at this, I don't quite know what to make of it yet, or how to deal with it. ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 7 05:59:54 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 7 Apr 2011 09:59:54 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Peter Cock. File __init__.py added Hi Cedar, I do think these are invalid GenBank files, but as a short term hack you could try this modified version of the code - install Biopython 1.57 and replace the Bio/GenBank/__init__.py file. You could comment out the warning if you like ;) This basically automates the removal of the join from the illegal locations, which seems to me to be the best way to salvage the location. I can then parse plastid1.genomic.gbff fine. I don't want to commit a fix unless the NCBI tell us these are valid location, and/or a more elegant fix can be implemented. This current hack will probably slow down general GenBank parsing. Peter ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From chapmanb at 50mail.com Thu Apr 7 10:52:31 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 7 Apr 2011 10:52:31 -0400 Subject: [Biopython-dev] Propsal Draft - Timeline. In-Reply-To: References: Message-ID: <20110407145231.GA20963@sobchak> Maximiliano and Reece; Great to see that the proposal is coming along. I'm cc'ing the developers mailing lists in case others have thoughts as well. I'll start by echoing some of Reece's comments: > - An overview -- without this, it's hard for readers to know how well you > understand the context or why the issue is relevant at all. ~5 sentences > should suffice. Please take a stab at it and I'll help. Yes, definitely. This is an application not to Reece, who knows about the project, but to the general developer community. You need to justify why this project is important and what you hope to accomplish. Generally you need to argue for why Google should fund this project over other equally deserving projects. > - Consider adding a short "about me" section. The reviewers will need detailed information about your background to assess your ability to be successful. You should add work you've done previously, especially related to Python. Ideally you will have links to some open source work you've done so reviewers can assess your programming experience. > I'm also cc'ing Brad who may have more input. The proposal timeline needs to be much more detailed. What it should look like is a week by week breakdown of what you hope to accomplish. This will be used by you and your mentors to help track progress and stay on track. These are the weekly milestones you mention in your proposal. Some specific suggestions: - All non-coding tasks (setting up version control) should be put in your timeline prior to the start of the coding period. - Your weekly goals need to be very specific. For instance 'Design the library API' does not tell a reviewer any details about what you hope to accomplish. You should have a general idea of what you plan to design now, and then be listing these in your plan. Hope this helps with getting everything finalized before tomorrow, Brad > > *Abstract:* > > *I am still working on it.* > > > > *Proposal Timeline:* > > > > *Before April 25:* > > > > - To familiarize myself with BioPython. > > - Experiment with PLY (Python Lex-Yacc) and Pyparsing. > > - Review some basic biology concepts: genomes, transcripts, proteins, > > genomic variation, and others suggested by my mentor. > > - To familiarize myself with HGVS nomenclature, and experiment using > > Mutalyzer 2.0 > > > > > > *April 27 - May 24 (Before the official coding time):* > > > > - Define the subset of the HGVS to be represented. > > - Identify variation types to be represented (SNV, CNV, repeats, > > inversions, etc). > > - Design a formal grammar that fully represents the subset of the HGVS > > chosen before. > > - Define a set of semantic validations for the represented variations. > > - Write a short document explaining how to properly extend the formal > > grammar defined before. > > > > > > *May 25 - July 12 (Official coding period starts):* > > > > - Set up a control version system and a bug tracker. > > - Define weekly milestones. > > - Design the library API. > > - Develop an abstract variant class and subclasses representing > > specific cases of them. > > - Design and implement a parser for the formal grammar defined before. > > - Test the code written up to now. > > > > > > *July 15: Midterm evaluation* > > > > *July 17 ? August 16:* > > > > - Work on semantic validations defined before. > > - Full testing of the whole library. > > - Integration of the library to BioPython. > > - Documentation of the whole library. > > - Implementation of a syntax checker as an example of the use of the > > library. Make it freely availably on the Internet. From redmine at redmine.open-bio.org Thu Apr 7 13:39:06 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 7 Apr 2011 17:39:06 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Cedar McKay. Peter, thanks as always for your quick and helpful response! I've emailed NCBI about these apparently illegal files, and I'll update this bug when I get a reply. In the meantime, I'm going to go ahead and use your hacked up version. Thanks! ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From chapmanb at 50mail.com Fri Apr 8 06:45:41 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 8 Apr 2011 06:45:41 -0400 Subject: [Biopython-dev] Proposal: almost finished. In-Reply-To: References: Message-ID: <20110408104541.GJ20963@sobchak> Maxi; (cc'ing the Biopython mailing list for suggestions) Thanks for this; it's looking really good. Some last minute thoughts: - The About Me section needs a link to code you've written. I couldn't find anything substantial i nthe Pep8fy or Cdpedia projects, so if you've contributed something large there please highlight it. Otherwise you should upload some code to bitbucket to demonstrate work you've done. This will be the first thing evaluators look at. - You should renumber your weeks so week 1 is the start of the coding period; you should keep the prep weeks as that is really useful information, but just mark them generally as the community bonding period. - When the coding period starts you should start, well, coding. So the specification/design work you have in weeks 5 and 6 should be moved to the community bonding/prep period, and code writing should begin on May 23rd. - You mention unit testing, but should go into specifics about what you plan to test. This demonstrates that you've thought about potential issues and how to avoid them. - The purpose of GSoC is open source code and integration with existing projects. So some of the late items (week 14/Make it freely available on the internet; week 17/integration of the library to Biopython) should be happening from week 1. The code should be freely available in an open source repository the entire time, and you should be talking with the Biopython community throughout. I'd suggest emphasizing those points in your text, and adding in work/tests/documentation for those weeks. Don't forget that this needs to be submitted to the GSoC website by the deadline: http://www.google-melange.com/gsoc/homepage/google/gsoc2011 Google can only evaluate proposals that are entered there. Thanks again for the work getting this together, Brad > Reece, Brad: > > I attach my proposal (odt and pdf versions). I have been working all the > evening. It is late here, so I am going to bed now. Tomorrow I will get up > early, read it one more time, read if you made any recommendation, and send > the proposal! :) > I think I can add more in "Design aspects" and "Implementation". > > Reece: I gave more importance to testing, adding weekly unit test, and 2 > instances of system test. I usually work with test driven development in my > university, so we can implement that if you want. > > Brad: I will try to extend a bit more about API design. > > Recommandations are welcomed > Thanks for your help! > > -- > Maxi. -------------- next part -------------- A non-text attachment was scrubbed... Name: Proposal Application.pdf Type: application/pdf Size: 110725 bytes Desc: not available URL: From updates at feedmyinbox.com Mon Apr 11 00:42:29 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Mon, 11 Apr 2011 00:42:29 -0400 Subject: [Biopython-dev] 4/11 active questions tagged biopython - Stack Overflow Message-ID: <4c9304139061a653fdbf5fa9899671bf@74.63.51.88> // Script for parsing a biological sequence from a public database in Python // April 10, 2011 at 3:33 PM http://stackoverflow.com/questions/5614180/script-for-parsing-a-biological-sequence-from-a-public-database-in-python Greetings to the stackoverflow community, I am currently following a bioinformatics module as part of a biomedical degree (I am basically a python newbie) and the following task is required as part of a Python programming assignment: extract motif sequences (amino acid sequences, so basically strings in programmatic-speak, that have been excised from algorithms implementing a multiple sequence alignment and subsequently iterative database scanning to generate the best conserved sequences. The ultimate idea is to infer functional significance from such "motifs"). These motifs are stored on a public database in files which have multiple data fields corresponding to each protein (uniprot ID, Accession Number, the alignment itself stored in a hyperlink .seq file), currently one of which is of interest in this scope. The data field is called "extracted motif sets". My question is how to go about writing a script that will essentially parse the "motif strings" and output them to a file. Very crudely, I believe the pseudocode would run something along these lines: motif_file = open("lysozyme.seq") # database files are saved as .seq for "extracted motif sets" in motif_file # motif extracting code goes here motif_file.close() There are well over a couple hundred .seq files, so I imagine a looping technique would be needed to scan a good part of the database. The excised motifs are on a file separated from the .seq by a hyperlink, but are of course subsequences of each of the entries in the Mult. Seq. Alignment files (.seq). Is there a way to effectively pick up the motif sequences (strings) from one file and do some mining on the alignment files to detect the same sequence? I apologize for the extensive text, I just hope to be a clear as possible. Thanks in advance for any help! -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From clementsgalaxy at gmail.com Mon Apr 11 11:57:48 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Mon, 11 Apr 2011 08:57:48 -0700 Subject: [Biopython-dev] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands In-Reply-To: References: Message-ID: Hello all, This is a reminder that early registration for the 2011 Galaxy Community Conference ends in less than two weeks. You can save 20% if you register on or before 24 April. http://galaxy.psu.edu/gcc2011/Register.html We've also added a partial list of confirmed speakers. More will be added in the coming weeks as the schedule firms up. http://galaxy.psu.edu/gcc2011/Programme.html Please let me know if you have any questions, and hope to see you in May, Dave C. On Thu, Feb 3, 2011 at 5:01 PM, Dave Clements wrote: > We are pleased to announce the *2011 Galaxy Community Conference*, being > held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature > two full days of presentations and discussion on extending Galaxy to use new > tools and data sources, deploying Galaxy at your organization, and best > practices for using Galaxy to further your own and your community's > research. See http://galaxy.psu.edu/gcc2011/* for complete details. > * > *About Galaxy: > *Galaxy is an open, web-based platform for *accessible, reproducible, and > transparent* computational biomedical research. > > - *Accessibility:* Galaxy enables users without programming experience > to easily specify parameters and run tools and workflows. > - *Reproducibility:* Galaxy captures all information necessary so that > any user can repeat and understand a complete computational analysis. > - *Transparency:* Galaxy enables users to share and publish analyses > via the web and create Pages--interactive, web-based documents that describe > a complete analysis. > > Galaxy is open source for all organizations. The public Galaxy service ( > http://usegalaxy.org) makes analysis tools, genomic data, > tutorial demonstrations, persistent workspaces, and publication services > available to any scientist that has access to the Internet. Local > Galaxy servers can be set up by downloading the Galaxy application and > customizing it to meet particular needs. > > *Conference Overview: > * > This event aims to engage a broader community of developers, data > producers, tool creators, and core facility and other research hub staff to > become an active part of the Galaxy community. We'll cover defining > resources in the Galaxy framework, increasing their visibility and making > them easier to use and integrate with other resources, how to extend Galaxy > to use custom data sources and custom tools, and best practices for using > Galaxy in your organization. > > Additional topics include, but are not limited to: > * Talks submitted by the Galaxy community > * Integration of tools (including NGS analysis tools) and distributed job > management > * Deployment of Galaxy instances on local resources and on the Cloud > * Management of large datasets with the Galaxy Library System > * Using the Galaxy LIMS functionality at NGS sequencing facilities > * Visualizing Data without leaving Galaxy > * Performing reproducible research > * Performing and sharing complex analyses with Workflows > * An "Introduction to Galaxy" session, offered on May 24, for Galaxy > newcomers. > > *Registration: > * > The conference fee is ?100 on or before April 24, and ?120 after that. The > meeting is being held at the Conference Centre De Werelt in Lunteren, The > Netherlands, which is also the conference hotel. You are encouraged to > register early, as space at the hotel (and at the "Intro to Galaxy" session) > is limited and is likely to fill up before the conference itself does. See > http://galaxy.psu.edu/gcc2011/Register.html > * > Abstract Submission: > * > Abstracts are now being accepted for short oral presentations. Proposals > on any topic of interest to the Galaxy community are welcome and > encouraged. The abstract submission deadline is the end of February 28. > See http://galaxy.psu.edu/gcc2011/Abstracts.html > * * > *Sponsors > * > The 2011 Galaxy Community Conference is co-sponsored by the US National > Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands > Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a > collaborative institute of the bioinformatics groups in the Netherlands. > Together, these groups perform cutting-edge research, develop novel tools > and support platforms, create an e-science infrastructure and educate the > next generations of bioinformaticians. > > We are looking forward to a great conference and hope to see you in the > Netherlands! > > The Galaxy and NBIC Teams > > -- > http://galaxy.psu.edu/gcc2011/ > http://getgalaxy.org > http://usegalaxy.org/ > -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From md.bustos90 at gmail.com Tue Apr 12 22:55:39 2011 From: md.bustos90 at gmail.com (Maximiliano David Bustos) Date: Tue, 12 Apr 2011 23:55:39 -0300 Subject: [Biopython-dev] Google Summer of Code Proposal Message-ID: Hello everybody, My name is Maximiliano David Bustos, I am a Computer Science student from La Rioja, Argentina. I joined the list some days ago to start collaborating with BioPython project and to get feedback in Google Summer of Code (GSoC). The proposal I submitted to GSoC is titled *"Variant representation, parser, generator, and coordinate converter"*. This idea was taken from BioPython wiki. The project mentor is Reece Hart, who had been helping me a lot in the elaboration of my proposal. Brad Chapman made great contributions too. Reece recommended me to send my proposal to the mailing list. I would really appreciate any feedback from you. Thanks in advance, Maxi. From p.j.a.cock at googlemail.com Wed Apr 13 05:16:42 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 13 Apr 2011 10:16:42 +0100 Subject: [Biopython-dev] Google Summer of Code Proposal In-Reply-To: References: Message-ID: On Wed, Apr 13, 2011 at 3:55 AM, Maximiliano David Bustos wrote: > Hello everybody, > > My name is Maximiliano David Bustos, I am a Computer Science student from La > Rioja, Argentina. I joined the list some days ago to start collaborating > with BioPython project and to get feedback in Google Summer of Code (GSoC). > The proposal I submitted to GSoC is titled *"Variant representation, parser, > generator, and coordinate > converter"*. > This idea was taken from BioPython wiki. > The project mentor is Reece Hart, who had been helping me a lot in the > elaboration of my proposal. Brad Chapman made great contributions too. > > Reece recommended me to send my proposal to the mailing list. I would really > appreciate any feedback from you. > > Thanks in advance, > > Maxi. Hi Maxi, Just a couple of quick initial thoughts on the implementation section, >> Implementation >> >> I will implement the library in Python 2.7, using PLY (Python Lex-Yacc) >> or Pyparsing. I will follow BioPython coding conventions and abstractions >> so the project can be integrated from the beginning. Currently Biopython supports Python 2.5 to 2.7 (and we're working on Python 3). If you target Python 2.7 specific features it would be a problem for integrating your work into Biopython. You would ideally also run and test your code on Python 2.5, and on Python 3. On the bright side, PLY (Python Lex-Yacc) and Pyparsing are pure python and *should* work cross platform (we do want to support Windows). On the other hand, if we can do without them and use the standard Python library only, I'd be happier as it will keep our dependencies down. This is important for making Biopython easy to install and use. In this case they are run time dependencies so it isn't critical. Peter From md.bustos90 at gmail.com Thu Apr 14 12:59:52 2011 From: md.bustos90 at gmail.com (Maximiliano David Bustos) Date: Thu, 14 Apr 2011 13:59:52 -0300 Subject: [Biopython-dev] Google Summer of Code Proposal In-Reply-To: References: Message-ID: Peter, Thanks for your feedback. I will consider this compatibility issues when implementing. Maxi. On Wed, Apr 13, 2011 at 6:16 AM, Peter Cock wrote: > On Wed, Apr 13, 2011 at 3:55 AM, Maximiliano David Bustos > wrote: > > Hello everybody, > > > > My name is Maximiliano David Bustos, I am a Computer Science student from > La > > Rioja, Argentina. I joined the list some days ago to start collaborating > > with BioPython project and to get feedback in Google Summer of Code > (GSoC). > > The proposal I submitted to GSoC is titled *"Variant representation, > parser, > > generator, and coordinate > > converter"*< > https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B1Q10jdy75U_YzE4ZmUzMGEtNjA5Ni00Mjc4LTgwYTQtZTI1MTdkNTJiODc4&hl=en&authkey=CN_Dm8ML > >. > > This idea was taken from BioPython wiki. > > The project mentor is Reece Hart, who had been helping me a lot in the > > elaboration of my proposal. Brad Chapman made great contributions too. > > > > Reece recommended me to send my proposal to the mailing list. I would > really > > appreciate any feedback from you. > > > > Thanks in advance, > > > > Maxi. > > Hi Maxi, > > Just a couple of quick initial thoughts on the implementation section, > > >> Implementation > >> > >> I will implement the library in Python 2.7, using PLY (Python Lex-Yacc) > >> or Pyparsing. I will follow BioPython coding conventions and > abstractions > >> so the project can be integrated from the beginning. > > Currently Biopython supports Python 2.5 to 2.7 (and we're working on Python > 3). > If you target Python 2.7 specific features it would be a problem for > integrating > your work into Biopython. You would ideally also run and test your code on > Python 2.5, and on Python 3. > > On the bright side, PLY (Python Lex-Yacc) and Pyparsing are pure python > and *should* work cross platform (we do want to support Windows). On > the other hand, if we can do without them and use the standard Python > library only, I'd be happier as it will keep our dependencies down. This is > important for making Biopython easy to install and use. In this case they > are run time dependencies so it isn't critical. > > Peter > From updates at feedmyinbox.com Sun Apr 17 00:38:16 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Sun, 17 Apr 2011 00:38:16 -0400 Subject: [Biopython-dev] 4/17 active questions tagged biopython - Stack Overflow Message-ID: <0ed8a84c3c0ad762f3f583f6db924c52@74.63.51.88> // Are there any function that can calculate score for the aligned sequences give parameters? // April 16, 2011 at 7:39 AM http://stackoverflow.com/questions/5686211/are-there-any-function-that-can-calculate-score-for-the-aligned-sequences-give-pa I try to score the already-aligned sequences. Let say seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE' seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE' with given parameters substitution matrix : blogsum62 gap open penalty : -5 gap extension penalty : -1 I did look through the biopython cookbook but all i can get is substitution matrix blogsum62 but I feel that it must have someone already implemented this kind of library. So can anyone suggest any libraries or shortest code that can solve my problem? Thx in advance -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From p.j.a.cock at googlemail.com Sun Apr 17 07:01:58 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 17 Apr 2011 12:01:58 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? Message-ID: Hi all, I realise the BOSC abstract deadline is now tomorrow (!) http://www.open-bio.org/wiki/BOSC_2011 I think it may be just me and Brad going - and we could certainly put together something... Who else is planning to attend BOSC 2011 in Vienna, and would you like to be involved? Peter From tiagoantao at gmail.com Sun Apr 17 11:51:33 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Sun, 17 Apr 2011 16:51:33 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: References: Message-ID: I might go the codefest. It all depends if my PhD is done or not and if I have to go nearby (I might visit south .CH, and thus it would be just a small deviation). If going to the codefest, I would maybe like suggesting spending sometime with infrastructure hardening (like cleaning up the integration testing script, discussing and making changes to the wiki - whatever things people think is important to "robustify"). But for now I am still "hibernating". Tiago On Sun, Apr 17, 2011 at 12:01 PM, Peter Cock wrote: > Hi all, > > I realise the BOSC abstract deadline is now tomorrow (!) > http://www.open-bio.org/wiki/BOSC_2011 > > I think it may be just me and Brad going - and we could > certainly put together something... Who else is planning > to attend BOSC 2011 in Vienna, and would you like to > be involved? > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From chapmanb at 50mail.com Sun Apr 17 12:03:27 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Sun, 17 Apr 2011 12:03:27 -0400 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: References: Message-ID: <20110417160327.GB2401@kunkel> Peter and Tiago; > > I realise the BOSC abstract deadline is now tomorrow (!) > > http://www.open-bio.org/wiki/BOSC_2011 > > > > I think it may be just me and Brad going - and we could > > certainly put together something... Who else is planning > > to attend BOSC 2011 in Vienna, and would you like to > > be involved? It would be great if you wanted to do a Biopython talk. BOSC was trying to deviate a bit from the project update format, but anything you are working on with respect to Biopython or new features added would be perfect. Personally, I'd be interested in hearing about the NGS work you are doing with Biopython and Galaxy. Democratizing analysis methods to allow biologists access is always a challenge, and I'd love to hear about how you've been approaching this. > I might go the codefest. It all depends if my PhD is done or not and > if I have to go nearby (I might visit south .CH, and thus it would be > just a small deviation). Tiago, good luck finishing up the degree. Hope you are done by the summer can make it out to Codefest, Brad From updates at feedmyinbox.com Mon Apr 18 00:38:18 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Mon, 18 Apr 2011 00:38:18 -0400 Subject: [Biopython-dev] 4/18 active questions tagged biopython - Stack Overflow Message-ID: // Are there any function that can calculate score for the aligned sequences give parameters? // April 16, 2011 at 7:39 AM http://stackoverflow.com/questions/5686211/are-there-any-function-that-can-calculate-score-for-the-aligned-sequences-give-pa I try to score the already-aligned sequences. Let say seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE' seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE' with given parameters substitution matrix : blogsum62 gap open penalty : -5 gap extension penalty : -1 I did look through the biopython cookbook but all i can get is substitution matrix blogsum62 but I feel that it must have someone already implemented this kind of library. So can anyone suggest any libraries or shortest code that can solve my problem? Thx in advance -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From p.j.a.cock at googlemail.com Mon Apr 18 05:03:01 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 18 Apr 2011 10:03:01 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: <20110417160327.GB2401@kunkel> References: <20110417160327.GB2401@kunkel> Message-ID: 2011/4/17 Brad Chapman : > Peter and Tiago; > >> > I realise the BOSC abstract deadline is now tomorrow (!) >> > http://www.open-bio.org/wiki/BOSC_2011 >> > >> > I think it may be just me and Brad going - and we could >> > certainly put together something... Who else is planning >> > to attend BOSC 2011 in Vienna, and would you like to >> > be involved? > > It would be great if you wanted to do a Biopython talk. BOSC was > trying to deviate a bit from the project update format, but anything > you are working on with respect to Biopython or new features added > would be perfect. One idea would be to go over the Bio.SeqIO.index_db(...) code and how this SQLite3 backend could be the basis of a new Bio* OBF version of OBDA (to supplement the existing flat file and BDB specifications). > Personally, I'd be interested in hearing about the > NGS work you are doing with Biopython and Galaxy. Democratizing > analysis methods to allow biologists access is always a challenge, > and I'd love to hear about how you've been approaching this. I'll be talking after BOSC during ISMB proper about some of my Galaxy work, but it isn't NGS focused - see Workshop 6 "Genomics for Non-Model Organisms" being organised by James Taylor and Anton Nekrutenko from Galaxy: http://www.iscb.org/ismbeccb2011-program/workshops#w6 In terms of Galaxy and NGS, I've finding my sequence file filtering tool very handy (FASTA, FASTQ and SFF) for a number of workflows including removing read contamination, mapped reads etc. This is on the Galaxy toolshed and uses Biopython (for SFF filtering): http://community.g2.bx.psu.edu/ >> I might go the codefest. It all depends if my PhD is done or not and >> if I have to go nearby (I might visit south .CH, and thus it would be >> just a small deviation). > > Tiago, good luck finishing up the degree. Hope you are done by the > summer can make it out to Codefest, +1 Peter From p.j.a.cock at googlemail.com Mon Apr 18 13:58:26 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 18 Apr 2011 18:58:26 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: References: <20110417160327.GB2401@kunkel> Message-ID: 2011/4/18 Peter Cock : > 2011/4/17 Brad Chapman : >> Peter and Tiago; >> >>> > I realise the BOSC abstract deadline is now tomorrow (!) >>> > http://www.open-bio.org/wiki/BOSC_2011 >>> > >>> > I think it may be just me and Brad going - and we could >>> > certainly put together something... Who else is planning >>> > to attend BOSC 2011 in Vienna, and would you like to >>> > be involved? >> >> It would be great if you wanted to do a Biopython talk. BOSC was >> trying to deviate a bit from the project update format, but anything >> you are working on with respect to Biopython or new features added >> would be perfect. > > One idea would be to go over the Bio.SeqIO.index_db(...) code > and how this SQLite3 backend could be the basis of a new Bio* > OBF version of OBDA (to supplement the existing flat file and > BDB specifications). > >> Personally, I'd be interested in hearing about the >> NGS work you are doing with Biopython and Galaxy. Democratizing >> analysis methods to allow biologists access is always a challenge, >> and I'd love to hear about how you've been approaching this. > > I'll be talking after BOSC during ISMB proper about some of > my Galaxy work, but it isn't NGS focused - see Workshop 6 > "Genomics for Non-Model Organisms" being organised by James > Taylor and Anton Nekrutenko from Galaxy: > http://www.iscb.org/ismbeccb2011-program/workshops#w6 > > In terms of Galaxy and NGS, I've finding my sequence file filtering > tool very handy (FASTA, FASTQ and SFF) for a number of workflows > including removing read contamination, mapped reads etc. This is > on the Galaxy toolshed and uses Biopython (for SFF filtering): > http://community.g2.bx.psu.edu/ > >>> I might go the codefest. It all depends if my PhD is done or not and >>> if I have to go nearby (I might visit south .CH, and thus it would be >>> just a small deviation). >> >> Tiago, good luck finishing up the degree. Hope you are done by the >> summer can make it out to Codefest, > > +1 > > Peter > I've uploaded an initial abstract (which I can still change until the deadline later tonight), if there are suggestions for improvements: In this talk we present the current status of the Biopython project (www.biopython.org), described in a application (Cock et al., 2009). Since BOSC 2010, we have made three releases. Touching on key functionality, Biopython 1.55 (August 2010) made our command line tool wrappers easier to use, Biopython 1.56 (November 2010) added a UniProt XML parser, and Biopython 1.57 (April 2011) added an SQLite based indexer for sequence flat files. All releases have seen more unit tests, more documentation, and more new contributors. In summer 2010 we had one Google Summer of Code (GSoC) project student, Joao Rodrigues working on protein structure (PDB) code for Biopython. Some of Joao?s work has already been included in Biopython releases, and he and his mentor Eric Talevich (himself a GSoC 2009 student) are working to merge the rest of this work. Additionally they hope to co-mentor a GSoC student this summer. For the last six months, we have been running a BuildBot server (see http://buildbot.net/), with the offline parts of the Biopython unit test suite scheduled every night on build slaves running on Linux, Windows and Mac OS X, and both ?C? Python and Jython (using the Java virtual machine). This has been beneficial in catching platform specific regressions, for example under Python 3 which we are still working towards fully supporting. The BuildBot server is running on an OBF maintained Amazon cloud server, while the slaves are initially all machines maintained by individual Biopython developers. Biopython is free open source software available from www.biopython.org under the Biopython License Agreement (an MIT style license, http://www.biopython.org/DIST/LICENSE). Peter From redmine at redmine.open-bio.org Tue Apr 19 20:37:36 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 00:37:36 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Cedar McKay. I got a response from NCBI, and those files were, in fact, defective. Their text below: 
Dear Cedar Mckay,
Thank you for reporting this. The developer staff have traced through the
problem and identified a solution for future FTP releases.

You can download the record from the NCBI web site in the meantime; however,
note that this problem feature is not included in that download. 

Apologies for the inconvenience and thanks again for reporting it.

Kim Pruitt
---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Tue Apr 19 23:06:21 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 03:06:21 +0000 Subject: [Biopython-dev] [Biopython - Bug #3211] (New) Enhancement for Tm calculation Message-ID: Issue #3211 has been reported by ogan abaan. ---------------------------------------- Bug #3211: Enhancement for Tm calculation https://redmine.open-bio.org/issues/3211 Author: ogan abaan Status: New Priority: Normal Assignee: Category: Target version: URL: I have created this Tm function with NN thermodynamics corrected for dna, Monovalent ions, Mg, dNTP, DMSO concentrations as published in the literature. Please feel free to provide your feedback. This function might be useful in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 04:00:31 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 08:00:31 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] (Resolved) SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Peter Cock. Status changed from New to Resolved % Done changed from 0 to 100 Thanks Cedar :) I think we can close this now - there will be a more helpful error in the next Biopython release, https://github.com/biopython/biopython/commit/cb270ea74e9ccb4ae6889dfb7570010d9bcbdb8a Peter ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: Resolved Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 11:05:16 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 15:05:16 +0000 Subject: [Biopython-dev] [Biopython - Bug #3212] (New) Enhancement for Bio.SeqUtils.MeltingTemp Message-ID: Issue #3212 has been reported by ogan abaan. ---------------------------------------- Bug #3212: Enhancement for Bio.SeqUtils.MeltingTemp https://redmine.open-bio.org/issues/3212 Author: ogan abaan Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: URL: Sorry, this is a repost. This was my first post and I realized that I left may things out. I couldn't update it or delete it sorry. Peter suggested that I post this here so you all can comment. I have created this Tm function with NN thermodynamics corrected for dna, Monovalent ions, Mg, dNTP, DMSO concentrations as published in the literature. Please feel free to provide your feedback. This function might be useful in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 11:05:17 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 15:05:17 +0000 Subject: [Biopython-dev] [Biopython - Bug #3212] (New) Enhancement for Bio.SeqUtils.MeltingTemp Message-ID: Issue #3212 has been reported by ogan abaan. ---------------------------------------- Bug #3212: Enhancement for Bio.SeqUtils.MeltingTemp https://redmine.open-bio.org/issues/3212 Author: ogan abaan Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: URL: Sorry, this is a repost. This was my first post and I realized that I left may things out. I couldn't update it or delete it sorry. Peter suggested that I post this here so you all can comment. I have created this Tm function with NN thermodynamics corrected for dna, Monovalent ions, Mg, dNTP, DMSO concentrations as published in the literature. Please feel free to provide your feedback. This function might be useful in Biopython. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From p.j.a.cock at googlemail.com Wed Apr 20 13:08:46 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 20 Apr 2011 18:08:46 +0100 Subject: [Biopython-dev] Interesting BLAST 2.2.25+ XML behaviour Message-ID: Hi all, Have a look at this XML file from a FASTA vs FASTA search using blastp from BLAST 2.2.25+ (current release), which is a test file I created for the BLAST+ wrappers in Galaxy: https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml I just put it though the Biopython BLAST XML parser, and was surprised not to get four records back (since as you might guess from the filename, there were four queries). It appears this version of BLAST+ is incrementing the iteration counter for each match... or something like that. Has anyone else noticed this? I wonder if it is accidental... Peter From updates at feedmyinbox.com Fri Apr 22 00:38:36 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Fri, 22 Apr 2011 00:38:36 -0400 Subject: [Biopython-dev] 4/22 active questions tagged biopython - Stack Overflow Message-ID: <8eaed29e41b889fff3193bf1aff57ba1@74.63.51.88> // Problem with GFF parser by BCBio // April 21, 2011 at 5:50 AM http://stackoverflow.com/questions/5742379/problem-with-gff-parser-by-bcbio Hi, I am trying to parse a GFF file using the BCBio GFF parser and I get the following error. Can anybody help me in resolving this problem? Traceback (most recent call last): File "gff_parse.py", line 6, in for rec in GFF.parse(in_handle): File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 709, in parse File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 299, in parse_in_parts File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 320, in parse_simple File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 603, in _gff_process File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 634, in _lines_to_out_info File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 183, in _gff_line_map ValueError: invalid literal for int() with base 10: 'New Start' Here is my code: from BCBio import GFF in_file = "infile.gff" in_handle = open(in_file) for rec in GFF.parse(in_handle): print rec in_handle.close() Thanks Tulika -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From redmine at redmine.open-bio.org Fri Apr 22 12:22:31 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Fri, 22 Apr 2011 16:22:31 +0000 Subject: [Biopython-dev] [Biopython - Bug #3009] (Closed) Check the FASTA m10 alignment parser works with FASTA36 References: Message-ID: Issue #3009 has been updated by Peter Cock. Status changed from New to Closed % Done changed from 0 to 100 Seemed to have been working fine up to and including fasta-36.2, I just found and fixed a problem with fasta-36.3 https://github.com/biopython/biopython/commit/f528bf583993efd7558173dff4309cf0821203a1 https://github.com/biopython/biopython/commit/f8373400a9dbe2cf54f5d0e73ccd5163e7ad4558 Marking this bug as fixed. ---------------------------------------- Bug #3009: Check the FASTA m10 alignment parser works with FASTA36 https://redmine.open-bio.org/issues/3009 Author: Peter Cock Status: Closed Priority: Normal Assignee: Biopython Dev Mailing List Category: Unit Tests Target version: Not Applicable URL: Bill Pearson has just announced the release of FASTA36: http://faculty.virginia.edu/wrpearson/fasta/fasta36/ >From his email, > This version is a major update from FASTA version 35. > It's main new feature is the ability to report all > statistically significant alignments between a query > and library sequence (equivalent to BLAST's multiple > HSPs). All previous versions of the FASTA program > reported only the best alignment between the query > and library sequence, a serious shortcoming when > comparing a query protein to a multi-exon gene or > multi-domain protein. We need to check the FASTA36 -m 10 output, add this to our unit tests, and update our parser as required. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Tue Apr 26 13:20:10 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Tue, 26 Apr 2011 17:20:10 +0000 Subject: [Biopython-dev] [Biopython - Bug #3009] (New) Check the FASTA m10 alignment parser works with FASTA36 References: Message-ID: Issue #3009 has been updated by Peter Cock. Category changed from Unit Tests to Main Distribution Status changed from Closed to New % Done changed from 100 to 0 Reopening bug, found some examples with multiple HSPs for the same query and match, separated by new line ">--". I will add an example to the test suite, but the parser will need revising (something I was looking at doing anyway for other reasons). ---------------------------------------- Bug #3009: Check the FASTA m10 alignment parser works with FASTA36 https://redmine.open-bio.org/issues/3009 Author: Peter Cock Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: Not Applicable URL: Bill Pearson has just announced the release of FASTA36: http://faculty.virginia.edu/wrpearson/fasta/fasta36/ >From his email, > This version is a major update from FASTA version 35. > It's main new feature is the ability to report all > statistically significant alignments between a query > and library sequence (equivalent to BLAST's multiple > HSPs). All previous versions of the FASTA program > reported only the best alignment between the query > and library sequence, a serious shortcoming when > comparing a query protein to a multi-exon gene or > multi-domain protein. We need to check the FASTA36 -m 10 output, add this to our unit tests, and update our parser as required. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 27 22:07:51 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 02:07:51 +0000 Subject: [Biopython-dev] [Biopython - Bug #2820] (Closed) Convert test_PDB.py to unittest References: Message-ID: Issue #2820 has been updated by Eric Talevich. Status changed from New to Closed % Done changed from 0 to 100 Wow, we took care of this a long time ago. Marking it closed. ---------------------------------------- Bug #2820: Convert test_PDB.py to unittest https://redmine.open-bio.org/issues/2820 Author: Eric Talevich Status: Closed Priority: Normal Assignee: Biopython Dev Mailing List Category: Unit Tests Target version: Not Applicable URL: The current test script for Bio.PDB uses the print-and-compare approach. I've written an equivalent test script using unittest, assuming that style is the preferred one. It was written to go with Bug 2754, but now lives on my pdbtidy branch: http://github.com/etal/biopython/tree/pdbtidy This script could also live alongside the original test_PDB.py for awhile, as an additional check on Bio.PDB's error handling. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 27 22:24:28 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 02:24:28 +0000 Subject: [Biopython-dev] [Biopython - Feature #3216] (New) Bio.Phylo.Applications support for PhyML Message-ID: Issue #3216 has been reported by Eric Talevich. ---------------------------------------- Feature #3216: Bio.Phylo.Applications support for PhyML https://redmine.open-bio.org/issues/3216 Author: Eric Talevich Status: New Priority: Low Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: http://www.atgc-montpellier.fr/phyml/ PhyML is another popular tool for inferring phylogenies by maximum likelihood, and can be also be considered reasonably best-practice (alongside RAxML, which isn't yet packaged). The Debian package for PhyML was recently updated to the latest version (3.0), and should be trickling down to the distros soon. Let's create a wrapper for it in Biopython. The input is just a Phylip alignment, so this should be easier than MrBayes. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 27 22:50:27 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 02:50:27 +0000 Subject: [Biopython-dev] [Biopython - Feature #3217] (New) Bio.Phylo I/O support for the NeXML format Message-ID: Issue #3217 has been reported by Eric Talevich. ---------------------------------------- Feature #3217: Bio.Phylo I/O support for the NeXML format https://redmine.open-bio.org/issues/3217 Author: Eric Talevich Status: New Priority: Normal Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: The future data exchange standard is... approaching rapidly. NeXML is going to become the format of choice for TreeBASE, Mesquite and probably MIAPA-targeted tools over the next year or two, and Biopython should be there to support it. Notes: * Another Python library, DendroPy, already supports (some of?) the NeXML format. Jeet Sukumaran and Mark Holder changed the license to BSD to allow other projects -- particularly us -- to share their code. So let's start there. * NeXML was designed so its elements can be treated as RDF triples, so see if RDFLib can help -- either as the underlying parser, or to provide some additional (optional) functionality. See: http://nexml.org/ http://packages.python.org/DendroPy/ http://www.rdflib.net/ ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 11:41:40 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 15:41:40 +0000 Subject: [Biopython-dev] [Biopython - Feature #3218] (New) Bio.Phylo.Applications support for RAxML Message-ID: Issue #3218 has been reported by Eric Talevich. ---------------------------------------- Feature #3218: Bio.Phylo.Applications support for RAxML https://redmine.open-bio.org/issues/3218 Author: Eric Talevich Status: New Priority: Low Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: RAxML is another popular tool for inferring phylogenies by maximum likelihood, and can be also be considered reasonably best-practice. Performance is good, and the command-line options are easy to understand. The Debian package for RAxML was uploaded to SVN today. Let's create a wrapper for it in Biopython. The input is a Phylip alignment, like PhyML. Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm NB: Frank Kauff wrote a separate wrapper for RAxML called PYRAXML. Check it out. http://www.lutzonilab.net/downloads/ Implementation note: Phylip alignment format truncates taxon names, but we can support longer names in intermediate Bio.Align.MultipleSeqAlignment objects by mapping sequence IDs to unique integers (for example). That function would be useful in several places in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:09:11 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:09:11 +0000 Subject: [Biopython-dev] [Biopython - Feature #3219] (New) Port Biopython documentation to Sphinx Message-ID: Issue #3219 has been reported by Eric Talevich. ---------------------------------------- Feature #3219: Port Biopython documentation to Sphinx https://redmine.open-bio.org/issues/3219 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: Currently we use Epydoc for the API reference documentation, and LaTeX (to PDF via pdflatex, and HTML via hevea) for the tutorial. There's some material on the wiki to consider, too. A number of Python projects, including CPython, now use Sphinx for documentation. Content is written in reStructuredText format, and can be pulled from both standalone .rst files and Python docstrings. This offers several advantages: (i) API documentation will be prettier and easier to navigate; (ii) the Tutorial will be easier to edit for those not fluent in LaTeX; (iii) Since the API reference and Tutorial will be written in the same markup, potentially even pulling from some shared sources, it will be easier to address redundant or overlapping portions between the two, avoiding inconsistencies. See: http://sphinx.pocoo.org/ http://docutils.sourceforge.net/ Mailing list discussion: http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html Numpy's approach: http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:09:11 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:09:11 +0000 Subject: [Biopython-dev] [Biopython - Feature #3219] (New) Port Biopython documentation to Sphinx Message-ID: Issue #3219 has been reported by Eric Talevich. ---------------------------------------- Feature #3219: Port Biopython documentation to Sphinx https://redmine.open-bio.org/issues/3219 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: Currently we use Epydoc for the API reference documentation, and LaTeX (to PDF via pdflatex, and HTML via hevea) for the tutorial. There's some material on the wiki to consider, too. A number of Python projects, including CPython, now use Sphinx for documentation. Content is written in reStructuredText format, and can be pulled from both standalone .rst files and Python docstrings. This offers several advantages: (i) API documentation will be prettier and easier to navigate; (ii) the Tutorial will be easier to edit for those not fluent in LaTeX; (iii) Since the API reference and Tutorial will be written in the same markup, potentially even pulling from some shared sources, it will be easier to address redundant or overlapping portions between the two, avoiding inconsistencies. See: http://sphinx.pocoo.org/ http://docutils.sourceforge.net/ Mailing list discussion: http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html Numpy's approach: http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:19:17 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:19:17 +0000 Subject: [Biopython-dev] [Biopython - Feature #3220] (New) Port Biopython docstrings to reStructuredText Message-ID: Issue #3220 has been reported by Eric Talevich. ---------------------------------------- Feature #3220: Port Biopython docstrings to reStructuredText https://redmine.open-bio.org/issues/3220 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work. Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from: 
__docformat__ = "epytext en"
to: 
__docformat__ = "restructuredtext en"
And changing any Epytext markup in the docstrings to valid rST. Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation. See: http://epydoc.sourceforge.net/manual-othermarkup.html http://docutils.sourceforge.net/rst.html -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:19:16 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:19:16 +0000 Subject: [Biopython-dev] [Biopython - Feature #3220] (New) Port Biopython docstrings to reStructuredText Message-ID: Issue #3220 has been reported by Eric Talevich. ---------------------------------------- Feature #3220: Port Biopython docstrings to reStructuredText https://redmine.open-bio.org/issues/3220 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work. Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from: 
__docformat__ = "epytext en"
to: 
__docformat__ = "restructuredtext en"
And changing any Epytext markup in the docstrings to valid rST. Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation. See: http://epydoc.sourceforge.net/manual-othermarkup.html http://docutils.sourceforge.net/rst.html ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:23:48 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:23:48 +0000 Subject: [Biopython-dev] [Biopython - Feature #3221] (New) Port the Biopython Tutorial to Sphinx/reStructuredText Message-ID: Issue #3221 has been reported by Eric Talevich. ---------------------------------------- Feature #3221: Port the Biopython Tutorial to Sphinx/reStructuredText https://redmine.open-bio.org/issues/3221 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: This is the second step in porting Biopython documentation to Sphinx -- port the Tutorial markup from LaTeX to reStructuredText, and split it into multiple files for Sphinx to process. While we're at it, we may want to slim down the Tutorial and move some of the more detailed material to a separate Reference based on the automated API docs. See the parent task for discussion. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:23:48 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:23:48 +0000 Subject: [Biopython-dev] [Biopython - Feature #3221] (New) Port the Biopython Tutorial to Sphinx/reStructuredText Message-ID: Issue #3221 has been reported by Eric Talevich. ---------------------------------------- Feature #3221: Port the Biopython Tutorial to Sphinx/reStructuredText https://redmine.open-bio.org/issues/3221 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: This is the second step in porting Biopython documentation to Sphinx -- port the Tutorial markup from LaTeX to reStructuredText, and split it into multiple files for Sphinx to process. While we're at it, we may want to slim down the Tutorial and move some of the more detailed material to a separate Reference based on the automated API docs. See the parent task for discussion. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:42:48 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:42:48 +0000 Subject: [Biopython-dev] [Biopython - Feature #3220] Port Biopython docstrings to reStructuredText References: Message-ID: Issue #3220 has been updated by Peter Cock. You linked to this on the parent bug #3319, but we should probably adopt (some of) the NumPy docstring conventions, which limit the amount of rich mark up so as not to make the plain text view too ugly. This is important when reading the API help text at the python prompt. https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt Also note that a large fraction of the current API docs are not even done in epytext, they are plain text. This would also be a nice point to standardise on the layout of things like function/method argument documentation. Again, I'd suggest following NumPy by default. ---------------------------------------- Feature #3220: Port Biopython docstrings to reStructuredText https://redmine.open-bio.org/issues/3220 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work. Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from: 
__docformat__ = "epytext en"
to: 
__docformat__ = "restructuredtext en"
And changing any Epytext markup in the docstrings to valid rST. Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation. See: http://epydoc.sourceforge.net/manual-othermarkup.html http://docutils.sourceforge.net/rst.html -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 12:45:16 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:45:16 +0000 Subject: [Biopython-dev] [Biopython - Feature #3221] Port the Biopython Tutorial to Sphinx/reStructuredText References: Message-ID: Issue #3221 has been updated by Peter Cock. Note that some of the examples in Tutorial.txt are written in doctest format and are now tested using the doctest library via test_Tutorial.py It would be nice to continue to have these examples run as part of our test suite, but it would require some markup convention (since not all doctest like examples should be tested). ---------------------------------------- Feature #3221: Port the Biopython Tutorial to Sphinx/reStructuredText https://redmine.open-bio.org/issues/3221 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: This is the second step in porting Biopython documentation to Sphinx -- port the Tutorial markup from LaTeX to reStructuredText, and split it into multiple files for Sphinx to process. While we're at it, we may want to slim down the Tutorial and move some of the more detailed material to a separate Reference based on the automated API docs. See the parent task for discussion. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From luizaugustomm at gmail.com Thu Apr 28 21:42:26 2011 From: luizaugustomm at gmail.com (=?ISO-8859-1?Q?Luiz_Augusto_Mac=EAdo_Morais?=) Date: Thu, 28 Apr 2011 22:42:26 -0300 Subject: [Biopython-dev] Translation of the tutorial about Biopython Message-ID: Hi everybody, My name is Luiz Augusto. I am a brazilian student of Computer Science and I am interested to translate to Portuguese the tutorial of the Biopython written by Jeff Chang et al. I begun to study Biopython this year and I noticed that there is not many materials about Biopython written in Portuguese. So, I want to know how get permission to translate that material. I tried send an e-mail to Jeff Chang, but his e-mail is not working. Yours faithfully, Luiz Augusto de Mac?do Morais From krother at rubor.de Fri Apr 29 03:37:28 2011 From: krother at rubor.de (Kristian Rother) Date: Fri, 29 Apr 2011 09:37:28 +0200 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: Hi, I've seen Sphinx being used on several projects (see e.g. http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one myself (2009). The system for mixing text+code and testing code examples is gorgeous! What I didn't like is that all Sphinx sites seem to look the same (including font sizes and colours). There probably is a place to apply a CSS stylesheet, but it was not easy to find. There might be some work at this point. Is someone trying to make a proof-of-concept on GIT or are we looking for a volunteer? Best regards, Kristian > > Issue #3219 has been reported by Eric Talevich. > > ---------------------------------------- > Feature #3219: Port Biopython documentation to Sphinx > https://redmine.open-bio.org/issues/3219 > > Author: Eric Talevich > Status: New > Priority: Low > Assignee: Biopython Dev Mailing List > Category: Documentation > Target version: > URL: > > > Currently we use Epydoc for the API reference documentation, and LaTeX (to > PDF via pdflatex, and HTML via hevea) for the tutorial. There's some > material on the wiki to consider, too. > > A number of Python projects, including CPython, now use Sphinx for > documentation. Content is written in reStructuredText format, and can be > pulled from both standalone .rst files and Python docstrings. > > This offers several advantages: (i) API documentation will be prettier and > easier to navigate; (ii) the Tutorial will be easier to edit for those not > fluent in LaTeX; (iii) Since the API reference and Tutorial will be > written in the same markup, potentially even pulling from some shared > sources, it will be easier to address redundant or overlapping portions > between the two, avoiding inconsistencies. > > See: > http://sphinx.pocoo.org/ > http://docutils.sourceforge.net/ > > Mailing list discussion: > http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html > > Numpy's approach: > http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt > > > > ---------------------------------------- > You have received this notification because this email was added to the > New Issue Alert plugin > > > -- > You have received this notification because you have either subscribed to > it, or are involved in it. > To change your notification preferences, please click here and login: > http://redmine.open-bio.org > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > > From p.j.a.cock at googlemail.com Fri Apr 29 03:55:40 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 29 Apr 2011 08:55:40 +0100 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: Re: Feature #3219: Port Biopython documentation to Sphinx https://redmine.open-bio.org/issues/3219 and this thread last year: http://portal.open-bio.org/pipermail/biopython-dev/2010-July/007977.html On Fri, Apr 29, 2011 at 8:37 AM, Kristian Rother wrote: > > Hi, > > I've seen Sphinx being used on several projects (see e.g. > http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one > myself (2009). The system for mixing text+code and testing code examples > is gorgeous! > > What I didn't like is that all Sphinx sites seem to look the same > (including font sizes and colours). There probably is a place to apply a > CSS stylesheet, but it was not easy to find. There might be some work at > this point. > > Is someone trying to make a proof-of-concept on GIT or are we looking for > a volunteer? > > Best regards, > ? Kristian I think there was an experimental branch on github already... by Eric and/or Vince, but his repository seems to have gone: https://github.com/vsbuffalo/ Peter From chapmanb at 50mail.com Fri Apr 29 08:17:29 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 29 Apr 2011 08:17:29 -0400 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: Message-ID: <20110429121729.GE27039@sobchak> Luiz; > My name is Luiz Augusto. I am a brazilian student of Computer Science and I > am interested to translate to Portuguese the tutorial of the Biopython > written by Jeff Chang et al. [...] > So, I want to know how get permission to translate that material. Yes, please. Portuguese translations of the documentation, cookbooks, or just code examples would be very useful. No permission needed, please go for it. When you have documentation available please let us know so we can link to it: http://biopython.org/wiki/Documentation Thanks much, Brad From idoerg at gmail.com Fri Apr 29 08:48:25 2011 From: idoerg at gmail.com (Iddo Friedberg) Date: Fri, 29 Apr 2011 08:48:25 -0400 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> Message-ID: Hey all, Prompted by this exchange: how about placing all the biopython docs under a creative commons license? Iddo Friedberg http://iddo-friedberg.net/contact.html On Apr 29, 2011 8:22 AM, "Brad Chapman" wrote: Luiz; > My name is Luiz Augusto. I am a brazilian student of Computer Science and I > am interested to tra... [...] > So, I want to know how get permission to translate that material. Yes, please. Portuguese translations of the documentation, cookbooks, or just code examples would be very useful. No permission needed, please go for it. When you have documentation available please let us know so we can link to it: http://biopython.org/wiki/Documentation Thanks much, Brad _______________________________________________ Biopython-dev mailing list Biopython-dev at lists.open-... From tiagoantao at gmail.com Fri Apr 29 08:51:04 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Fri, 29 Apr 2011 13:51:04 +0100 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> Message-ID: 2011/4/29 Iddo Friedberg : > Prompted by this exchange: how about placing all the biopython docs under a > creative commons license? +1 From p.j.a.cock at googlemail.com Fri Apr 29 09:15:47 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 29 Apr 2011 14:15:47 +0100 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> Message-ID: <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> On 29 Apr 2011, at 13:51, Tiago Ant?o wrote: > 2011/4/29 Iddo Friedberg : >> Prompted by this exchange: how about placing all the biopython docs under a >> creative commons license? > > +1 > _______________________________________________ > We'd have to check with at least the named authors... but it seems like a good idea. Peter From eric.talevich at gmail.com Fri Apr 29 10:13:17 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Fri, 29 Apr 2011 10:13:17 -0400 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: On Fri, Apr 29, 2011 at 3:55 AM, Peter Cock wrote: > Re: Feature #3219: Port Biopython documentation to Sphinx > https://redmine.open-bio.org/issues/3219 > > and this thread last year: > http://portal.open-bio.org/pipermail/biopython-dev/2010-July/007977.html > > On Fri, Apr 29, 2011 at 8:37 AM, Kristian Rother wrote: > > > > Hi, > > > > I've seen Sphinx being used on several projects (see e.g. > > http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one > > myself (2009). The system for mixing text+code and testing code examples > > is gorgeous! > > > > What I didn't like is that all Sphinx sites seem to look the same > > (including font sizes and colours). There probably is a place to apply a > > CSS stylesheet, but it was not easy to find. There might be some work at > > this point. > > > > Is someone trying to make a proof-of-concept on GIT or are we looking for > > a volunteer? > > > > Best regards, > > Kristian > > I think there was an experimental branch on github already... by Eric > and/or > Vince, but his repository seems to have gone: > https://github.com/vsbuffalo/ > > I don't have a branch for this yet, but I filed the bugs on Redmine to get this big to-do item out of my head and onto the web. I expect to have a little bit more time this summer to work on Bio.Phylo and Bio.PDB/Struct, and I'm going to start by converting the docstrings in Bio.Phylo to reStructuredText. This won't take much time, and once we merge that branch and make the Docutils dependency official (for building Epydoc documentation), that will reduce the activation energy for porting the rest of our docstrings. If anyone else wants to port some docstrings independently, that's cool too, and I don't think it will cause any conflict in the code base. Once that's done, we can start seriously considering the switch from Epydoc to Sphinx. Sound like a plan? Cheers, Eric From eric.talevich at gmail.com Fri Apr 29 10:25:18 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Fri, 29 Apr 2011 10:25:18 -0400 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> Message-ID: 2011/4/29 Peter Cock > > > On 29 Apr 2011, at 13:51, Tiago Ant?o wrote: > > > 2011/4/29 Iddo Friedberg : > >> Prompted by this exchange: how about placing all the biopython docs > under a > >> creative commons license? > > > > +1 > > _______________________________________________ > > > > We'd have to check with at least the named authors... but it seems like a > good idea. > > Peter > > +1. Right now the LICENSE file refers to both "this software and its documentation", so the docs are already legally free to modify, translate and redistribute. The Tutorial doesn't have a copyright notice in the comments at the top -- should it? -Eric From luizaugustomm at gmail.com Fri Apr 29 17:10:33 2011 From: luizaugustomm at gmail.com (=?ISO-8859-1?Q?Luiz_Augusto_Mac=EAdo_Morais?=) Date: Fri, 29 Apr 2011 18:10:33 -0300 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> Message-ID: Thank you folks. So, I'll start to translate. Brad, when it's done, I'll send the material to this mailing list. Luiz Augusto Em 29 de abril de 2011 11:25, Eric Talevich escreveu: > 2011/4/29 Peter Cock > >> >> >> On 29 Apr 2011, at 13:51, Tiago Ant?o wrote: >> >> > 2011/4/29 Iddo Friedberg : >> >> Prompted by this exchange: how about placing all the biopython docs >> under a >> >> creative commons license? >> > >> > +1 >> > _______________________________________________ >> > >> >> We'd have to check with at least the named authors... but it seems like a >> good idea. >> >> Peter >> >> > +1. Right now the LICENSE file refers to both "this software and its > documentation", so the docs are already legally free to modify, translate > and redistribute. The Tutorial doesn't have a copyright notice in the > comments at the top -- should it? > > -Eric > From p.j.a.cock at googlemail.com Fri Apr 29 19:47:35 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 30 Apr 2011 00:47:35 +0100 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: On Friday, April 29, 2011, Eric Talevich wrote: > > I don't have a branch for this yet, but I filed the bugs on Redmine to get this big to-do item out of my head and onto the web. I expect to have a little bit more time this summer to work on Bio.Phylo and Bio.PDB/Struct, and I'm going to start by converting the docstrings in Bio.Phylo to reStructuredText. This won't take much time, and once we merge that branch and make the Docutils dependency official (for building Epydoc documentation), that will reduce the activation energy for porting the rest of our docstrings. > > If anyone else wants to port some docstrings independently, that's cool too, and I don't think it will cause any conflict in the code base. > > Once that's done, we can start seriously considering the switch from Epydoc to Sphinx. Sound like a plan? > > Cheers, > Eric > Yes, sounds good. Peter From mdipierro at cs.depaul.edu Fri Apr 29 09:34:34 2011 From: mdipierro at cs.depaul.edu (Massimo Di Pierro) Date: Fri, 29 Apr 2011 08:34:34 -0500 Subject: [Biopython-dev] biopython web interface In-Reply-To: <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> Message-ID: <57629245-F184-4143-8B18-80E69BC2C351@cs.depaul.edu> Hello everybody, I am new to biopython and I have some silly questions. Does biopython have a web interface? If not, would you be interested in help developing one? What kind of features would you be interested in? Reason for my question: I am a physicist and a professor of CS. I am working with a few different groups to build a unified platform to bring scientific data online. The main idea is that of having a tool that requires no programming and scientists can use to introspect an existing directory and turn it into dynamical web pages. Those pages can then be edited and re-oreganized like a CMS. The system should be able to recognize basic file types, group, tag and categorize them. It should them be possible to register algorithms, run them on the server, create a workflow. The system will also have an interface for mobile. Here is a first prototype for physics data that interface with the National Energy Research Computing Center: http://tests.web2py.com/nersc Since we are doing this it would be great to have as many community on board as possible so that we can write specs that are broad enough. We can do all the work or you can help us if you want. So, if you have a wish list please share it with me. Personally, I need to be educated on biopython since I do not fully understand what are the basic file types it handles, what are the most popular algorithms it provides, nor I am familiar with the typical usage workflow. Massimo From eric.talevich at gmail.com Sat Apr 30 10:49:52 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Sat, 30 Apr 2011 10:49:52 -0400 Subject: [Biopython-dev] biopython web interface In-Reply-To: <57629245-F184-4143-8B18-80E69BC2C351@cs.depaul.edu> References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> <57629245-F184-4143-8B18-80E69BC2C351@cs.depaul.edu> Message-ID: Hi Massimo, On Fri, Apr 29, 2011 at 9:34 AM, Massimo Di Pierro wrote: > > Does biopython have a web interface? > If not, would you be interested in help developing one? > What kind of features would you be interested in? > Biopython is only a library, but can be useful for building web interfaces for biological workflows. Have you looked at Galaxy yet? http://galaxy.psu.edu/ http://usegalaxy.org/ http://getgalaxy.org/ I think it may provide most of what you're interested in. It provides a web interface for biological workflows; it requires no programming to use, but it can also be easily extended with a small amount of code to incorporate new command-line tools into a workflow. It already handles most of the common file formats for biological data, too. Reason for my question: I am a physicist and a professor of CS. I am working > with a few different groups to build a unified platform to bring scientific > data online. The main idea is that of having a tool that requires no > programming and scientists can use to introspect an existing directory and > turn it into dynamical web pages. Those pages can then be edited and > re-oreganized like a CMS. The system should be able to recognize basic file > types, group, tag and categorize them. It should them be possible to > register algorithms, run them on the server, create a workflow. The system > will also have an interface for mobile. > > Here is a first prototype for physics data that interface with the National > Energy Research Computing Center: > http://tests.web2py.com/nersc > Interesting, something keep an eye on as it develops. Cheers, Eric From andrea at biocomp.unibo.it Sat Apr 30 13:03:46 2011 From: andrea at biocomp.unibo.it (Andrea Pierleoni) Date: Sat, 30 Apr 2011 19:03:46 +0200 (CEST) Subject: [Biopython-dev] biopython web interface In-Reply-To: References: Message-ID: <3a649ae478daf0c2e544dc573a15f3b5.squirrel@lipid.biocomp.unibo.it> > > Message: 3 > Date: Fri, 29 Apr 2011 08:34:34 -0500 > From: Massimo Di Pierro > Subject: [Biopython-dev] biopython web interface > To: > Message-ID: <57629245-F184-4143-8B18-80E69BC2C351 at cs.depaul.edu> > Content-Type: text/plain; charset="us-ascii" > > Hello everybody, > > I am new to biopython and I have some silly questions. > > Does biopython have a web interface? > If not, would you be interested in help developing one? > What kind of features would you be interested in? > > Reason for my question: I am a physicist and a professor of CS. I am > working with a few different groups to build a unified platform to bring > scientific data online. The main idea is that of having a tool that > requires no programming and scientists can use to introspect an existing > directory and turn it into dynamical web pages. Those pages can then be > edited and re-oreganized like a CMS. The system should be able to > recognize basic file types, group, tag and categorize them. It should them > be possible to register algorithms, run them on the server, create a > workflow. The system will also have an interface for mobile. > > Here is a first prototype for physics data that interface with the > National Energy Research Computing Center: > http://tests.web2py.com/nersc > > Since we are doing this it would be great to have as many community on > board as possible so that we can write specs that are broad enough. > We can do all the work or you can help us if you want. > > So, if you have a wish list please share it with me. > > Personally, I need to be educated on biopython since I do not fully > understand what are the basic file types it handles, what are the most > popular algorithms it provides, nor I am familiar with the typical usage > workflow. > > Massimo > > > Hi Massimo, BioPython itself is a python library, but a web interface would enable many functions to biological scientist with no programming expertise. There are some parts of the library that cope well with a web-interface/server, in particular the BioSQL modules. The BioSQL schema is a relational database model to store biological data. I do have working code for using the BioPython BioSQL functions (and more) with the web2py DAL, and I'm working on a complete web2py-based opensource webserver to store and manage biological sequences/entities. If you (or any other) are interested and want to contribute, let me know. There are many things in common between what I'm doing and what you want to do, so maybe its a good idea to work together. Andrea Pierleoni From rodrigo.faccioli at gmail.com Sat Apr 30 13:55:59 2011 From: rodrigo.faccioli at gmail.com (Rodrigo Faccioli) Date: Sat, 30 Apr 2011 14:55:59 -0300 Subject: [Biopython-dev] biopython web interface In-Reply-To: <3a649ae478daf0c2e544dc573a15f3b5.squirrel@lipid.biocomp.unibo.it> References: <3a649ae478daf0c2e544dc573a15f3b5.squirrel@lipid.biocomp.unibo.it> Message-ID: Hello, The messages before described about BioPython and BioSQL projects. Furthermore, they commented how you are able to develop your system with those projects. I would like to show the project which I have been working. Although you're using web2py framework, I would like to show my project which don't use framework, yet. We develop its front-end in jsp. However, its back-end is written with BioPython. Please, see [1]. [1] http://glu.fcfrp.usp.br:8180/prometheus/ -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-8739 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 Personal Blogg - http://rodrigofaccioli.blogspot.com/ On Sat, Apr 30, 2011 at 2:03 PM, Andrea Pierleoni wrote: > > > > > Message: 3 > > Date: Fri, 29 Apr 2011 08:34:34 -0500 > > From: Massimo Di Pierro > > Subject: [Biopython-dev] biopython web interface > > To: > > Message-ID: <57629245-F184-4143-8B18-80E69BC2C351 at cs.depaul.edu> > > Content-Type: text/plain; charset="us-ascii" > > > > Hello everybody, > > > > I am new to biopython and I have some silly questions. > > > > Does biopython have a web interface? > > If not, would you be interested in help developing one? > > What kind of features would you be interested in? > > > > Reason for my question: I am a physicist and a professor of CS. I am > > working with a few different groups to build a unified platform to bring > > scientific data online. The main idea is that of having a tool that > > requires no programming and scientists can use to introspect an existing > > directory and turn it into dynamical web pages. Those pages can then be > > edited and re-oreganized like a CMS. The system should be able to > > recognize basic file types, group, tag and categorize them. It should > them > > be possible to register algorithms, run them on the server, create a > > workflow. The system will also have an interface for mobile. > > > > Here is a first prototype for physics data that interface with the > > National Energy Research Computing Center: > > http://tests.web2py.com/nersc > > > > Since we are doing this it would be great to have as many community on > > board as possible so that we can write specs that are broad enough. > > We can do all the work or you can help us if you want. > > > > So, if you have a wish list please share it with me. > > > > Personally, I need to be educated on biopython since I do not fully > > understand what are the basic file types it handles, what are the most > > popular algorithms it provides, nor I am familiar with the typical usage > > workflow. > > > > Massimo > > > > > > > > > Hi Massimo, > BioPython itself is a python library, but a web interface would enable many > functions to biological scientist with no programming expertise. > There are some parts of the library that cope well with a > web-interface/server, > in particular the BioSQL modules. > The BioSQL schema is a relational database model to store biological data. > I do have working code for using the BioPython BioSQL functions (and more) > with > the web2py DAL, and I'm working on a complete web2py-based opensource > webserver to store and manage biological sequences/entities. > If you (or any other) are interested and want to contribute, let me know. > There are many things in common between what I'm doing and what you want > to do, > so maybe its a good idea to work together. > > Andrea Pierleoni > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > From chapmanb at 50mail.com Fri Apr 1 10:37:26 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 1 Apr 2011 06:37:26 -0400 Subject: [Biopython-dev] GSoC: "Variant representation, parser, generator, and coordinate converter" In-Reply-To: References: <4D953DA3.7010408@cornell.edu> Message-ID: <20110401103726.GB2330@kunkel> Maximiliano; Thanks for the introduction and interest in the project. I'm cc'ing in the mailing list and Reece, who is the primary mentor. > >> My name is Maximiliano David Bustos, I am from La Rioja, Argentina. I am > >> 20 years old, and currently studying Computer Science at "Facultad de > >> Matem?tica Astronom?a y F?sica" (Fa.M.A.F - UNC). > >> > >> I have read about your organization, in I like the projects that you are > >> developing. I am really interested in contributing in the project > >> "Variant representation, parser, generator, and coordinate converter", > >> taken from your wiki. > >> > >> I want to read more about the topic before writing to the corresponding > >> mailing list. Great to hear. Could you provide some more background and details about why you are interested in the project and what areas you would like to read more on? It would be really helpful to understand how comfortable you are with Python programming, with the Biopython project, and with the biological concepts (variations, genes, proteins). Thanks again, Brad From p.j.a.cock at googlemail.com Fri Apr 1 10:48:21 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 1 Apr 2011 11:48:21 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> Message-ID: On Tue, Mar 29, 2011 at 1:26 PM, Peter Cock wrote: > On Tue, Mar 29, 2011 at 1:05 PM, Brad Chapman wrote: >> Peter; >> >>> > What is our timeline for 1.57? >> >>> I was hoping for some more comments on the tutorial, and ideally fix >>> http://lists.open-bio.org/pipermail/biopython/2011-March/007130.html >>> but other than that we're good to go. Do you want to do the honours? >> >> For your fastq file examples, we could use the EBI short read >> archive, which is staying around for a while longer: >> >> ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/ > > Good plan - why didn't I think of that the other night when I was > looking at this? I may even be able to find the equivalent files to > the ones we used to use from the NCBI SRA. I'll try and sort > that today or tomorrow... Good news - the tutorial update is nearly done now. Bad news - I updated to NCBI BLAST 2.2.25+ and the unit test is complaining about some new switches like -db_hard_mask which we'll need to add and then white-list in test_NCBI_BLAST_tools.py (or just turn off this bit of the tests) Peter From p.j.a.cock at googlemail.com Fri Apr 1 16:35:58 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 1 Apr 2011 17:35:58 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> Message-ID: On Fri, Apr 1, 2011 at 11:48 AM, Peter Cock wrote: > > Good news - the tutorial update is nearly done now. > > Bad news - I updated to NCBI BLAST 2.2.25+ and the unit test is > complaining about some new switches like -db_hard_mask which > we'll need to add and then white-list in test_NCBI_BLAST_tools.py > (or just turn off this bit of the tests) > OK, I think both the SRA links in the Tutorial and the new arguments added to the BLAST+ tools are done. We are also all green on the buildbot (I just forced a set of builds after making those commits): http://testing.open-bio.org/biopython/grid Ready when you are Brad, and if you'd like to wait until after April 1st is over to avoid any jokes, that's OK with me ;) Peter From chapmanb at 50mail.com Fri Apr 1 18:50:42 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 1 Apr 2011 14:50:42 -0400 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> Message-ID: <20110401185042.GG2330@kunkel> Peter; Thanks for fixing the BLAST+ issue and the tutorial. We'll plan for a release later this evening or tomorrow morning, so everyone please hold off commits until it's finished. Below are the release notes and contributors list for the release. Please let me know anything or anyone is missing; additionally if anyone wants to clean up the text or add more flourishes of brilliance, that would be very welcome. Thanks everyone for all the hard work for the release, Brad In progress: Biopython 1.57 (not yet released). Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary. Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the ability to run the BLAST tools and save the output as ASN.1 format, and then convert this to any other supported BLAST ouput format (plain text, tabular, XML, or HTML) with the blast_formatter tool. The wrappers were also updated to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask. The SeqRecord object now has a reverse_complement method (similar to that of the Seq object). This is most useful to reversing per-letter-annotation (such as quality scores from FASTQ) or features (such as annotation from GenBank). Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now uses an optimised routine for FASTQ to QUAL making this much faster. Biopython can now be installed with pip. Thanks to David Koppstein and James Casbon for reporting the problem. Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and IMGT output. The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary (previously it was a list of key,value tuples) to better match the standard. (At least) 14 people have contributed to this release, including 5 new people: Brad Chapman Eric Talevich Erick Matsen (first contribution) Hongbo Zhu Jeffrey Finkelstein (first contribution) Joanna & Dominik Kasprzak (first contribution) Joao Rodrigues Kristian Rother Leighton Pritchard Michiel de Hoon Peter Cock Phillip Garland Walter Gillett (first contribution) From eric.talevich at gmail.com Fri Apr 1 22:08:14 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Fri, 1 Apr 2011 18:08:14 -0400 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: <20110401185042.GG2330@kunkel> References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: On Fri, Apr 1, 2011 at 2:50 PM, Brad Chapman wrote: > > Below are the release notes and contributors list for the release. > Please let me know anything or anyone is missing; additionally if > anyone wants to clean up the text or add more flourishes of > brilliance, that would be very welcome. > > Thanks everyone for all the hard work for the release, > Brad > > > In progress: Biopython 1.57 (not yet released). > > Bio.SeqIO now includes an index_db() function which extends the existing > indexing functionality to allow indexing many files, and more importantly > this keeps the index on disk in a simple SQLite3 database rather than in > memory in a Python dictionary. > > Bio.Blast.Applications now includes a wrapper for the BLAST+ > blast_formatter > tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the > ability to run the BLAST tools and save the output as ASN.1 format, and > then > convert this to any other supported BLAST ouput format (plain text, > tabular, > XML, or HTML) with the blast_formatter tool. The wrappers were also updated > to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask. > > The SeqRecord object now has a reverse_complement method (similar to that > of > the Seq object). This is most useful to reversing per-letter-annotation > (such > as quality scores from FASTQ) or features (such as annotation from > GenBank). > > Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now > uses an optimised routine for FASTQ to QUAL making this much faster. > > Biopython can now be installed with pip. Thanks to David Koppstein and > James Casbon for reporting the problem. > > Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and > IMGT output. > > The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary > (previously it was a list of key,value tuples) to better match the > standard. > > The Bio.PDB module received several fixes and improvements. We've started merging Jo?o's work from GSoC 2010, and consequently Atom objects now know their element type and IUPAC mass. (The new features that use these attributes won't be included in Biopython until the next release, though, so stay tuned.) -E From updates at feedmyinbox.com Sat Apr 2 08:09:17 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Sat, 2 Apr 2011 04:09:17 -0400 Subject: [Biopython-dev] 4/2 active questions tagged biopython - Stack Overflow Message-ID: <11b208e29a7233e2df1e3969f1afc4b9@74.63.51.88> // Bio.IUPAC problem in Biopython // April 1, 2011 at 5:28 PM http://stackoverflow.com/questions/5519081/bio-iupac-problem-in-biopython i was testing this simple code from Bio.Alphabet import IUPAC from Bio import Seq my_prot=Seq("AGTACACTGGT",IUPAC.protein) and it gives me this error TypeError: 'module' object is not callable can anyone explain why this is happening? PS: this is an Example from the BioPython's Cookbook -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From weichen302 at aol.com Sat Apr 2 08:49:13 2011 From: weichen302 at aol.com (Chen Wei) Date: Sat, 2 Apr 2011 16:49:13 +0800 Subject: [Biopython-dev] 4/2 active questions tagged biopython - Stack Overflow In-Reply-To: <11b208e29a7233e2df1e3969f1afc4b9@74.63.51.88> References: <11b208e29a7233e2df1e3969f1afc4b9@74.63.51.88> Message-ID: <20110402084913.GA9993@Tungsten.DarkStar> On Sat, Apr 02, 2011 at 04:09:17AM -0400, Feed My Inbox wrote: > from Bio.Alphabet import IUPAC > from Bio import Seq > my_prot=Seq("AGTACACTGGT",IUPAC.protein) > > and it gives me this error > > TypeError: 'module' object is not callable > it is a namespace problem, Seq is a class lives inside module Seq. Take a look at Bio/Seq.py. u can either change the code to: my_prot=Seq.Seq("AGTACACTGGT",IUPAC.protein) or use: from Bio.Seq import Seq -- Chen Wei From p.j.a.cock at googlemail.com Sat Apr 2 13:43:30 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 2 Apr 2011 14:43:30 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: Thanks Brad :) http://news.open-bio.org/news/2011/04/biopython-1-57-released/ I'll get the Windows installers done on Monday. Peter From redmine at redmine.open-bio.org Sat Apr 2 14:25:57 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Sat, 2 Apr 2011 14:25:57 +0000 Subject: [Biopython-dev] [Biopython - Feature #3193] (New) Bio.Phylo.Applications support for MrBayes Message-ID: Issue #3193 has been reported by Eric Talevich. ---------------------------------------- Feature #3193: Bio.Phylo.Applications support for MrBayes https://redmine.open-bio.org/issues/3193 Author: Eric Talevich Status: New Priority: Normal Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: MrBayes is a popular tool for inferring phylogenies, reasonably best-practice, open-source, and packaged for Debian. Let's create a wrapper for it in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Sat Apr 2 14:59:29 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Sat, 2 Apr 2011 14:59:29 +0000 Subject: [Biopython-dev] [Biopython - Feature #3194] (New) Bio.Phylo export to 'ape' via Rpy2 Message-ID: Issue #3194 has been reported by Eric Talevich. ---------------------------------------- Feature #3194: Bio.Phylo export to 'ape' via Rpy2 https://redmine.open-bio.org/issues/3194 Author: Eric Talevich Status: New Priority: Low Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: There are many more packages for working with phylogenetic data in R, and most of these operate on the basic tree object defined in the ape package. Let's support interoperability through Rpy2. The trivial way to do this is serialize a tree to a Newick string, then feed that to the read.tree() function. Maybe we can build the tree object in R directly and retain the tree annotations that Newick doesn't handle. See: http://ape.mpl.ird.fr/ http://rpy.sourceforge.net/rpy2.html ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From eric.talevich at gmail.com Sat Apr 2 19:16:32 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Sat, 2 Apr 2011 15:16:32 -0400 Subject: [Biopython-dev] New functions in Bio.PDB: renumber_residues(), remove_disordered_atoms() In-Reply-To: References: Message-ID: Hi Jo?o, Now that Biopython 1.57 is out, I'd like to try merging some more features into the trunk. I'm looking at this branch: https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements Can I pull and merge the whole branch, or should I cherry-pick certain commits? And, have you already squashed the history to your own satisfaction? Thanks, Eric On Thu, Feb 17, 2011 at 7:59 AM, Jo?o Rodrigues wrote: > Hey Kristian, > > To Tests/test_pdb.py ? Just to make sure that the renumbering acts on both > accordingly? I agree. > > Jo?o > > On Thu, Feb 17, 2011 at 7:54 AM, Kristian Rother wrote: > > Hi Joao, > > I think we should add a simple test function that ensures consistency of > child_dict and child_list upon renumbering. Let me know if you'd prefer me > to explain in Python what I mean. > > Kristian > > > > > Dear All, > > > > I've been working on the above-mentioned functions following really great > > feedback from Eric, Kristian, and Peter. I've been also using them > > routinely > > and I've had no problems yet so they should be stable enough. Therefore I > > think they can be cherry-picked from my pdb_enhancements branch and added > > to > > the main branch. Let me know what you think. > > > > Cheers, > > > > Jo??o > > > > _______________________________________________ > From p.j.a.cock at googlemail.com Mon Apr 4 08:57:51 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Apr 2011 09:57:51 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: On Sat, Apr 2, 2011 at 2:43 PM, Peter Cock wrote: > Thanks Brad :) > > http://news.open-bio.org/news/2011/04/biopython-1-57-released/ > > I'll get the Windows installers done on Monday. > > Peter They're up. I included one for Python 2.4 put stuck 'unsupported' at the end of its filename. I'm wondering if we should make a couple for Python 3.1 and 3.2 but clearly mark them as alpha quality? Perhaps a little branch on github just to change the version to 1.57a and edit the setup.py description? Speaking of which, I found our first bug: I didn't add do2to3.py to the manifest, so it isn't included in the tar ball or zip. This means you can't install from a source release under Python 3. Not a big issue as we haven't claimed to support Python 3 yet: https://github.com/biopython/biopython/commit/4b1cc1e501a136188c41c1345c1d22ceb11cdb0c Peter From chapmanb at 50mail.com Mon Apr 4 12:51:49 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Mon, 4 Apr 2011 08:51:49 -0400 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> Message-ID: <20110404125149.GB17045@sobchak> Peter; [Windows installers] > They're up. I included one for Python 2.4 put stuck 'unsupported' > at the end of its filename. Awesome, thanks much. > I'm wondering if we should make a couple for Python 3.1 and 3.2 > but clearly mark them as alpha quality? Perhaps a little branch > on github just to change the version to 1.57a and edit the setup.py > description? This is a good idea and could help us get a sense of if people are using Python 3 yet. > Speaking of which, I found our first bug: I didn't add do2to3.py > to the manifest, so it isn't included in the tar ball or zip. This > means you can't install from a source release under Python 3. > Not a big issue as we haven't claimed to support Python 3 yet: > https://github.com/biopython/biopython/commit/4b1cc1e501a136188c41c1345c1d22ceb11cdb0c Whoops. Should we freshen up the tarballs with this or wait until the next release? For your manifest fix, we should add do2to3.py to the MANIFEST.in instead of checking in the MANIFEST directly, since the MANIFEST is generated during building the release. Brad From p.j.a.cock at googlemail.com Mon Apr 4 13:10:19 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Apr 2011 14:10:19 +0100 Subject: [Biopython-dev] 1.57 release plans In-Reply-To: <20110404125149.GB17045@sobchak> References: <20110328133639.GD26383@sobchak> <20110329120532.GL26383@sobchak> <20110401185042.GG2330@kunkel> <20110404125149.GB17045@sobchak> Message-ID: On Mon, Apr 4, 2011 at 1:51 PM, Brad Chapman wrote: > Peter; > > [Windows installers] >> They're up. I included one for Python 2.4 put stuck 'unsupported' >> at the end of its filename. > > Awesome, thanks much. > >> I'm wondering if we should make a couple for Python 3.1 and 3.2 >> but clearly mark them as alpha quality? Perhaps a little branch >> on github just to change the version to 1.57a and edit the setup.py >> description? > > This is a good idea and could help us get a sense of if people are > using Python 3 yet. > >> Speaking of which, I found our first bug: I didn't add do2to3.py >> to the manifest, so it isn't included in the tar ball or zip. This >> means you can't install from a source release under Python 3. >> Not a big issue as we haven't claimed to support Python 3 yet: >> https://github.com/biopython/biopython/commit/4b1cc1e501a136188c41c1345c1d22ceb11cdb0c > > Whoops. Should we freshen up the tarballs with this or wait until > the next release? I'm tempted to leave it as is. Anyone keen to use Biopython from source under Python 3 can try from git. > For your manifest fix, we should add do2to3.py to the MANIFEST.in > instead of checking in the MANIFEST directly, since the MANIFEST is > generated during building the release. Good catch - that's what I meant to do, I guess I missed the extension in my git add command (over reliant on tab auto completion). Fixed now. Peter From bjclavijo at gmail.com Mon Apr 4 16:28:50 2011 From: bjclavijo at gmail.com (Bernardo Clavijo) Date: Mon, 4 Apr 2011 13:28:50 -0300 Subject: [Biopython-dev] DAS implementation Message-ID: Hello everyone, new subscriber here, hopefully lending a hand around from now on (Python fan working on bioinformatics, so this is the place). I've been searching for a DAS server/client but found none written in python. Since I'm writting some Chado+Gbrowse+tools web glue in python, don't want to attach a perl implementation or such. Have anyone some code for this? Maybe it's just that my googling skills aren't so good. If not, wouldn't it be nice to have such a module in biopython? I'm not the best developer in the world, but maybe I could code something that serves us all and then it could be included in biopython. Well, that all for now... hope to hear some answers, and if you think that impelmenting DAS would be a nice idea, I'm sure you could provide me with a hint in how I could design it (a module interacting with Seq? Is there some webserver capabilities, or just write functions and let the code ready to glue into a webserver?, etc). Greets bj From p.j.a.cock at googlemail.com Mon Apr 4 16:35:02 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 4 Apr 2011 17:35:02 +0100 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo wrote: > Hello everyone, new subscriber here, hopefully lending a hand around > from now on (Python fan working on bioinformatics, so this is the > place). > I've been searching for a DAS server/client but found none written in > python. Since I'm writting some Chado+Gbrowse+tools web glue in > python, don't want to attach a perl implementation or such. > Have anyone some code for this? Maybe it's just that my googling > skills aren't so good. If not, wouldn't it be nice to have such a > module in biopython? > I'm not the best developer in the world, but maybe I could code > something that serves us all and then it could be included in > biopython. > Well, that all for now... hope to hear some answers, and if you think > that impelmenting DAS would be a nice idea, I'm sure you could provide > me with a hint in how I could design it (a module interacting with > Seq? Is there some webserver capabilities, or just write functions and > let the code ready to glue into a webserver?, etc). > > Greets > > bj Hi Bernardo, Andrea Pierleoni started looking at a DAS client last year: http://github.com/apierleoni/biopython/tree/das-client http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html More eyes on this code would be good :) Peter From bjclavijo at gmail.com Mon Apr 4 16:44:41 2011 From: bjclavijo at gmail.com (Bernardo Clavijo) Date: Mon, 4 Apr 2011 13:44:41 -0300 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: On Mon, Apr 4, 2011 at 1:35 PM, Peter Cock wrote: > On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo wrote: >> Hello everyone, new subscriber here, hopefully lending a hand around >> from now on (Python fan working on bioinformatics, so this is the >> place). >> I've been searching for a DAS server/client but found none written in >> python. Since I'm writting some Chado+Gbrowse+tools web glue in >> python, don't want to attach a perl implementation or such. >> Have anyone some code for this? Maybe it's just that my googling >> skills aren't so good. If not, wouldn't it be nice to have such a >> module in biopython? >> I'm not the best developer in the world, but maybe I could code >> something that serves us all and then it could be included in >> biopython. >> Well, that all for now... hope to hear some answers, and if you think >> that impelmenting DAS would be a nice idea, I'm sure you could provide >> me with a hint in how I could design it (a module interacting with >> Seq? Is there some webserver capabilities, or just write functions and >> let the code ready to glue into a webserver?, etc). >> >> Greets >> >> bj > > Hi Bernardo, > > Andrea Pierleoni started looking at a DAS client last year: > http://github.com/apierleoni/biopython/tree/das-client > http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html > > More eyes on this code would be good :) > > Peter > Great! a starting point for the client part... i'll check it out that for a starting point, I see there are some "TODO" parts... i'll try to handle those. Anyone having something similar as for the server part? Greets bj From bpederse at gmail.com Mon Apr 4 19:31:51 2011 From: bpederse at gmail.com (Brent Pedersen) Date: Mon, 4 Apr 2011 13:31:51 -0600 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: On Mon, Apr 4, 2011 at 10:44 AM, Bernardo Clavijo wrote: > On Mon, Apr 4, 2011 at 1:35 PM, Peter Cock wrote: >> On Mon, Apr 4, 2011 at 5:28 PM, Bernardo Clavijo wrote: >>> Hello everyone, new subscriber here, hopefully lending a hand around >>> from now on (Python fan working on bioinformatics, so this is the >>> place). >>> I've been searching for a DAS server/client but found none written in >>> python. Since I'm writting some Chado+Gbrowse+tools web glue in >>> python, don't want to attach a perl implementation or such. >>> Have anyone some code for this? Maybe it's just that my googling >>> skills aren't so good. If not, wouldn't it be nice to have such a >>> module in biopython? >>> I'm not the best developer in the world, but maybe I could code >>> something that serves us all and then it could be included in >>> biopython. >>> Well, that all for now... hope to hear some answers, and if you think >>> that impelmenting DAS would be a nice idea, I'm sure you could provide >>> me with a hint in how I could design it (a module interacting with >>> Seq? Is there some webserver capabilities, or just write functions and >>> let the code ready to glue into a webserver?, etc). >>> >>> Greets >>> >>> bj >> >> Hi Bernardo, >> >> Andrea Pierleoni started looking at a DAS client last year: >> http://github.com/apierleoni/biopython/tree/das-client >> http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008047.html >> >> More eyes on this code would be good :) >> >> Peter >> > > Great! a starting point for the client part... i'll check it out that > for a starting point, I see there are some "TODO" parts... i'll try to > handle those. > Anyone having something similar as for the server part? > > Greets > > bj > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > if you fork this on github (and especially if you start the server stuff) and link back here, perhaps you'll get some help. i'd be very interested in server and client for biodas in biopython. -brentp From jblanca at upv.es Tue Apr 5 06:58:41 2011 From: jblanca at upv.es (Jose Blanca) Date: Tue, 05 Apr 2011 08:58:41 +0200 Subject: [Biopython-dev] DAS implementation In-Reply-To: References: Message-ID: <4D9ABDA1.7090505@btc.upv.es> El 04/04/11 18:28, Bernardo Clavijo escribi?: > Hello everyone, new subscriber here, hopefully lending a hand around > from now on (Python fan working on bioinformatics, so this is the > place). > I've been searching for a DAS server/client but found none written in > python. Since I'm writting some Chado+Gbrowse+tools web glue in > python, don't want to attach a perl implementation or such. Hi: I've no idea about the DAS server, but I'm very interested in the Chado stuff. We're building a django application to browse a Chado database. It is still not completely ready, but you can take a look at: http://bioinf.comav.upv.es/git//?p=gene_web.git;a=summary We were thinking about showing this code in the Chado mailing list once completed in case anyone could be interested in using it and improving it. But here it is. If anyone could be interested, it is free software, we like AGPL, but we're open about other free software licences. Regards, Jose Blanca > Have anyone some code for this? Maybe it's just that my googling > skills aren't so good. If not, wouldn't it be nice to have such a > module in biopython? > I'm not the best developer in the world, but maybe I could code > something that serves us all and then it could be included in > biopython. > Well, that all for now... hope to hear some answers, and if you think > that impelmenting DAS would be a nice idea, I'm sure you could provide > me with a hint in how I could design it (a module interacting with > Seq? Is there some webserver capabilities, or just write functions and > let the code ready to glue into a webserver?, etc). > > Greets > > bj > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > -- Jose M. Blanca Postigo Instituto Universitario de Conservacion y Mejora de la Agrodiversidad Valenciana (COMAV) Universidad Politecnica de Valencia (UPV) Edificio CPI (Ciudad Politecnica de la Innovacion), 8E 46022 Valencia (SPAIN) Tlf.:+34-96-3877000 (ext 88473) From anaryin at gmail.com Tue Apr 5 15:50:34 2011 From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=) Date: Tue, 5 Apr 2011 17:50:34 +0200 Subject: [Biopython-dev] New functions in Bio.PDB: renumber_residues(), remove_disordered_atoms() In-Reply-To: References: Message-ID: Hey Eric, Let me write the Tests Kristian proposed. I haven't had time to do it yet and those are quite important :) I'll update the branch with the current version, correct some bugs that might show up with the merging, write the tests, clean the history, and let you know. I think merging should be good, but cherry-picking is safer I guess! Cheers, J From andrea at biocomp.unibo.it Tue Apr 5 16:08:21 2011 From: andrea at biocomp.unibo.it (Andrea Pierleoni) Date: Tue, 5 Apr 2011 18:08:21 +0200 (CEST) Subject: [Biopython-dev] DAS implementation (Bernardo Clavijo) In-Reply-To: References: Message-ID: <3b5245fb50ceea358894429e89dc1464.squirrel@lipid.biocomp.unibo.it> Bernardo if you want I can grant you access to the DAS repository in my github profile. so we can work on the same version. Regarding the DAS server implementation, how could this be included in Biopython? A DAS server will require a webserver. Andrea From bjclavijo at gmail.com Tue Apr 5 18:28:42 2011 From: bjclavijo at gmail.com (Bernardo Clavijo) Date: Tue, 5 Apr 2011 15:28:42 -0300 Subject: [Biopython-dev] DAS implementation (Bernardo Clavijo) In-Reply-To: <3b5245fb50ceea358894429e89dc1464.squirrel@lipid.biocomp.unibo.it> References: <3b5245fb50ceea358894429e89dc1464.squirrel@lipid.biocomp.unibo.it> Message-ID: That would be great (the client access) i'll send you a private mail later. As for the server, I'll try to create a class that handles all the back functions (generating the responses from the Bio.Seq module, for example, maybe it's not the best design). As for the web server, we could just let it open for anyone to glue it on (it's just a matter of passing the requests), or use one of the simple http modules already in python (I didn't know if some module is already used in another point in biopython). Greets bj On Tue, Apr 5, 2011 at 1:08 PM, Andrea Pierleoni wrote: > Bernardo if you want I can grant you access to the DAS repository in my > github profile. so we can work on the same version. > Regarding the DAS server implementation, how could this be included in > Biopython? > A DAS server will require a webserver. > > Andrea > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > From redmine at redmine.open-bio.org Wed Apr 6 23:26:08 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 6 Apr 2011 23:26:08 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] (New) SeqIO parse error with some genbank files Message-ID: Issue #3197 has been reported by Cedar McKay. ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Category: Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 6 23:42:54 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 6 Apr 2011 23:42:54 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Peter Cock. Assignee set to Biopython Dev Mailing List ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 7 01:01:11 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 7 Apr 2011 01:01:11 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Cedar McKay. I did a little more poking, and it really seems like a common mistake. I'm working with this file: ftp://ftp.ncbi.nih.gov/refseq/release/plastid/plastid1.genomic.gbff.gz which is a file containing all plastid genomes in genbank. It has 208 records, and of those, 124 have an illegal location containing the string 'order(join(' One thing that I noticed is that all but two examples of 'order(join(' that appear across those 124 records are describing the location of a ycf3 feature! Strange! I'll send them an email about it, but I'm not really sure what is going on. I followed your suggestion for my test file, and changed the the location of that misc_feature. It got hung up on yet another ycf3 gene: 
     misc_feature    complement(order(42643..42645,42652..42654,42664..42666,
                     43470..43472,43515..43517,43524..43526,43536..43538,
                     43572..43574,43626..43628,43635..43637,43647..43649,
                     join(43683..43684,44430)))
                     /gene="ycf3"
I got rid of the join there too, and finally it could be parsed. Thanks for looking at this, I don't quite know what to make of it yet, or how to deal with it. ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 7 09:59:54 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 7 Apr 2011 09:59:54 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Peter Cock. File __init__.py added Hi Cedar, I do think these are invalid GenBank files, but as a short term hack you could try this modified version of the code - install Biopython 1.57 and replace the Bio/GenBank/__init__.py file. You could comment out the warning if you like ;) This basically automates the removal of the join from the illegal locations, which seems to me to be the best way to salvage the location. I can then parse plastid1.genomic.gbff fine. I don't want to commit a fix unless the NCBI tell us these are valid location, and/or a more elegant fix can be implemented. This current hack will probably slow down general GenBank parsing. Peter ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From chapmanb at 50mail.com Thu Apr 7 14:52:31 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 7 Apr 2011 10:52:31 -0400 Subject: [Biopython-dev] Propsal Draft - Timeline. In-Reply-To: References: Message-ID: <20110407145231.GA20963@sobchak> Maximiliano and Reece; Great to see that the proposal is coming along. I'm cc'ing the developers mailing lists in case others have thoughts as well. I'll start by echoing some of Reece's comments: > - An overview -- without this, it's hard for readers to know how well you > understand the context or why the issue is relevant at all. ~5 sentences > should suffice. Please take a stab at it and I'll help. Yes, definitely. This is an application not to Reece, who knows about the project, but to the general developer community. You need to justify why this project is important and what you hope to accomplish. Generally you need to argue for why Google should fund this project over other equally deserving projects. > - Consider adding a short "about me" section. The reviewers will need detailed information about your background to assess your ability to be successful. You should add work you've done previously, especially related to Python. Ideally you will have links to some open source work you've done so reviewers can assess your programming experience. > I'm also cc'ing Brad who may have more input. The proposal timeline needs to be much more detailed. What it should look like is a week by week breakdown of what you hope to accomplish. This will be used by you and your mentors to help track progress and stay on track. These are the weekly milestones you mention in your proposal. Some specific suggestions: - All non-coding tasks (setting up version control) should be put in your timeline prior to the start of the coding period. - Your weekly goals need to be very specific. For instance 'Design the library API' does not tell a reviewer any details about what you hope to accomplish. You should have a general idea of what you plan to design now, and then be listing these in your plan. Hope this helps with getting everything finalized before tomorrow, Brad > > *Abstract:* > > *I am still working on it.* > > > > *Proposal Timeline:* > > > > *Before April 25:* > > > > - To familiarize myself with BioPython. > > - Experiment with PLY (Python Lex-Yacc) and Pyparsing. > > - Review some basic biology concepts: genomes, transcripts, proteins, > > genomic variation, and others suggested by my mentor. > > - To familiarize myself with HGVS nomenclature, and experiment using > > Mutalyzer 2.0 > > > > > > *April 27 - May 24 (Before the official coding time):* > > > > - Define the subset of the HGVS to be represented. > > - Identify variation types to be represented (SNV, CNV, repeats, > > inversions, etc). > > - Design a formal grammar that fully represents the subset of the HGVS > > chosen before. > > - Define a set of semantic validations for the represented variations. > > - Write a short document explaining how to properly extend the formal > > grammar defined before. > > > > > > *May 25 - July 12 (Official coding period starts):* > > > > - Set up a control version system and a bug tracker. > > - Define weekly milestones. > > - Design the library API. > > - Develop an abstract variant class and subclasses representing > > specific cases of them. > > - Design and implement a parser for the formal grammar defined before. > > - Test the code written up to now. > > > > > > *July 15: Midterm evaluation* > > > > *July 17 ? August 16:* > > > > - Work on semantic validations defined before. > > - Full testing of the whole library. > > - Integration of the library to BioPython. > > - Documentation of the whole library. > > - Implementation of a syntax checker as an example of the use of the > > library. Make it freely availably on the Internet. From redmine at redmine.open-bio.org Thu Apr 7 17:39:06 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 7 Apr 2011 17:39:06 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Cedar McKay. Peter, thanks as always for your quick and helpful response! I've emailed NCBI about these apparently illegal files, and I'll update this bug when I get a reply. In the meantime, I'm going to go ahead and use your hacked up version. Thanks! ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From chapmanb at 50mail.com Fri Apr 8 10:45:41 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 8 Apr 2011 06:45:41 -0400 Subject: [Biopython-dev] Proposal: almost finished. In-Reply-To: References: Message-ID: <20110408104541.GJ20963@sobchak> Maxi; (cc'ing the Biopython mailing list for suggestions) Thanks for this; it's looking really good. Some last minute thoughts: - The About Me section needs a link to code you've written. I couldn't find anything substantial i nthe Pep8fy or Cdpedia projects, so if you've contributed something large there please highlight it. Otherwise you should upload some code to bitbucket to demonstrate work you've done. This will be the first thing evaluators look at. - You should renumber your weeks so week 1 is the start of the coding period; you should keep the prep weeks as that is really useful information, but just mark them generally as the community bonding period. - When the coding period starts you should start, well, coding. So the specification/design work you have in weeks 5 and 6 should be moved to the community bonding/prep period, and code writing should begin on May 23rd. - You mention unit testing, but should go into specifics about what you plan to test. This demonstrates that you've thought about potential issues and how to avoid them. - The purpose of GSoC is open source code and integration with existing projects. So some of the late items (week 14/Make it freely available on the internet; week 17/integration of the library to Biopython) should be happening from week 1. The code should be freely available in an open source repository the entire time, and you should be talking with the Biopython community throughout. I'd suggest emphasizing those points in your text, and adding in work/tests/documentation for those weeks. Don't forget that this needs to be submitted to the GSoC website by the deadline: http://www.google-melange.com/gsoc/homepage/google/gsoc2011 Google can only evaluate proposals that are entered there. Thanks again for the work getting this together, Brad > Reece, Brad: > > I attach my proposal (odt and pdf versions). I have been working all the > evening. It is late here, so I am going to bed now. Tomorrow I will get up > early, read it one more time, read if you made any recommendation, and send > the proposal! :) > I think I can add more in "Design aspects" and "Implementation". > > Reece: I gave more importance to testing, adding weekly unit test, and 2 > instances of system test. I usually work with test driven development in my > university, so we can implement that if you want. > > Brad: I will try to extend a bit more about API design. > > Recommandations are welcomed > Thanks for your help! > > -- > Maxi. -------------- next part -------------- A non-text attachment was scrubbed... Name: Proposal Application.pdf Type: application/pdf Size: 110725 bytes Desc: not available URL: From updates at feedmyinbox.com Mon Apr 11 04:42:29 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Mon, 11 Apr 2011 00:42:29 -0400 Subject: [Biopython-dev] 4/11 active questions tagged biopython - Stack Overflow Message-ID: <4c9304139061a653fdbf5fa9899671bf@74.63.51.88> // Script for parsing a biological sequence from a public database in Python // April 10, 2011 at 3:33 PM http://stackoverflow.com/questions/5614180/script-for-parsing-a-biological-sequence-from-a-public-database-in-python Greetings to the stackoverflow community, I am currently following a bioinformatics module as part of a biomedical degree (I am basically a python newbie) and the following task is required as part of a Python programming assignment: extract motif sequences (amino acid sequences, so basically strings in programmatic-speak, that have been excised from algorithms implementing a multiple sequence alignment and subsequently iterative database scanning to generate the best conserved sequences. The ultimate idea is to infer functional significance from such "motifs"). These motifs are stored on a public database in files which have multiple data fields corresponding to each protein (uniprot ID, Accession Number, the alignment itself stored in a hyperlink .seq file), currently one of which is of interest in this scope. The data field is called "extracted motif sets". My question is how to go about writing a script that will essentially parse the "motif strings" and output them to a file. Very crudely, I believe the pseudocode would run something along these lines: motif_file = open("lysozyme.seq") # database files are saved as .seq for "extracted motif sets" in motif_file # motif extracting code goes here motif_file.close() There are well over a couple hundred .seq files, so I imagine a looping technique would be needed to scan a good part of the database. The excised motifs are on a file separated from the .seq by a hyperlink, but are of course subsequences of each of the entries in the Mult. Seq. Alignment files (.seq). Is there a way to effectively pick up the motif sequences (strings) from one file and do some mining on the alignment files to detect the same sequence? I apologize for the extensive text, I just hope to be a clear as possible. Thanks in advance for any help! -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From clementsgalaxy at gmail.com Mon Apr 11 15:57:48 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Mon, 11 Apr 2011 08:57:48 -0700 Subject: [Biopython-dev] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands In-Reply-To: References: Message-ID: Hello all, This is a reminder that early registration for the 2011 Galaxy Community Conference ends in less than two weeks. You can save 20% if you register on or before 24 April. http://galaxy.psu.edu/gcc2011/Register.html We've also added a partial list of confirmed speakers. More will be added in the coming weeks as the schedule firms up. http://galaxy.psu.edu/gcc2011/Programme.html Please let me know if you have any questions, and hope to see you in May, Dave C. On Thu, Feb 3, 2011 at 5:01 PM, Dave Clements wrote: > We are pleased to announce the *2011 Galaxy Community Conference*, being > held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature > two full days of presentations and discussion on extending Galaxy to use new > tools and data sources, deploying Galaxy at your organization, and best > practices for using Galaxy to further your own and your community's > research. See http://galaxy.psu.edu/gcc2011/* for complete details. > * > *About Galaxy: > *Galaxy is an open, web-based platform for *accessible, reproducible, and > transparent* computational biomedical research. > > - *Accessibility:* Galaxy enables users without programming experience > to easily specify parameters and run tools and workflows. > - *Reproducibility:* Galaxy captures all information necessary so that > any user can repeat and understand a complete computational analysis. > - *Transparency:* Galaxy enables users to share and publish analyses > via the web and create Pages--interactive, web-based documents that describe > a complete analysis. > > Galaxy is open source for all organizations. The public Galaxy service ( > http://usegalaxy.org) makes analysis tools, genomic data, > tutorial demonstrations, persistent workspaces, and publication services > available to any scientist that has access to the Internet. Local > Galaxy servers can be set up by downloading the Galaxy application and > customizing it to meet particular needs. > > *Conference Overview: > * > This event aims to engage a broader community of developers, data > producers, tool creators, and core facility and other research hub staff to > become an active part of the Galaxy community. We'll cover defining > resources in the Galaxy framework, increasing their visibility and making > them easier to use and integrate with other resources, how to extend Galaxy > to use custom data sources and custom tools, and best practices for using > Galaxy in your organization. > > Additional topics include, but are not limited to: > * Talks submitted by the Galaxy community > * Integration of tools (including NGS analysis tools) and distributed job > management > * Deployment of Galaxy instances on local resources and on the Cloud > * Management of large datasets with the Galaxy Library System > * Using the Galaxy LIMS functionality at NGS sequencing facilities > * Visualizing Data without leaving Galaxy > * Performing reproducible research > * Performing and sharing complex analyses with Workflows > * An "Introduction to Galaxy" session, offered on May 24, for Galaxy > newcomers. > > *Registration: > * > The conference fee is ?100 on or before April 24, and ?120 after that. The > meeting is being held at the Conference Centre De Werelt in Lunteren, The > Netherlands, which is also the conference hotel. You are encouraged to > register early, as space at the hotel (and at the "Intro to Galaxy" session) > is limited and is likely to fill up before the conference itself does. See > http://galaxy.psu.edu/gcc2011/Register.html > * > Abstract Submission: > * > Abstracts are now being accepted for short oral presentations. Proposals > on any topic of interest to the Galaxy community are welcome and > encouraged. The abstract submission deadline is the end of February 28. > See http://galaxy.psu.edu/gcc2011/Abstracts.html > * * > *Sponsors > * > The 2011 Galaxy Community Conference is co-sponsored by the US National > Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands > Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a > collaborative institute of the bioinformatics groups in the Netherlands. > Together, these groups perform cutting-edge research, develop novel tools > and support platforms, create an e-science infrastructure and educate the > next generations of bioinformaticians. > > We are looking forward to a great conference and hope to see you in the > Netherlands! > > The Galaxy and NBIC Teams > > -- > http://galaxy.psu.edu/gcc2011/ > http://getgalaxy.org > http://usegalaxy.org/ > -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From md.bustos90 at gmail.com Wed Apr 13 02:55:39 2011 From: md.bustos90 at gmail.com (Maximiliano David Bustos) Date: Tue, 12 Apr 2011 23:55:39 -0300 Subject: [Biopython-dev] Google Summer of Code Proposal Message-ID: Hello everybody, My name is Maximiliano David Bustos, I am a Computer Science student from La Rioja, Argentina. I joined the list some days ago to start collaborating with BioPython project and to get feedback in Google Summer of Code (GSoC). The proposal I submitted to GSoC is titled *"Variant representation, parser, generator, and coordinate converter"*. This idea was taken from BioPython wiki. The project mentor is Reece Hart, who had been helping me a lot in the elaboration of my proposal. Brad Chapman made great contributions too. Reece recommended me to send my proposal to the mailing list. I would really appreciate any feedback from you. Thanks in advance, Maxi. From p.j.a.cock at googlemail.com Wed Apr 13 09:16:42 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 13 Apr 2011 10:16:42 +0100 Subject: [Biopython-dev] Google Summer of Code Proposal In-Reply-To: References: Message-ID: On Wed, Apr 13, 2011 at 3:55 AM, Maximiliano David Bustos wrote: > Hello everybody, > > My name is Maximiliano David Bustos, I am a Computer Science student from La > Rioja, Argentina. I joined the list some days ago to start collaborating > with BioPython project and to get feedback in Google Summer of Code (GSoC). > The proposal I submitted to GSoC is titled *"Variant representation, parser, > generator, and coordinate > converter"*. > This idea was taken from BioPython wiki. > The project mentor is Reece Hart, who had been helping me a lot in the > elaboration of my proposal. Brad Chapman made great contributions too. > > Reece recommended me to send my proposal to the mailing list. I would really > appreciate any feedback from you. > > Thanks in advance, > > Maxi. Hi Maxi, Just a couple of quick initial thoughts on the implementation section, >> Implementation >> >> I will implement the library in Python 2.7, using PLY (Python Lex-Yacc) >> or Pyparsing. I will follow BioPython coding conventions and abstractions >> so the project can be integrated from the beginning. Currently Biopython supports Python 2.5 to 2.7 (and we're working on Python 3). If you target Python 2.7 specific features it would be a problem for integrating your work into Biopython. You would ideally also run and test your code on Python 2.5, and on Python 3. On the bright side, PLY (Python Lex-Yacc) and Pyparsing are pure python and *should* work cross platform (we do want to support Windows). On the other hand, if we can do without them and use the standard Python library only, I'd be happier as it will keep our dependencies down. This is important for making Biopython easy to install and use. In this case they are run time dependencies so it isn't critical. Peter From md.bustos90 at gmail.com Thu Apr 14 16:59:52 2011 From: md.bustos90 at gmail.com (Maximiliano David Bustos) Date: Thu, 14 Apr 2011 13:59:52 -0300 Subject: [Biopython-dev] Google Summer of Code Proposal In-Reply-To: References: Message-ID: Peter, Thanks for your feedback. I will consider this compatibility issues when implementing. Maxi. On Wed, Apr 13, 2011 at 6:16 AM, Peter Cock wrote: > On Wed, Apr 13, 2011 at 3:55 AM, Maximiliano David Bustos > wrote: > > Hello everybody, > > > > My name is Maximiliano David Bustos, I am a Computer Science student from > La > > Rioja, Argentina. I joined the list some days ago to start collaborating > > with BioPython project and to get feedback in Google Summer of Code > (GSoC). > > The proposal I submitted to GSoC is titled *"Variant representation, > parser, > > generator, and coordinate > > converter"*< > https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B1Q10jdy75U_YzE4ZmUzMGEtNjA5Ni00Mjc4LTgwYTQtZTI1MTdkNTJiODc4&hl=en&authkey=CN_Dm8ML > >. > > This idea was taken from BioPython wiki. > > The project mentor is Reece Hart, who had been helping me a lot in the > > elaboration of my proposal. Brad Chapman made great contributions too. > > > > Reece recommended me to send my proposal to the mailing list. I would > really > > appreciate any feedback from you. > > > > Thanks in advance, > > > > Maxi. > > Hi Maxi, > > Just a couple of quick initial thoughts on the implementation section, > > >> Implementation > >> > >> I will implement the library in Python 2.7, using PLY (Python Lex-Yacc) > >> or Pyparsing. I will follow BioPython coding conventions and > abstractions > >> so the project can be integrated from the beginning. > > Currently Biopython supports Python 2.5 to 2.7 (and we're working on Python > 3). > If you target Python 2.7 specific features it would be a problem for > integrating > your work into Biopython. You would ideally also run and test your code on > Python 2.5, and on Python 3. > > On the bright side, PLY (Python Lex-Yacc) and Pyparsing are pure python > and *should* work cross platform (we do want to support Windows). On > the other hand, if we can do without them and use the standard Python > library only, I'd be happier as it will keep our dependencies down. This is > important for making Biopython easy to install and use. In this case they > are run time dependencies so it isn't critical. > > Peter > From updates at feedmyinbox.com Sun Apr 17 04:38:16 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Sun, 17 Apr 2011 00:38:16 -0400 Subject: [Biopython-dev] 4/17 active questions tagged biopython - Stack Overflow Message-ID: <0ed8a84c3c0ad762f3f583f6db924c52@74.63.51.88> // Are there any function that can calculate score for the aligned sequences give parameters? // April 16, 2011 at 7:39 AM http://stackoverflow.com/questions/5686211/are-there-any-function-that-can-calculate-score-for-the-aligned-sequences-give-pa I try to score the already-aligned sequences. Let say seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE' seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE' with given parameters substitution matrix : blogsum62 gap open penalty : -5 gap extension penalty : -1 I did look through the biopython cookbook but all i can get is substitution matrix blogsum62 but I feel that it must have someone already implemented this kind of library. So can anyone suggest any libraries or shortest code that can solve my problem? Thx in advance -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From p.j.a.cock at googlemail.com Sun Apr 17 11:01:58 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sun, 17 Apr 2011 12:01:58 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? Message-ID: Hi all, I realise the BOSC abstract deadline is now tomorrow (!) http://www.open-bio.org/wiki/BOSC_2011 I think it may be just me and Brad going - and we could certainly put together something... Who else is planning to attend BOSC 2011 in Vienna, and would you like to be involved? Peter From tiagoantao at gmail.com Sun Apr 17 15:51:33 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Sun, 17 Apr 2011 16:51:33 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: References: Message-ID: I might go the codefest. It all depends if my PhD is done or not and if I have to go nearby (I might visit south .CH, and thus it would be just a small deviation). If going to the codefest, I would maybe like suggesting spending sometime with infrastructure hardening (like cleaning up the integration testing script, discussing and making changes to the wiki - whatever things people think is important to "robustify"). But for now I am still "hibernating". Tiago On Sun, Apr 17, 2011 at 12:01 PM, Peter Cock wrote: > Hi all, > > I realise the BOSC abstract deadline is now tomorrow (!) > http://www.open-bio.org/wiki/BOSC_2011 > > I think it may be just me and Brad going - and we could > certainly put together something... Who else is planning > to attend BOSC 2011 in Vienna, and would you like to > be involved? > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From chapmanb at 50mail.com Sun Apr 17 16:03:27 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Sun, 17 Apr 2011 12:03:27 -0400 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: References: Message-ID: <20110417160327.GB2401@kunkel> Peter and Tiago; > > I realise the BOSC abstract deadline is now tomorrow (!) > > http://www.open-bio.org/wiki/BOSC_2011 > > > > I think it may be just me and Brad going - and we could > > certainly put together something... Who else is planning > > to attend BOSC 2011 in Vienna, and would you like to > > be involved? It would be great if you wanted to do a Biopython talk. BOSC was trying to deviate a bit from the project update format, but anything you are working on with respect to Biopython or new features added would be perfect. Personally, I'd be interested in hearing about the NGS work you are doing with Biopython and Galaxy. Democratizing analysis methods to allow biologists access is always a challenge, and I'd love to hear about how you've been approaching this. > I might go the codefest. It all depends if my PhD is done or not and > if I have to go nearby (I might visit south .CH, and thus it would be > just a small deviation). Tiago, good luck finishing up the degree. Hope you are done by the summer can make it out to Codefest, Brad From updates at feedmyinbox.com Mon Apr 18 04:38:18 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Mon, 18 Apr 2011 00:38:18 -0400 Subject: [Biopython-dev] 4/18 active questions tagged biopython - Stack Overflow Message-ID: // Are there any function that can calculate score for the aligned sequences give parameters? // April 16, 2011 at 7:39 AM http://stackoverflow.com/questions/5686211/are-there-any-function-that-can-calculate-score-for-the-aligned-sequences-give-pa I try to score the already-aligned sequences. Let say seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE' seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE' with given parameters substitution matrix : blogsum62 gap open penalty : -5 gap extension penalty : -1 I did look through the biopython cookbook but all i can get is substitution matrix blogsum62 but I feel that it must have someone already implemented this kind of library. So can anyone suggest any libraries or shortest code that can solve my problem? Thx in advance -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From p.j.a.cock at googlemail.com Mon Apr 18 09:03:01 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 18 Apr 2011 10:03:01 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: <20110417160327.GB2401@kunkel> References: <20110417160327.GB2401@kunkel> Message-ID: 2011/4/17 Brad Chapman : > Peter and Tiago; > >> > I realise the BOSC abstract deadline is now tomorrow (!) >> > http://www.open-bio.org/wiki/BOSC_2011 >> > >> > I think it may be just me and Brad going - and we could >> > certainly put together something... Who else is planning >> > to attend BOSC 2011 in Vienna, and would you like to >> > be involved? > > It would be great if you wanted to do a Biopython talk. BOSC was > trying to deviate a bit from the project update format, but anything > you are working on with respect to Biopython or new features added > would be perfect. One idea would be to go over the Bio.SeqIO.index_db(...) code and how this SQLite3 backend could be the basis of a new Bio* OBF version of OBDA (to supplement the existing flat file and BDB specifications). > Personally, I'd be interested in hearing about the > NGS work you are doing with Biopython and Galaxy. Democratizing > analysis methods to allow biologists access is always a challenge, > and I'd love to hear about how you've been approaching this. I'll be talking after BOSC during ISMB proper about some of my Galaxy work, but it isn't NGS focused - see Workshop 6 "Genomics for Non-Model Organisms" being organised by James Taylor and Anton Nekrutenko from Galaxy: http://www.iscb.org/ismbeccb2011-program/workshops#w6 In terms of Galaxy and NGS, I've finding my sequence file filtering tool very handy (FASTA, FASTQ and SFF) for a number of workflows including removing read contamination, mapped reads etc. This is on the Galaxy toolshed and uses Biopython (for SFF filtering): http://community.g2.bx.psu.edu/ >> I might go the codefest. It all depends if my PhD is done or not and >> if I have to go nearby (I might visit south .CH, and thus it would be >> just a small deviation). > > Tiago, good luck finishing up the degree. Hope you are done by the > summer can make it out to Codefest, +1 Peter From p.j.a.cock at googlemail.com Mon Apr 18 17:58:26 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 18 Apr 2011 18:58:26 +0100 Subject: [Biopython-dev] Biopython project update at BOSC 2011? In-Reply-To: References: <20110417160327.GB2401@kunkel> Message-ID: 2011/4/18 Peter Cock : > 2011/4/17 Brad Chapman : >> Peter and Tiago; >> >>> > I realise the BOSC abstract deadline is now tomorrow (!) >>> > http://www.open-bio.org/wiki/BOSC_2011 >>> > >>> > I think it may be just me and Brad going - and we could >>> > certainly put together something... Who else is planning >>> > to attend BOSC 2011 in Vienna, and would you like to >>> > be involved? >> >> It would be great if you wanted to do a Biopython talk. BOSC was >> trying to deviate a bit from the project update format, but anything >> you are working on with respect to Biopython or new features added >> would be perfect. > > One idea would be to go over the Bio.SeqIO.index_db(...) code > and how this SQLite3 backend could be the basis of a new Bio* > OBF version of OBDA (to supplement the existing flat file and > BDB specifications). > >> Personally, I'd be interested in hearing about the >> NGS work you are doing with Biopython and Galaxy. Democratizing >> analysis methods to allow biologists access is always a challenge, >> and I'd love to hear about how you've been approaching this. > > I'll be talking after BOSC during ISMB proper about some of > my Galaxy work, but it isn't NGS focused - see Workshop 6 > "Genomics for Non-Model Organisms" being organised by James > Taylor and Anton Nekrutenko from Galaxy: > http://www.iscb.org/ismbeccb2011-program/workshops#w6 > > In terms of Galaxy and NGS, I've finding my sequence file filtering > tool very handy (FASTA, FASTQ and SFF) for a number of workflows > including removing read contamination, mapped reads etc. This is > on the Galaxy toolshed and uses Biopython (for SFF filtering): > http://community.g2.bx.psu.edu/ > >>> I might go the codefest. It all depends if my PhD is done or not and >>> if I have to go nearby (I might visit south .CH, and thus it would be >>> just a small deviation). >> >> Tiago, good luck finishing up the degree. Hope you are done by the >> summer can make it out to Codefest, > > +1 > > Peter > I've uploaded an initial abstract (which I can still change until the deadline later tonight), if there are suggestions for improvements: In this talk we present the current status of the Biopython project (www.biopython.org), described in a application (Cock et al., 2009). Since BOSC 2010, we have made three releases. Touching on key functionality, Biopython 1.55 (August 2010) made our command line tool wrappers easier to use, Biopython 1.56 (November 2010) added a UniProt XML parser, and Biopython 1.57 (April 2011) added an SQLite based indexer for sequence flat files. All releases have seen more unit tests, more documentation, and more new contributors. In summer 2010 we had one Google Summer of Code (GSoC) project student, Joao Rodrigues working on protein structure (PDB) code for Biopython. Some of Joao?s work has already been included in Biopython releases, and he and his mentor Eric Talevich (himself a GSoC 2009 student) are working to merge the rest of this work. Additionally they hope to co-mentor a GSoC student this summer. For the last six months, we have been running a BuildBot server (see http://buildbot.net/), with the offline parts of the Biopython unit test suite scheduled every night on build slaves running on Linux, Windows and Mac OS X, and both ?C? Python and Jython (using the Java virtual machine). This has been beneficial in catching platform specific regressions, for example under Python 3 which we are still working towards fully supporting. The BuildBot server is running on an OBF maintained Amazon cloud server, while the slaves are initially all machines maintained by individual Biopython developers. Biopython is free open source software available from www.biopython.org under the Biopython License Agreement (an MIT style license, http://www.biopython.org/DIST/LICENSE). Peter From redmine at redmine.open-bio.org Wed Apr 20 00:37:36 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 00:37:36 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Cedar McKay. I got a response from NCBI, and those files were, in fact, defective. Their text below: 
Dear Cedar Mckay,
Thank you for reporting this. The developer staff have traced through the
problem and identified a solution for future FTP releases.

You can download the record from the NCBI web site in the meantime; however,
note that this problem feature is not included in that download. 

Apologies for the inconvenience and thanks again for reporting it.

Kim Pruitt
---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 03:06:21 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 03:06:21 +0000 Subject: [Biopython-dev] [Biopython - Bug #3211] (New) Enhancement for Tm calculation Message-ID: Issue #3211 has been reported by ogan abaan. ---------------------------------------- Bug #3211: Enhancement for Tm calculation https://redmine.open-bio.org/issues/3211 Author: ogan abaan Status: New Priority: Normal Assignee: Category: Target version: URL: I have created this Tm function with NN thermodynamics corrected for dna, Monovalent ions, Mg, dNTP, DMSO concentrations as published in the literature. Please feel free to provide your feedback. This function might be useful in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 08:00:31 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 08:00:31 +0000 Subject: [Biopython-dev] [Biopython - Bug #3197] (Resolved) SeqIO parse error with some genbank files References: Message-ID: Issue #3197 has been updated by Peter Cock. Status changed from New to Resolved % Done changed from 0 to 100 Thanks Cedar :) I think we can close this now - there will be a more helpful error in the next Biopython release, https://github.com/biopython/biopython/commit/cb270ea74e9ccb4ae6889dfb7570010d9bcbdb8a Peter ---------------------------------------- Bug #3197: SeqIO parse error with some genbank files https://redmine.open-bio.org/issues/3197 Author: Cedar McKay Status: Resolved Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: 1.56 URL: I've found a file that seems to choke SeqIO genbank parsing. I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location? Please let me know if I can provide any other information! Thanks! Cedar >>> from Bio import SeqIO >>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank') Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read first = iterator.next() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse for r in i: File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records record = self.parse(handle, do_features) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse if self.feed(handle, consumer, do_features): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed self._feed_feature_table(consumer, self.parse_features(skip=False)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table consumer.location(location_string) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location raise LocationParserError(location_line) Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 15:05:16 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 15:05:16 +0000 Subject: [Biopython-dev] [Biopython - Bug #3212] (New) Enhancement for Bio.SeqUtils.MeltingTemp Message-ID: Issue #3212 has been reported by ogan abaan. ---------------------------------------- Bug #3212: Enhancement for Bio.SeqUtils.MeltingTemp https://redmine.open-bio.org/issues/3212 Author: ogan abaan Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: URL: Sorry, this is a repost. This was my first post and I realized that I left may things out. I couldn't update it or delete it sorry. Peter suggested that I post this here so you all can comment. I have created this Tm function with NN thermodynamics corrected for dna, Monovalent ions, Mg, dNTP, DMSO concentrations as published in the literature. Please feel free to provide your feedback. This function might be useful in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Wed Apr 20 15:05:17 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Wed, 20 Apr 2011 15:05:17 +0000 Subject: [Biopython-dev] [Biopython - Bug #3212] (New) Enhancement for Bio.SeqUtils.MeltingTemp Message-ID: Issue #3212 has been reported by ogan abaan. ---------------------------------------- Bug #3212: Enhancement for Bio.SeqUtils.MeltingTemp https://redmine.open-bio.org/issues/3212 Author: ogan abaan Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: URL: Sorry, this is a repost. This was my first post and I realized that I left may things out. I couldn't update it or delete it sorry. Peter suggested that I post this here so you all can comment. I have created this Tm function with NN thermodynamics corrected for dna, Monovalent ions, Mg, dNTP, DMSO concentrations as published in the literature. Please feel free to provide your feedback. This function might be useful in Biopython. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From p.j.a.cock at googlemail.com Wed Apr 20 17:08:46 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 20 Apr 2011 18:08:46 +0100 Subject: [Biopython-dev] Interesting BLAST 2.2.25+ XML behaviour Message-ID: Hi all, Have a look at this XML file from a FASTA vs FASTA search using blastp from BLAST 2.2.25+ (current release), which is a test file I created for the BLAST+ wrappers in Galaxy: https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml I just put it though the Biopython BLAST XML parser, and was surprised not to get four records back (since as you might guess from the filename, there were four queries). It appears this version of BLAST+ is incrementing the iteration counter for each match... or something like that. Has anyone else noticed this? I wonder if it is accidental... Peter From updates at feedmyinbox.com Fri Apr 22 04:38:36 2011 From: updates at feedmyinbox.com (Feed My Inbox) Date: Fri, 22 Apr 2011 00:38:36 -0400 Subject: [Biopython-dev] 4/22 active questions tagged biopython - Stack Overflow Message-ID: <8eaed29e41b889fff3193bf1aff57ba1@74.63.51.88> // Problem with GFF parser by BCBio // April 21, 2011 at 5:50 AM http://stackoverflow.com/questions/5742379/problem-with-gff-parser-by-bcbio Hi, I am trying to parse a GFF file using the BCBio GFF parser and I get the following error. Can anybody help me in resolving this problem? Traceback (most recent call last): File "gff_parse.py", line 6, in for rec in GFF.parse(in_handle): File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 709, in parse File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 299, in parse_in_parts File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 320, in parse_simple File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 603, in _gff_process File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 634, in _lines_to_out_info File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 183, in _gff_line_map ValueError: invalid literal for int() with base 10: 'New Start' Here is my code: from BCBio import GFF in_file = "infile.gff" in_handle = open(in_file) for rec in GFF.parse(in_handle): print rec in_handle.close() Thanks Tulika -- Website: http://stackoverflow.com/questions/tagged/?tagnames=biopython&sort=active Account Login: https://www.feedmyinbox.com/members/login/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/630208/9a33fac9c8e89861715f609a2333362c8425e495/?utm_source=fmi&utm_medium=email&utm_campaign=feed-email -- This email was carefully delivered by FeedMyInbox.com. PO Box 682532 Franklin, TN 37068 From redmine at redmine.open-bio.org Fri Apr 22 16:22:31 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Fri, 22 Apr 2011 16:22:31 +0000 Subject: [Biopython-dev] [Biopython - Bug #3009] (Closed) Check the FASTA m10 alignment parser works with FASTA36 References: Message-ID: Issue #3009 has been updated by Peter Cock. Status changed from New to Closed % Done changed from 0 to 100 Seemed to have been working fine up to and including fasta-36.2, I just found and fixed a problem with fasta-36.3 https://github.com/biopython/biopython/commit/f528bf583993efd7558173dff4309cf0821203a1 https://github.com/biopython/biopython/commit/f8373400a9dbe2cf54f5d0e73ccd5163e7ad4558 Marking this bug as fixed. ---------------------------------------- Bug #3009: Check the FASTA m10 alignment parser works with FASTA36 https://redmine.open-bio.org/issues/3009 Author: Peter Cock Status: Closed Priority: Normal Assignee: Biopython Dev Mailing List Category: Unit Tests Target version: Not Applicable URL: Bill Pearson has just announced the release of FASTA36: http://faculty.virginia.edu/wrpearson/fasta/fasta36/ >From his email, > This version is a major update from FASTA version 35. > It's main new feature is the ability to report all > statistically significant alignments between a query > and library sequence (equivalent to BLAST's multiple > HSPs). All previous versions of the FASTA program > reported only the best alignment between the query > and library sequence, a serious shortcoming when > comparing a query protein to a multi-exon gene or > multi-domain protein. We need to check the FASTA36 -m 10 output, add this to our unit tests, and update our parser as required. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Tue Apr 26 17:20:10 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Tue, 26 Apr 2011 17:20:10 +0000 Subject: [Biopython-dev] [Biopython - Bug #3009] (New) Check the FASTA m10 alignment parser works with FASTA36 References: Message-ID: Issue #3009 has been updated by Peter Cock. Category changed from Unit Tests to Main Distribution Status changed from Closed to New % Done changed from 100 to 0 Reopening bug, found some examples with multiple HSPs for the same query and match, separated by new line ">--". I will add an example to the test suite, but the parser will need revising (something I was looking at doing anyway for other reasons). ---------------------------------------- Bug #3009: Check the FASTA m10 alignment parser works with FASTA36 https://redmine.open-bio.org/issues/3009 Author: Peter Cock Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: Not Applicable URL: Bill Pearson has just announced the release of FASTA36: http://faculty.virginia.edu/wrpearson/fasta/fasta36/ >From his email, > This version is a major update from FASTA version 35. > It's main new feature is the ability to report all > statistically significant alignments between a query > and library sequence (equivalent to BLAST's multiple > HSPs). All previous versions of the FASTA program > reported only the best alignment between the query > and library sequence, a serious shortcoming when > comparing a query protein to a multi-exon gene or > multi-domain protein. We need to check the FASTA36 -m 10 output, add this to our unit tests, and update our parser as required. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 02:07:51 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 02:07:51 +0000 Subject: [Biopython-dev] [Biopython - Bug #2820] (Closed) Convert test_PDB.py to unittest References: Message-ID: Issue #2820 has been updated by Eric Talevich. Status changed from New to Closed % Done changed from 0 to 100 Wow, we took care of this a long time ago. Marking it closed. ---------------------------------------- Bug #2820: Convert test_PDB.py to unittest https://redmine.open-bio.org/issues/2820 Author: Eric Talevich Status: Closed Priority: Normal Assignee: Biopython Dev Mailing List Category: Unit Tests Target version: Not Applicable URL: The current test script for Bio.PDB uses the print-and-compare approach. I've written an equivalent test script using unittest, assuming that style is the preferred one. It was written to go with Bug 2754, but now lives on my pdbtidy branch: http://github.com/etal/biopython/tree/pdbtidy This script could also live alongside the original test_PDB.py for awhile, as an additional check on Bio.PDB's error handling. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 02:24:28 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 02:24:28 +0000 Subject: [Biopython-dev] [Biopython - Feature #3216] (New) Bio.Phylo.Applications support for PhyML Message-ID: Issue #3216 has been reported by Eric Talevich. ---------------------------------------- Feature #3216: Bio.Phylo.Applications support for PhyML https://redmine.open-bio.org/issues/3216 Author: Eric Talevich Status: New Priority: Low Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: http://www.atgc-montpellier.fr/phyml/ PhyML is another popular tool for inferring phylogenies by maximum likelihood, and can be also be considered reasonably best-practice (alongside RAxML, which isn't yet packaged). The Debian package for PhyML was recently updated to the latest version (3.0), and should be trickling down to the distros soon. Let's create a wrapper for it in Biopython. The input is just a Phylip alignment, so this should be easier than MrBayes. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 02:50:27 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 02:50:27 +0000 Subject: [Biopython-dev] [Biopython - Feature #3217] (New) Bio.Phylo I/O support for the NeXML format Message-ID: Issue #3217 has been reported by Eric Talevich. ---------------------------------------- Feature #3217: Bio.Phylo I/O support for the NeXML format https://redmine.open-bio.org/issues/3217 Author: Eric Talevich Status: New Priority: Normal Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: The future data exchange standard is... approaching rapidly. NeXML is going to become the format of choice for TreeBASE, Mesquite and probably MIAPA-targeted tools over the next year or two, and Biopython should be there to support it. Notes: * Another Python library, DendroPy, already supports (some of?) the NeXML format. Jeet Sukumaran and Mark Holder changed the license to BSD to allow other projects -- particularly us -- to share their code. So let's start there. * NeXML was designed so its elements can be treated as RDF triples, so see if RDFLib can help -- either as the underlying parser, or to provide some additional (optional) functionality. See: http://nexml.org/ http://packages.python.org/DendroPy/ http://www.rdflib.net/ ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 15:41:40 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 15:41:40 +0000 Subject: [Biopython-dev] [Biopython - Feature #3218] (New) Bio.Phylo.Applications support for RAxML Message-ID: Issue #3218 has been reported by Eric Talevich. ---------------------------------------- Feature #3218: Bio.Phylo.Applications support for RAxML https://redmine.open-bio.org/issues/3218 Author: Eric Talevich Status: New Priority: Low Assignee: Eric Talevich Category: Main Distribution Target version: Not Applicable URL: RAxML is another popular tool for inferring phylogenies by maximum likelihood, and can be also be considered reasonably best-practice. Performance is good, and the command-line options are easy to understand. The Debian package for RAxML was uploaded to SVN today. Let's create a wrapper for it in Biopython. The input is a Phylip alignment, like PhyML. Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm NB: Frank Kauff wrote a separate wrapper for RAxML called PYRAXML. Check it out. http://www.lutzonilab.net/downloads/ Implementation note: Phylip alignment format truncates taxon names, but we can support longer names in intermediate Bio.Align.MultipleSeqAlignment objects by mapping sequence IDs to unique integers (for example). That function would be useful in several places in Biopython. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:09:11 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:09:11 +0000 Subject: [Biopython-dev] [Biopython - Feature #3219] (New) Port Biopython documentation to Sphinx Message-ID: Issue #3219 has been reported by Eric Talevich. ---------------------------------------- Feature #3219: Port Biopython documentation to Sphinx https://redmine.open-bio.org/issues/3219 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: Currently we use Epydoc for the API reference documentation, and LaTeX (to PDF via pdflatex, and HTML via hevea) for the tutorial. There's some material on the wiki to consider, too. A number of Python projects, including CPython, now use Sphinx for documentation. Content is written in reStructuredText format, and can be pulled from both standalone .rst files and Python docstrings. This offers several advantages: (i) API documentation will be prettier and easier to navigate; (ii) the Tutorial will be easier to edit for those not fluent in LaTeX; (iii) Since the API reference and Tutorial will be written in the same markup, potentially even pulling from some shared sources, it will be easier to address redundant or overlapping portions between the two, avoiding inconsistencies. See: http://sphinx.pocoo.org/ http://docutils.sourceforge.net/ Mailing list discussion: http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html Numpy's approach: http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:09:11 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:09:11 +0000 Subject: [Biopython-dev] [Biopython - Feature #3219] (New) Port Biopython documentation to Sphinx Message-ID: Issue #3219 has been reported by Eric Talevich. ---------------------------------------- Feature #3219: Port Biopython documentation to Sphinx https://redmine.open-bio.org/issues/3219 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: Currently we use Epydoc for the API reference documentation, and LaTeX (to PDF via pdflatex, and HTML via hevea) for the tutorial. There's some material on the wiki to consider, too. A number of Python projects, including CPython, now use Sphinx for documentation. Content is written in reStructuredText format, and can be pulled from both standalone .rst files and Python docstrings. This offers several advantages: (i) API documentation will be prettier and easier to navigate; (ii) the Tutorial will be easier to edit for those not fluent in LaTeX; (iii) Since the API reference and Tutorial will be written in the same markup, potentially even pulling from some shared sources, it will be easier to address redundant or overlapping portions between the two, avoiding inconsistencies. See: http://sphinx.pocoo.org/ http://docutils.sourceforge.net/ Mailing list discussion: http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html Numpy's approach: http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:19:17 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:19:17 +0000 Subject: [Biopython-dev] [Biopython - Feature #3220] (New) Port Biopython docstrings to reStructuredText Message-ID: Issue #3220 has been reported by Eric Talevich. ---------------------------------------- Feature #3220: Port Biopython docstrings to reStructuredText https://redmine.open-bio.org/issues/3220 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work. Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from: 
__docformat__ = "epytext en"
to: 
__docformat__ = "restructuredtext en"
And changing any Epytext markup in the docstrings to valid rST. Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation. See: http://epydoc.sourceforge.net/manual-othermarkup.html http://docutils.sourceforge.net/rst.html -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:19:16 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:19:16 +0000 Subject: [Biopython-dev] [Biopython - Feature #3220] (New) Port Biopython docstrings to reStructuredText Message-ID: Issue #3220 has been reported by Eric Talevich. ---------------------------------------- Feature #3220: Port Biopython docstrings to reStructuredText https://redmine.open-bio.org/issues/3220 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work. Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from: 
__docformat__ = "epytext en"
to: 
__docformat__ = "restructuredtext en"
And changing any Epytext markup in the docstrings to valid rST. Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation. See: http://epydoc.sourceforge.net/manual-othermarkup.html http://docutils.sourceforge.net/rst.html ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:23:48 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:23:48 +0000 Subject: [Biopython-dev] [Biopython - Feature #3221] (New) Port the Biopython Tutorial to Sphinx/reStructuredText Message-ID: Issue #3221 has been reported by Eric Talevich. ---------------------------------------- Feature #3221: Port the Biopython Tutorial to Sphinx/reStructuredText https://redmine.open-bio.org/issues/3221 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: This is the second step in porting Biopython documentation to Sphinx -- port the Tutorial markup from LaTeX to reStructuredText, and split it into multiple files for Sphinx to process. While we're at it, we may want to slim down the Tutorial and move some of the more detailed material to a separate Reference based on the automated API docs. See the parent task for discussion. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:23:48 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:23:48 +0000 Subject: [Biopython-dev] [Biopython - Feature #3221] (New) Port the Biopython Tutorial to Sphinx/reStructuredText Message-ID: Issue #3221 has been reported by Eric Talevich. ---------------------------------------- Feature #3221: Port the Biopython Tutorial to Sphinx/reStructuredText https://redmine.open-bio.org/issues/3221 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: This is the second step in porting Biopython documentation to Sphinx -- port the Tutorial markup from LaTeX to reStructuredText, and split it into multiple files for Sphinx to process. While we're at it, we may want to slim down the Tutorial and move some of the more detailed material to a separate Reference based on the automated API docs. See the parent task for discussion. ---------------------------------------- You have received this notification because this email was added to the New Issue Alert plugin -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:42:48 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:42:48 +0000 Subject: [Biopython-dev] [Biopython - Feature #3220] Port Biopython docstrings to reStructuredText References: Message-ID: Issue #3220 has been updated by Peter Cock. You linked to this on the parent bug #3319, but we should probably adopt (some of) the NumPy docstring conventions, which limit the amount of rich mark up so as not to make the plain text view too ugly. This is important when reading the API help text at the python prompt. https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt Also note that a large fraction of the current API docs are not even done in epytext, they are plain text. This would also be a nice point to standardise on the layout of things like function/method argument documentation. Again, I'd suggest following NumPy by default. ---------------------------------------- Feature #3220: Port Biopython docstrings to reStructuredText https://redmine.open-bio.org/issues/3220 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work. Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from: 
__docformat__ = "epytext en"
to: 
__docformat__ = "restructuredtext en"
And changing any Epytext markup in the docstrings to valid rST. Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation. See: http://epydoc.sourceforge.net/manual-othermarkup.html http://docutils.sourceforge.net/rst.html -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From redmine at redmine.open-bio.org Thu Apr 28 16:45:16 2011 From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org) Date: Thu, 28 Apr 2011 16:45:16 +0000 Subject: [Biopython-dev] [Biopython - Feature #3221] Port the Biopython Tutorial to Sphinx/reStructuredText References: Message-ID: Issue #3221 has been updated by Peter Cock. Note that some of the examples in Tutorial.txt are written in doctest format and are now tested using the doctest library via test_Tutorial.py It would be nice to continue to have these examples run as part of our test suite, but it would require some markup convention (since not all doctest like examples should be tested). ---------------------------------------- Feature #3221: Port the Biopython Tutorial to Sphinx/reStructuredText https://redmine.open-bio.org/issues/3221 Author: Eric Talevich Status: New Priority: Low Assignee: Biopython Dev Mailing List Category: Documentation Target version: URL: This is the second step in porting Biopython documentation to Sphinx -- port the Tutorial markup from LaTeX to reStructuredText, and split it into multiple files for Sphinx to process. While we're at it, we may want to slim down the Tutorial and move some of the more detailed material to a separate Reference based on the automated API docs. See the parent task for discussion. -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org From luizaugustomm at gmail.com Fri Apr 29 01:42:26 2011 From: luizaugustomm at gmail.com (=?ISO-8859-1?Q?Luiz_Augusto_Mac=EAdo_Morais?=) Date: Thu, 28 Apr 2011 22:42:26 -0300 Subject: [Biopython-dev] Translation of the tutorial about Biopython Message-ID: Hi everybody, My name is Luiz Augusto. I am a brazilian student of Computer Science and I am interested to translate to Portuguese the tutorial of the Biopython written by Jeff Chang et al. I begun to study Biopython this year and I noticed that there is not many materials about Biopython written in Portuguese. So, I want to know how get permission to translate that material. I tried send an e-mail to Jeff Chang, but his e-mail is not working. Yours faithfully, Luiz Augusto de Mac?do Morais From krother at rubor.de Fri Apr 29 07:37:28 2011 From: krother at rubor.de (Kristian Rother) Date: Fri, 29 Apr 2011 09:37:28 +0200 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: Hi, I've seen Sphinx being used on several projects (see e.g. http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one myself (2009). The system for mixing text+code and testing code examples is gorgeous! What I didn't like is that all Sphinx sites seem to look the same (including font sizes and colours). There probably is a place to apply a CSS stylesheet, but it was not easy to find. There might be some work at this point. Is someone trying to make a proof-of-concept on GIT or are we looking for a volunteer? Best regards, Kristian > > Issue #3219 has been reported by Eric Talevich. > > ---------------------------------------- > Feature #3219: Port Biopython documentation to Sphinx > https://redmine.open-bio.org/issues/3219 > > Author: Eric Talevich > Status: New > Priority: Low > Assignee: Biopython Dev Mailing List > Category: Documentation > Target version: > URL: > > > Currently we use Epydoc for the API reference documentation, and LaTeX (to > PDF via pdflatex, and HTML via hevea) for the tutorial. There's some > material on the wiki to consider, too. > > A number of Python projects, including CPython, now use Sphinx for > documentation. Content is written in reStructuredText format, and can be > pulled from both standalone .rst files and Python docstrings. > > This offers several advantages: (i) API documentation will be prettier and > easier to navigate; (ii) the Tutorial will be easier to edit for those not > fluent in LaTeX; (iii) Since the API reference and Tutorial will be > written in the same markup, potentially even pulling from some shared > sources, it will be easier to address redundant or overlapping portions > between the two, avoiding inconsistencies. > > See: > http://sphinx.pocoo.org/ > http://docutils.sourceforge.net/ > > Mailing list discussion: > http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html > > Numpy's approach: > http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt > > > > ---------------------------------------- > You have received this notification because this email was added to the > New Issue Alert plugin > > > -- > You have received this notification because you have either subscribed to > it, or are involved in it. > To change your notification preferences, please click here and login: > http://redmine.open-bio.org > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > > From p.j.a.cock at googlemail.com Fri Apr 29 07:55:40 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 29 Apr 2011 08:55:40 +0100 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: Re: Feature #3219: Port Biopython documentation to Sphinx https://redmine.open-bio.org/issues/3219 and this thread last year: http://portal.open-bio.org/pipermail/biopython-dev/2010-July/007977.html On Fri, Apr 29, 2011 at 8:37 AM, Kristian Rother wrote: > > Hi, > > I've seen Sphinx being used on several projects (see e.g. > http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one > myself (2009). The system for mixing text+code and testing code examples > is gorgeous! > > What I didn't like is that all Sphinx sites seem to look the same > (including font sizes and colours). There probably is a place to apply a > CSS stylesheet, but it was not easy to find. There might be some work at > this point. > > Is someone trying to make a proof-of-concept on GIT or are we looking for > a volunteer? > > Best regards, > ? Kristian I think there was an experimental branch on github already... by Eric and/or Vince, but his repository seems to have gone: https://github.com/vsbuffalo/ Peter From chapmanb at 50mail.com Fri Apr 29 12:17:29 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 29 Apr 2011 08:17:29 -0400 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: Message-ID: <20110429121729.GE27039@sobchak> Luiz; > My name is Luiz Augusto. I am a brazilian student of Computer Science and I > am interested to translate to Portuguese the tutorial of the Biopython > written by Jeff Chang et al. [...] > So, I want to know how get permission to translate that material. Yes, please. Portuguese translations of the documentation, cookbooks, or just code examples would be very useful. No permission needed, please go for it. When you have documentation available please let us know so we can link to it: http://biopython.org/wiki/Documentation Thanks much, Brad From idoerg at gmail.com Fri Apr 29 12:48:25 2011 From: idoerg at gmail.com (Iddo Friedberg) Date: Fri, 29 Apr 2011 08:48:25 -0400 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> Message-ID: Hey all, Prompted by this exchange: how about placing all the biopython docs under a creative commons license? Iddo Friedberg http://iddo-friedberg.net/contact.html On Apr 29, 2011 8:22 AM, "Brad Chapman" wrote: Luiz; > My name is Luiz Augusto. I am a brazilian student of Computer Science and I > am interested to tra... [...] > So, I want to know how get permission to translate that material. Yes, please. Portuguese translations of the documentation, cookbooks, or just code examples would be very useful. No permission needed, please go for it. When you have documentation available please let us know so we can link to it: http://biopython.org/wiki/Documentation Thanks much, Brad _______________________________________________ Biopython-dev mailing list Biopython-dev at lists.open-... From tiagoantao at gmail.com Fri Apr 29 12:51:04 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Fri, 29 Apr 2011 13:51:04 +0100 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> Message-ID: 2011/4/29 Iddo Friedberg : > Prompted by this exchange: how about placing all the biopython docs under a > creative commons license? +1 From p.j.a.cock at googlemail.com Fri Apr 29 13:15:47 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 29 Apr 2011 14:15:47 +0100 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> Message-ID: <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> On 29 Apr 2011, at 13:51, Tiago Ant?o wrote: > 2011/4/29 Iddo Friedberg : >> Prompted by this exchange: how about placing all the biopython docs under a >> creative commons license? > > +1 > _______________________________________________ > We'd have to check with at least the named authors... but it seems like a good idea. Peter From eric.talevich at gmail.com Fri Apr 29 14:13:17 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Fri, 29 Apr 2011 10:13:17 -0400 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: On Fri, Apr 29, 2011 at 3:55 AM, Peter Cock wrote: > Re: Feature #3219: Port Biopython documentation to Sphinx > https://redmine.open-bio.org/issues/3219 > > and this thread last year: > http://portal.open-bio.org/pipermail/biopython-dev/2010-July/007977.html > > On Fri, Apr 29, 2011 at 8:37 AM, Kristian Rother wrote: > > > > Hi, > > > > I've seen Sphinx being used on several projects (see e.g. > > http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one > > myself (2009). The system for mixing text+code and testing code examples > > is gorgeous! > > > > What I didn't like is that all Sphinx sites seem to look the same > > (including font sizes and colours). There probably is a place to apply a > > CSS stylesheet, but it was not easy to find. There might be some work at > > this point. > > > > Is someone trying to make a proof-of-concept on GIT or are we looking for > > a volunteer? > > > > Best regards, > > Kristian > > I think there was an experimental branch on github already... by Eric > and/or > Vince, but his repository seems to have gone: > https://github.com/vsbuffalo/ > > I don't have a branch for this yet, but I filed the bugs on Redmine to get this big to-do item out of my head and onto the web. I expect to have a little bit more time this summer to work on Bio.Phylo and Bio.PDB/Struct, and I'm going to start by converting the docstrings in Bio.Phylo to reStructuredText. This won't take much time, and once we merge that branch and make the Docutils dependency official (for building Epydoc documentation), that will reduce the activation energy for porting the rest of our docstrings. If anyone else wants to port some docstrings independently, that's cool too, and I don't think it will cause any conflict in the code base. Once that's done, we can start seriously considering the switch from Epydoc to Sphinx. Sound like a plan? Cheers, Eric From eric.talevich at gmail.com Fri Apr 29 14:25:18 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Fri, 29 Apr 2011 10:25:18 -0400 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> Message-ID: 2011/4/29 Peter Cock > > > On 29 Apr 2011, at 13:51, Tiago Ant?o wrote: > > > 2011/4/29 Iddo Friedberg : > >> Prompted by this exchange: how about placing all the biopython docs > under a > >> creative commons license? > > > > +1 > > _______________________________________________ > > > > We'd have to check with at least the named authors... but it seems like a > good idea. > > Peter > > +1. Right now the LICENSE file refers to both "this software and its documentation", so the docs are already legally free to modify, translate and redistribute. The Tutorial doesn't have a copyright notice in the comments at the top -- should it? -Eric From luizaugustomm at gmail.com Fri Apr 29 21:10:33 2011 From: luizaugustomm at gmail.com (=?ISO-8859-1?Q?Luiz_Augusto_Mac=EAdo_Morais?=) Date: Fri, 29 Apr 2011 18:10:33 -0300 Subject: [Biopython-dev] Translation of the tutorial about Biopython In-Reply-To: References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> Message-ID: Thank you folks. So, I'll start to translate. Brad, when it's done, I'll send the material to this mailing list. Luiz Augusto Em 29 de abril de 2011 11:25, Eric Talevich escreveu: > 2011/4/29 Peter Cock > >> >> >> On 29 Apr 2011, at 13:51, Tiago Ant?o wrote: >> >> > 2011/4/29 Iddo Friedberg : >> >> Prompted by this exchange: how about placing all the biopython docs >> under a >> >> creative commons license? >> > >> > +1 >> > _______________________________________________ >> > >> >> We'd have to check with at least the named authors... but it seems like a >> good idea. >> >> Peter >> >> > +1. Right now the LICENSE file refers to both "this software and its > documentation", so the docs are already legally free to modify, translate > and redistribute. The Tutorial doesn't have a copyright notice in the > comments at the top -- should it? > > -Eric > From p.j.a.cock at googlemail.com Fri Apr 29 23:47:35 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 30 Apr 2011 00:47:35 +0100 Subject: [Biopython-dev] Port Biopython documentation to Sphinx In-Reply-To: References: Message-ID: On Friday, April 29, 2011, Eric Talevich wrote: > > I don't have a branch for this yet, but I filed the bugs on Redmine to get this big to-do item out of my head and onto the web. I expect to have a little bit more time this summer to work on Bio.Phylo and Bio.PDB/Struct, and I'm going to start by converting the docstrings in Bio.Phylo to reStructuredText. This won't take much time, and once we merge that branch and make the Docutils dependency official (for building Epydoc documentation), that will reduce the activation energy for porting the rest of our docstrings. > > If anyone else wants to port some docstrings independently, that's cool too, and I don't think it will cause any conflict in the code base. > > Once that's done, we can start seriously considering the switch from Epydoc to Sphinx. Sound like a plan? > > Cheers, > Eric > Yes, sounds good. Peter From mdipierro at cs.depaul.edu Fri Apr 29 13:34:34 2011 From: mdipierro at cs.depaul.edu (Massimo Di Pierro) Date: Fri, 29 Apr 2011 08:34:34 -0500 Subject: [Biopython-dev] biopython web interface In-Reply-To: <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> Message-ID: <57629245-F184-4143-8B18-80E69BC2C351@cs.depaul.edu> Hello everybody, I am new to biopython and I have some silly questions. Does biopython have a web interface? If not, would you be interested in help developing one? What kind of features would you be interested in? Reason for my question: I am a physicist and a professor of CS. I am working with a few different groups to build a unified platform to bring scientific data online. The main idea is that of having a tool that requires no programming and scientists can use to introspect an existing directory and turn it into dynamical web pages. Those pages can then be edited and re-oreganized like a CMS. The system should be able to recognize basic file types, group, tag and categorize them. It should them be possible to register algorithms, run them on the server, create a workflow. The system will also have an interface for mobile. Here is a first prototype for physics data that interface with the National Energy Research Computing Center: http://tests.web2py.com/nersc Since we are doing this it would be great to have as many community on board as possible so that we can write specs that are broad enough. We can do all the work or you can help us if you want. So, if you have a wish list please share it with me. Personally, I need to be educated on biopython since I do not fully understand what are the basic file types it handles, what are the most popular algorithms it provides, nor I am familiar with the typical usage workflow. Massimo From eric.talevich at gmail.com Sat Apr 30 14:49:52 2011 From: eric.talevich at gmail.com (Eric Talevich) Date: Sat, 30 Apr 2011 10:49:52 -0400 Subject: [Biopython-dev] biopython web interface In-Reply-To: <57629245-F184-4143-8B18-80E69BC2C351@cs.depaul.edu> References: <20110429121729.GE27039@sobchak> <2A78A174-11CA-440C-A0B8-DF4563616290@googlemail.com> <57629245-F184-4143-8B18-80E69BC2C351@cs.depaul.edu> Message-ID: Hi Massimo, On Fri, Apr 29, 2011 at 9:34 AM, Massimo Di Pierro wrote: > > Does biopython have a web interface? > If not, would you be interested in help developing one? > What kind of features would you be interested in? > Biopython is only a library, but can be useful for building web interfaces for biological workflows. Have you looked at Galaxy yet? http://galaxy.psu.edu/ http://usegalaxy.org/ http://getgalaxy.org/ I think it may provide most of what you're interested in. It provides a web interface for biological workflows; it requires no programming to use, but it can also be easily extended with a small amount of code to incorporate new command-line tools into a workflow. It already handles most of the common file formats for biological data, too. Reason for my question: I am a physicist and a professor of CS. I am working > with a few different groups to build a unified platform to bring scientific > data online. The main idea is that of having a tool that requires no > programming and scientists can use to introspect an existing directory and > turn it into dynamical web pages. Those pages can then be edited and > re-oreganized like a CMS. The system should be able to recognize basic file > types, group, tag and categorize them. It should them be possible to > register algorithms, run them on the server, create a workflow. The system > will also have an interface for mobile. > > Here is a first prototype for physics data that interface with the National > Energy Research Computing Center: > http://tests.web2py.com/nersc > Interesting, something keep an eye on as it develops. Cheers, Eric From andrea at biocomp.unibo.it Sat Apr 30 17:03:46 2011 From: andrea at biocomp.unibo.it (Andrea Pierleoni) Date: Sat, 30 Apr 2011 19:03:46 +0200 (CEST) Subject: [Biopython-dev] biopython web interface In-Reply-To: References: Message-ID: <3a649ae478daf0c2e544dc573a15f3b5.squirrel@lipid.biocomp.unibo.it> > > Message: 3 > Date: Fri, 29 Apr 2011 08:34:34 -0500 > From: Massimo Di Pierro > Subject: [Biopython-dev] biopython web interface > To: > Message-ID: <57629245-F184-4143-8B18-80E69BC2C351 at cs.depaul.edu> > Content-Type: text/plain; charset="us-ascii" > > Hello everybody, > > I am new to biopython and I have some silly questions. > > Does biopython have a web interface? > If not, would you be interested in help developing one? > What kind of features would you be interested in? > > Reason for my question: I am a physicist and a professor of CS. I am > working with a few different groups to build a unified platform to bring > scientific data online. The main idea is that of having a tool that > requires no programming and scientists can use to introspect an existing > directory and turn it into dynamical web pages. Those pages can then be > edited and re-oreganized like a CMS. The system should be able to > recognize basic file types, group, tag and categorize them. It should them > be possible to register algorithms, run them on the server, create a > workflow. The system will also have an interface for mobile. > > Here is a first prototype for physics data that interface with the > National Energy Research Computing Center: > http://tests.web2py.com/nersc > > Since we are doing this it would be great to have as many community on > board as possible so that we can write specs that are broad enough. > We can do all the work or you can help us if you want. > > So, if you have a wish list please share it with me. > > Personally, I need to be educated on biopython since I do not fully > understand what are the basic file types it handles, what are the most > popular algorithms it provides, nor I am familiar with the typical usage > workflow. > > Massimo > > > Hi Massimo, BioPython itself is a python library, but a web interface would enable many functions to biological scientist with no programming expertise. There are some parts of the library that cope well with a web-interface/server, in particular the BioSQL modules. The BioSQL schema is a relational database model to store biological data. I do have working code for using the BioPython BioSQL functions (and more) with the web2py DAL, and I'm working on a complete web2py-based opensource webserver to store and manage biological sequences/entities. If you (or any other) are interested and want to contribute, let me know. There are many things in common between what I'm doing and what you want to do, so maybe its a good idea to work together. Andrea Pierleoni From rodrigo.faccioli at gmail.com Sat Apr 30 17:55:59 2011 From: rodrigo.faccioli at gmail.com (Rodrigo Faccioli) Date: Sat, 30 Apr 2011 14:55:59 -0300 Subject: [Biopython-dev] biopython web interface In-Reply-To: <3a649ae478daf0c2e544dc573a15f3b5.squirrel@lipid.biocomp.unibo.it> References: <3a649ae478daf0c2e544dc573a15f3b5.squirrel@lipid.biocomp.unibo.it> Message-ID: Hello, The messages before described about BioPython and BioSQL projects. Furthermore, they commented how you are able to develop your system with those projects. I would like to show the project which I have been working. Although you're using web2py framework, I would like to show my project which don't use framework, yet. We develop its front-end in jsp. However, its back-end is written with BioPython. Please, see [1]. [1] http://glu.fcfrp.usp.br:8180/prometheus/ -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-8739 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 Personal Blogg - http://rodrigofaccioli.blogspot.com/ On Sat, Apr 30, 2011 at 2:03 PM, Andrea Pierleoni wrote: > > > > > Message: 3 > > Date: Fri, 29 Apr 2011 08:34:34 -0500 > > From: Massimo Di Pierro > > Subject: [Biopython-dev] biopython web interface > > To: > > Message-ID: <57629245-F184-4143-8B18-80E69BC2C351 at cs.depaul.edu> > > Content-Type: text/plain; charset="us-ascii" > > > > Hello everybody, > > > > I am new to biopython and I have some silly questions. > > > > Does biopython have a web interface? > > If not, would you be interested in help developing one? > > What kind of features would you be interested in? > > > > Reason for my question: I am a physicist and a professor of CS. I am > > working with a few different groups to build a unified platform to bring > > scientific data online. The main idea is that of having a tool that > > requires no programming and scientists can use to introspect an existing > > directory and turn it into dynamical web pages. Those pages can then be > > edited and re-oreganized like a CMS. The system should be able to > > recognize basic file types, group, tag and categorize them. It should > them > > be possible to register algorithms, run them on the server, create a > > workflow. The system will also have an interface for mobile. > > > > Here is a first prototype for physics data that interface with the > > National Energy Research Computing Center: > > http://tests.web2py.com/nersc > > > > Since we are doing this it would be great to have as many community on > > board as possible so that we can write specs that are broad enough. > > We can do all the work or you can help us if you want. > > > > So, if you have a wish list please share it with me. > > > > Personally, I need to be educated on biopython since I do not fully > > understand what are the basic file types it handles, what are the most > > popular algorithms it provides, nor I am familiar with the typical usage > > workflow. > > > > Massimo > > > > > > > > > Hi Massimo, > BioPython itself is a python library, but a web interface would enable many > functions to biological scientist with no programming expertise. > There are some parts of the library that cope well with a > web-interface/server, > in particular the BioSQL modules. > The BioSQL schema is a relational database model to store biological data. > I do have working code for using the BioPython BioSQL functions (and more) > with > the web2py DAL, and I'm working on a complete web2py-based opensource > webserver to store and manage biological sequences/entities. > If you (or any other) are interested and want to contribute, let me know. > There are many things in common between what I'm doing and what you want > to do, > so maybe its a good idea to work together. > > Andrea Pierleoni > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev >