From rmb32 at cornell.edu Sun Aug 1 15:17:14 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sun, 01 Aug 2010 12:17:14 -0700 Subject: [Biopython] GMOD Evo Hackathon Open Call for Participation Message-ID: <4C55C83A.3060700@cornell.edu> We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From phosse1 at students.towson.edu Tue Aug 3 19:53:33 2010 From: phosse1 at students.towson.edu (Parsa Hosseini) Date: Tue, 3 Aug 2010 19:53:33 -0400 Subject: [Biopython] Biopython SUBA interface Message-ID: Hi everyone, I have some python cgi scripts which interface with the Arabidopsis thaliana SUBA database. I'd like to contribute such scripts (and hopefully much more). I was curious how I can go about submitting such code and/or if anyone would find such a script/interface of use? Thanks alot, -------------------------------------------- Parsa Hosseini Parsa.Hosseini at ars.usda.gov http://tiger.towson.edu/~phosse1/ 301-875-6525 From biopython at maubp.freeserve.co.uk Wed Aug 4 04:12:07 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 4 Aug 2010 09:12:07 +0100 Subject: [Biopython] Biopython SUBA interface In-Reply-To: References: Message-ID: On Wed, Aug 4, 2010 at 12:53 AM, Parsa Hosseini wrote: > Hi everyone, > I have some python cgi scripts which interface with the Arabidopsis > thaliana SUBA database. > I'd like to contribute such scripts (and hopefully much more). I was > curious how I can go about submitting such code and/or if anyone > would find such a script/interface of use? > Thanks alot, Hi Parsa, Are these stand alone scripts that you would use at the command line, or a Python module you can use in a Python script? Either way we could include them... I had a quick look at http://suba.plantenergy.uwa.edu.au/ and it isn't clear if they have an official API. Are you doing this by building the HTTP request and then parsing the HTML results? If so, that is worrying for two reasons. First, it is fragile and will need updates whenever the site makes changes to their layout (something that has happened to other HTML parsers in Biopython that have since been deprecated and removed). Secondly, in the absence of an official API are there any usage guidelines? The SUBA team may not be happy with people running scripts that could use up far more resources than several people using the website interface. As to would anyone find such a script/interface of use, well, personally probably not in my current work. But I'm sure there are people using Biopython working on plant genomes and Arabidopsis thaliana. Regards, Peter From biopython at maubp.freeserve.co.uk Wed Aug 11 11:14:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 11 Aug 2010 16:14:27 +0100 Subject: [Biopython] Using a dictionary rather than list for hierachy in Bio.SCOP.Cla Message-ID: Dear Biopythoneers - especially those using SCOP, Jeffrey Finkelstein has proposed a change to the Record class in Bio.SCOP.Cla to use a dictionary rather than a list for the hierarchy member to better match the SCOP specification, see his email quoted below and Bug 3109 for details: http://bugzilla.open-bio.org/show_bug.cgi?id=3109 This would be a backwards incompatible change, so feedback from anyone using Biopython's SCOP module would be important in deciding how to proceed. Comments please? Thank you, Peter On the dev list Jeffrey Finkelstein wrote: > I have submitted a bug report and a patch for a current feature of the > Bio.SCOP.Cla module that makes using it somewhat difficult. Specifically, > the Bio.Scop.Cla.Record class has a "hierarchy" member which is currently a > list, but should be a dictionary, according to the SCOP parseable > classification file format "specification" (it is an informal specification) > here: > http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html#scop-parseable-files. > > For a usage example, see the comments I have made at: > http://bugzilla.open-bio.org/show_bug.cgi?id=3109 > > I have CC'ed the original author of the module. Gavin (or anyone else), do > you have any objections to this change? > > Jeffrey See http://lists.open-bio.org/pipermail/biopython-dev/2010-August/008134.html From biopython at maubp.freeserve.co.uk Thu Aug 19 11:43:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 19 Aug 2010 16:43:56 +0100 Subject: [Biopython] Biopython 1.55 beta released Message-ID: Dear Biopythoneers, We?ve just released a beta of Biopython 1.55 for user testing, as announced on the news server (which has RSS and atom feeds) and on twitter: http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ http://twitter.com/biopython Since Biopython 1.54 was released three months ago, we?ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we?ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we?ve accidentally broken things ? which is why we?re doing this beta release. In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 10 people have contributed to this release (so far), including 5 new people - thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download Feedback is welcome through the mailing lists (or bugzilla), especially if you find something that doesn't work. Thank you, Peter From rmb32 at cornell.edu Thu Aug 19 13:09:45 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 19 Aug 2010 10:09:45 -0700 Subject: [Biopython] reminder: Aug 25 deadline for GMOD Hackathon application Message-ID: <4C6D6559.3080809@cornell.edu> Hi all, This is your one-week reminder: the deadline for open applications to the GMOD Evo hackathon is Wednesday, August 25th. Rob ======================================== We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From biopython at maubp.freeserve.co.uk Mon Aug 23 12:05:43 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 23 Aug 2010 17:05:43 +0100 Subject: [Biopython] Biopython 1.55 beta released In-Reply-To: References: Message-ID: On Thu, Aug 19, 2010 at 4:43 PM, Peter wrote: > Dear Biopythoneers, > > We?ve just released a beta of Biopython 1.55 for user testing, as > announced on the news server (which has RSS and atom feeds) and on > twitter: > http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ > http://twitter.com/biopython > > ... > > Feedback is welcome through the mailing lists (or bugzilla), > especially if you find something that doesn't work. Hi all, Is no news good news? So far there have been no problems reported. I've had a least one person report (off list) that the windows installers worked fine for them on Windows XP (32bit). Any other feedback on the beta? Thanks Peter From cgohlke at uci.edu Mon Aug 23 16:43:20 2010 From: cgohlke at uci.edu (Christoph Gohlke) Date: Mon, 23 Aug 2010 13:43:20 -0700 Subject: [Biopython] Biopython 1.55 beta released (Peter) In-Reply-To: References: Message-ID: <4C72DD68.20309@uci.edu> > Dear Biopythoneers, > > We?ve just released a beta of Biopython 1.55 for user testing, as > announced on the news server (which has RSS and atom feeds) and on > twitter: > http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ > http://twitter.com/biopython > > Since Biopython 1.54 was released three months ago, we?ve made a good > start on work for Python 3 support (via the 2to3 script), but as a > side effect of this we?ve had to update quite a lot of the older parts > of the library. Although the unit tests are all fine, there is a small > but real chance that we?ve accidentally broken things ? which is why > we?re doing this beta release. > > In terms of new features, the most noticeable highlight is that the > command line tool application wrapper classes are now executable, > which should make it much easier to call external tools. This is > described in the updated documentation. > http://biopython.org/DIST/docs/tutorial/Tutorial.html > http://biopython.org/DIST/docs/tutorial/Tutorial.pdf > > Note we are phasing out support for Python 2.4. We will continue to > support it for at least one further release (i.e. Biopython 1.56). > This could be delayed given feedback from our users (e.g. if this > proves to be a problem in combination with other libraries or a > popular Linux distribution). > > (At least) 10 people have contributed to this release (so far), > including 5 new people - thank you all: > > * Andres Colubri (first contribution) > * Carlos Rios Vera (first contribution) > * Claude Paroz (first contribution) > * Eric Talevich > * Frank Kauff > * Joao Rodrigues (first contribution) > * Konstantin Okonechnikov (first contribution) > * Michiel de Hoon > * Peter Cock > * Tiago Antao > > Source distributions and Windows installers are available from the > downloads page on the Biopython website: > http://www.biopython.org/wiki/Download > > Feedback is welcome through the mailing lists (or bugzilla), > especially if you find something that doesn't work. > > Thank you, > > Peter > Looks good. There are no test failures for the 32/64 bit msvc9 builds for Python 2.6/2.7 and numpy 1.4.1/1.5b2. -- Christoph From biopython at maubp.freeserve.co.uk Tue Aug 24 05:26:17 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 24 Aug 2010 10:26:17 +0100 Subject: [Biopython] Biopython 1.55 beta released (Peter) In-Reply-To: <4C72DD68.20309@uci.edu> References: <4C72DD68.20309@uci.edu> Message-ID: On Mon, Aug 23, 2010 at 9:43 PM, Christoph Gohlke wrote: > > Looks good. There are no test failures for the 32/64 bit msvc9 builds for > Python 2.6/2.7 and numpy 1.4.1/1.5b2. > Thank you - as far as I know you are the only person building Biopython on Windows 64 bit, so that is reassuring. Peter From schaefer at rostlab.org Tue Aug 24 09:37:19 2010 From: schaefer at rostlab.org (Christian Schaefer) Date: Tue, 24 Aug 2010 15:37:19 +0200 Subject: [Biopython] Contact Area Difference as an alternative to RMSD Message-ID: <4C73CB0F.7060100@rostlab.org> Hi, I'd be interested in the above alternative measure for structural difference as desribed in [1]. I know that there exists an implementation to make it useable via Python: It's a wrapper around icm-browser [2] implemented in the Biskit library [3]. However, it's a real pain to get the whole pipeline working and I haven't succeeded so far. So, does anybody know of an alternative implementation of CAD that is easy to use via python? Thanks, Chris [1] Abagyan RA, Totrov MM. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol. 1997 May 9;268(3):678-85. [2] http://www.molsoft.com/index.html [3] http://biskit.pasteur.fr/ -- Dipl.-Bioinf. Christian Schaefer Technical University Munich Department for Bioinformatics Faculty of Computer Science/I12 Boltzmannstr. 3 D-85748 Garching b. Muenchen Germany http://www.rostlab.org/~schaefer From vishal4linux2 at gmail.com Wed Aug 25 07:12:38 2010 From: vishal4linux2 at gmail.com (vishal bhardwa) Date: Wed, 25 Aug 2010 16:42:38 +0530 Subject: [Biopython] installing Biopython in Centos Message-ID: hello sir/mam how can i install biopython on Centos System Pls tell me any solution Vishal Bhardwaj Mb:-91-7696619429 From mitlox at op.pl Wed Aug 25 07:22:24 2010 From: mitlox at op.pl (xyz) Date: Wed, 25 Aug 2010 21:22:24 +1000 Subject: [Biopython] Writting fasta file Message-ID: <4C74FCF0.4070401@op.pl> Hello, the following code saves a multiple fasta file in a list and after reverse complement it writes the content back in a fasta file. in_handle = open(opts.inputFasta, "r") records = list(SeqIO.parse(in_handle, "fasta")) for record in records: record.seq = record.seq.reverse_complement() out_handle = open(opts.outputFasta, "w") SeqIO.write(records, out_handle, "fasta") How is it possible to do it without a list? Thank you in advance. From mitlox at op.pl Wed Aug 25 08:02:00 2010 From: mitlox at op.pl (xyz) Date: Wed, 25 Aug 2010 22:02:00 +1000 Subject: [Biopython] installing Biopython in Centos In-Reply-To: References: Message-ID: <4C750638.8090007@op.pl> Hi, I use Cent OS, but Python 2.6.5 is in my home directory installed and following both methods working fine for me: http://biopython.org/wiki/Download#Installation_Instructions http://biopython.org/wiki/Download#Easy_Install Cheers, On 25/08/10 21:12, vishal bhardwa wrote: > hello sir/mam > > how can i install biopython on Centos System Pls tell me any > solution > > > > > > Vishal Bhardwaj > Mb:-91-7696619429 > _______________________________________________ > Biopython mailing list - Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > > From biopython at maubp.freeserve.co.uk Wed Aug 25 08:59:58 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 25 Aug 2010 13:59:58 +0100 Subject: [Biopython] installing Biopython in Centos In-Reply-To: References: Message-ID: On Wed, Aug 25, 2010 at 12:12 PM, vishal bhardwa wrote: > hello sir/mam > > ? ? ? ? how can i install biopython on Centos System Pls tell me any > solution > > Vishal Bhardwaj > Mb:-91-7696619429 Hello Vishal, CentOS currently comes with Python 2.4, so you should be able to use that and install Biopython from source as normal. However, Python 2.4 is now very out of date so many packages don't support it anymore. It lacks a few useful modules like SQLite3 support and ElementTree for XML parser. It is also noticeable slower than more recent releases, but that may not be an issue for you. NumPy still supports Python 2.4, and Biopython still supports Python 2.4, but we plan to drop support for Python 2.4 after Biopython 1.56 is released (which will be some time later this year). We have servers running CentOS release 5.4 (Final) and CentOS 5.5 (final) where the administrator has installed Python 2.6 at /usr/local/bin/python2.6 or Python 2.7 at /usr/local/bin/python2.7 and Biopython works fine there. It would be worth considering installing Python 2.6 or 2.7. Ask your systems administrator if they can do this for you, or do it yourself under your user directory as "xyz" suggested. Peter From biopython at maubp.freeserve.co.uk Wed Aug 25 09:08:41 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 25 Aug 2010 14:08:41 +0100 Subject: [Biopython] Writting fasta file In-Reply-To: <4C74FCF0.4070401@op.pl> References: <4C74FCF0.4070401@op.pl> Message-ID: On Wed, Aug 25, 2010 at 12:22 PM, xyz wrote: > Hello, > the following code saves a multiple fasta file in a list and after reverse > complement it writes the content back in a fasta file. > > ?in_handle = open(opts.inputFasta, "r") > ?records = list(SeqIO.parse(in_handle, "fasta")) > > ?for record in records: > ? ? ?record.seq = record.seq.reverse_complement() > > ?out_handle = open(opts.outputFasta, "w") > ?SeqIO.write(records, out_handle, "fasta") > > How is it possible to do it without a list? > > Thank you in advance. Hi "xyz", Did you try looking in the tutorial? i.e. http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement You could modify your code to use a generator expression like this: def make_rc(record): """Modifies a SeqRecord in place, and returns it.""" record.seq = record.seq.reverse_complement() return record records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) SeqIO.write(records, out_opts.outputFasta, "fasta") I also changed it to pass filenames directly to SeqIO - its shorter ;) See also this thread about adding a reverse complement method to the SeqRecord which would make this easier: http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html Peter From mjldehoon at yahoo.com Wed Aug 25 09:52:58 2010 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 25 Aug 2010 06:52:58 -0700 (PDT) Subject: [Biopython] Deprecated code to be removed from Biopython Message-ID: <556514.21952.qm@web62405.mail.re1.yahoo.com> Dear all, Below are the bits of code in Biopython that are currently deprecated (with a DeprecationWarning). These have been deprecated since Biopython 1.51, and we are considering to remove them completely for the final release of Biopython 1.55. Any objections? Is anybody still using any of this code? Thanks, --Michiel. Bio.Align.FormatConvert Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter Bio.Entrez.efetch: rettype="genbank" option Bio.Fasta Bio.SCOP.Dom.Parser Bio.SwissProt.SProt Bio.Transcribe Bio.Translate BioSQL.BioSeqDatabase.open_database: driver="psycopg" option From ajperry at pansapiens.com Thu Aug 26 00:03:46 2010 From: ajperry at pansapiens.com (Andrew Perry) Date: Thu, 26 Aug 2010 14:03:46 +1000 Subject: [Biopython] Deprecated code to be removed from Biopython In-Reply-To: <556514.21952.qm@web62405.mail.re1.yahoo.com> References: <556514.21952.qm@web62405.mail.re1.yahoo.com> Message-ID: On 25 August 2010 23:52, Michiel de Hoon wrote: > Dear all, > > Below are the bits of code in Biopython that are currently deprecated (with > a DeprecationWarning). These have been deprecated since Biopython 1.51, and > we are considering to remove them completely for the final release of > Biopython 1.55. Any objections? Is anybody still using any of this code? > > Thanks, > --Michiel. > > Bio.Align.FormatConvert > Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter > Bio.Entrez.efetch: rettype="genbank" option > Bio.Fasta > Bio.SCOP.Dom.Parser > Bio.SwissProt.SProt > Bio.Transcribe > Bio.Translate > BioSQL.BioSeqDatabase.open_database: driver="psycopg" option > > No objections here. I did a quick grep over some of my code from the last two or three years - while I'm still using things like Bio.Align.FormatConvert (probably because I was cut and pasting from even older code), and Bio.SwissProt.SProt in some even older scripts, a quick look at the API documentation for these deprecated parts provides clear and simple pointers on how to migrate, so I'm happy. Good work on the docs in this respect ! Andrew Perry From biopython at maubp.freeserve.co.uk Thu Aug 26 06:57:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 11:57:27 +0100 Subject: [Biopython] Problem with biopython.org domain Message-ID: Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter From jfi.mamede at gmail.com Thu Aug 26 07:02:30 2010 From: jfi.mamede at gmail.com (=?ISO-8859-1?Q?Jo=E3o_Mamede?=) Date: Thu, 26 Aug 2010 13:02:30 +0200 Subject: [Biopython] Something happened to the domain? Message-ID: <4C7649C6.1080503@gmail.com> I was trying to see the new changes in biopython in the website, however when I type biopython.org it asks me if I want to rent the domain. What's the direct ip if the machine is up? Thanks From biopython at maubp.freeserve.co.uk Thu Aug 26 07:15:35 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 12:15:35 +0100 Subject: [Biopython] Something happened to the domain? In-Reply-To: <4C7649C6.1080503@gmail.com> References: <4C7649C6.1080503@gmail.com> Message-ID: On Thu, Aug 26, 2010 at 12:02 PM, Jo?o Mamede wrote: > ?I was trying to see the new changes in biopython in the website, however > when I type biopython.org it asks me if I want to rent the domain. > What's the direct ip if the machine is up? > > Thanks Hi Jo?o, I sent out an email shortly before your query - hopefully you've received it now: http://lists.open-bio.org/pipermail/biopython/2010-August/006712.html Peter From dag at sonsorol.org Thu Aug 26 07:26:57 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 26 Aug 2010 07:26:57 -0400 Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: References: Message-ID: <4C764F81.1060100@sonsorol.org> I manage or am the admin/technical/billing account holder for 24 domains, among them most of the open-bio.org ones. Biopython.org is one that I do not own. Actually since NetSol is offering to let me change DNS maybe I'm the technical contact - have to wait and see on this. Normally for domains I control netsol starts email nagging me constantly - never got emails about this one. However, Networksolutions allows *anyone* with a payment method to renew any domain for any reason. I've renewed biopython.org for a 2-year term, paying out of pocket like I do for all OBF domains so our $$ stays in our bank account. > Order Confirmation > > Order Number: 375229424 > Today's Charges: $65.98 > Future Charges: $0.00 > Credit Card: xxxxxxxxxxx1002 The site should be back up soonish. I can't change the DNS entry that points the website to the expired splash page until netsol processes the renewal. Upcoming domain expiration dates: biomoby.org will expire Oct 1 bior.org will expire Nov 5 biosoap.org will expire Oct 9 -Chris Peter wrote: > Hi all, > > We appear to have a temporary problem with our biopython.org domain, > which I trust the OBF admin team will address shortly. > > As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page > and http://biopython.open-bio.org/DIST/ for the downloads. > > Source code is hosted separately on github, > http://github.com/biopython/biopython/ > > Apologies, > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From mitlox at op.pl Thu Aug 26 07:27:31 2010 From: mitlox at op.pl (xyz) Date: Thu, 26 Aug 2010 21:27:31 +1000 Subject: [Biopython] Writting fasta file In-Reply-To: References: <4C74FCF0.4070401@op.pl> Message-ID: <4C764FA3.6080805@op.pl> On 25/08/10 23:08, Peter wrote: > > Hi "xyz", > > Did you try looking in the tutorial? i.e. > http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement > > You could modify your code to use a generator expression like this: > > def make_rc(record): > """Modifies a SeqRecord in place, and returns it.""" > record.seq = record.seq.reverse_complement() > return record > records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) > SeqIO.write(records, out_opts.outputFasta, "fasta") > > I also changed it to pass filenames directly to SeqIO - its shorter ;) > > See also this thread about adding a reverse complement > method to the SeqRecord which would make this easier: > http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html > > Peter > Thank you for your code it looks much better than mine. In order to save memory is it possible to write each record ie. one by one with SeqIO.write instead of all records at once? From biopython at maubp.freeserve.co.uk Thu Aug 26 07:59:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 12:59:56 +0100 Subject: [Biopython] Writting fasta file In-Reply-To: <4C764FA3.6080805@op.pl> References: <4C74FCF0.4070401@op.pl> <4C764FA3.6080805@op.pl> Message-ID: On Thu, Aug 26, 2010 at 12:27 PM, xyz wrote: > On 25/08/10 23:08, Peter wrote: >> >> Hi "xyz", >> >> Did you try looking in the tutorial? i.e. >> >> http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement >> >> You could modify your code to use a generator expression like this: >> >> def make_rc(record): >> ? ? """Modifies a SeqRecord in place, and returns it.""" >> ? ? record.seq = record.seq.reverse_complement() >> ? ? return record >> records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) >> SeqIO.write(records, out_opts.outputFasta, "fasta") >> >> I also changed it to pass filenames directly to SeqIO - its shorter ;) > > Thank you for your code it looks much better than mine. > > In order to save memory is it possible to write each record ie. one by one > with SeqIO.write instead of all records at once? The code is already doing it one by one. It uses a generator expression (rather than a list or list comprehension which would put all the records into memory at once) to make the reverse complemented records: For writing FASTA files (and most other formats), SeqIO.write() only needs to look at one record at a time, and won't load them all into memory. Peter From chapmanb at 50mail.com Thu Aug 26 07:55:17 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 26 Aug 2010 07:55:17 -0400 Subject: [Biopython] Writting fasta file In-Reply-To: <4C764FA3.6080805@op.pl> References: <4C74FCF0.4070401@op.pl> <4C764FA3.6080805@op.pl> Message-ID: <20100826115517.GW23299@sobchak.mgh.harvard.edu> Hello; > >Did you try looking in the tutorial? i.e. > >http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement > > > >You could modify your code to use a generator expression like this: > > > >def make_rc(record): > > """Modifies a SeqRecord in place, and returns it.""" > > record.seq = record.seq.reverse_complement() > > return record > >records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) > >SeqIO.write(records, out_opts.outputFasta, "fasta") [...] > In order to save memory is it possible to write each record ie. one > by one with SeqIO.write instead of all records at once? That's what Peter's code does. The write function pulls one record at a time from the records generator. In addition to the Biopython documentation, Andrew has a nice tutorial which goes into the details of generators: http://www.dalkescientific.com/writings/NBN/generators.html Brad From biopython at maubp.freeserve.co.uk Thu Aug 26 08:03:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 13:03:48 +0100 Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 domains, > among them most of the open-bio.org ones. > > Biopython.org is one that I do not own. Actually since NetSol is offering to > let me change DNS maybe I'm the technical contact - have to wait and see on > this. Normally for domains I control netsol starts email nagging me > constantly - never got emails about this one. > > > However, Networksolutions allows *anyone* with a payment method to renew any > domain for any reason. > > I've renewed biopython.org for a 2-year term, paying out of pocket like I do > for all OBF domains so our $$ stays in our bank account. > > >> Order Confirmation >> >> Order Number: 375229424 >> Today's Charges: $65.98 >> Future Charges: $0.00 >> Credit Card: xxxxxxxxxxx1002 > > The site should be back up soonish. I can't change the DNS entry that points > the website to the expired splash page until netsol processes the renewal. > > Upcoming domain expiration dates: > > biomoby.org will expire Oct 1 > bior.org will expire Nov 5 > biosoap.org will expire Oct 9 > > > -Chris Thanks Chris :) Will you be able to update the domain's contact details to be consistent with the other Bio* domains? Peter From vishal4linux2 at gmail.com Thu Aug 26 08:16:20 2010 From: vishal4linux2 at gmail.com (vishal bhardwa) Date: Thu, 26 Aug 2010 05:16:20 -0700 Subject: [Biopython] vishal bhardwa wants to chat Message-ID: ----------------------------------------------------------------------- vishal bhardwa wants to stay in better touch using some of Google's coolest new products. If you already have Gmail or Google Talk, visit: http://mail.google.com/mail/b-fa78ca1c25-6ed1ae4af1-rxWDot9g7gySnmbrqygKhSfE2Ro You'll need to click this link to be able to chat with vishal bhardwa. 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From biopython at maubp.freeserve.co.uk Thu Aug 26 08:28:18 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 13:28:18 +0100 Subject: [Biopython] vishal bhardwa wants to chat In-Reply-To: References: Message-ID: On Thu, Aug 26, 2010 at 1:16 PM, vishal bhardwa wrote: > ----------------------------------------------------------------------- > > vishal bhardwa wants to stay in better touch using some of Google's coolest new > products. > > If you already have Gmail or Google Talk, visit ... Hi all, Vishal and other - please try not to sending these kinds of product or service adverts to mailing lists. Thank you, Peter From nje5 at georgetown.edu Thu Aug 26 21:43:08 2010 From: nje5 at georgetown.edu (Nathan J. Edwards) Date: Thu, 26 Aug 2010 21:43:08 -0400 Subject: [Biopython] Problem with Bio.Entrez... Message-ID: <4C77182C.40007@georgetown.edu> Seems to be a problem with Entrez XML parsing: from Bio import Entrez Entrez.email = 'xxxyy at georgetown.edu' handle = Entrez.einfo(db='pubmed') result = Entrez.read(handle) results in: Traceback (most recent call last): File "C:/Documents and Settings/Nathan/My Documents/BCHB524/testing.py", line 5, in result = Entrez.read(handle) File "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py", line 261, in read record = handler.read(handle) File "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 150, in read self.parser.ParseFile(handle) File "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 295, in endElementHandler current[name] = value TypeError: 'str' object does not support item assignment error is in Parser.endElementHandler: current = self.stack[-1] try: current.append(value) except AttributeError: 295: current[name] = value because current is the empty string "". The problem is probably that the empty string shouldn't be on the stack, given the logic here and elsewhere, but a simple test for the empty string does get things working again. current = self.stack[-1] if current == "": return try: current.append(value) except AttributeError: 295: current[name] = value Cheers! - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From mjldehoon at yahoo.com Thu Aug 26 22:40:52 2010 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Thu, 26 Aug 2010 19:40:52 -0700 (PDT) Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C77182C.40007@georgetown.edu> Message-ID: <108175.26561.qm@web62405.mail.re1.yahoo.com> The problem is with the XML returned by NCBI. Currently, the XML returned by einfo contains elements that are not described in the corresponding DTD (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The parser therefore doesn't know how to handle them. Could you write an email to NCBI that einfo generates XML that is inconsistent with the corresponding DTD? Best, --Michiel. --- On Thu, 8/26/10, Nathan J. Edwards wrote: > From: Nathan J. Edwards > Subject: [Biopython] Problem with Bio.Entrez... > To: biopython at lists.open-bio.org > Date: Thursday, August 26, 2010, 9:43 PM > > Seems to be a problem with Entrez XML parsing: > > from Bio import Entrez > Entrez.email = 'xxxyy at georgetown.edu' > > handle = Entrez.einfo(db='pubmed') > result = Entrez.read(handle) > > results in: > > Traceback (most recent call last): > ? File "C:/Documents and Settings/Nathan/My > Documents/BCHB524/testing.py", line 5, in > ? ? result = Entrez.read(handle) > ? File > "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py", > line 261, in read > ? ? record = handler.read(handle) > ? File > "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", > line 150, in read > ? ? self.parser.ParseFile(handle) > ? File > "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", > line 295, in endElementHandler > ? ? current[name] = value > TypeError: 'str' object does not support item assignment > > error is in Parser.endElementHandler: > > ? ? ? ? ? ? current = > self.stack[-1] > ? ? ? ? ? ? try: > ? ? ? ? ? ? ? ? > current.append(value) > ? ? ? ? ? ? except > AttributeError: > 295:? ? ? ? ? ? current[name] > = value > > because current is the empty string "". > > The problem is probably that the empty string shouldn't be > on the stack, given the logic here and elsewhere, but a > simple test for the empty string does get things working > again. > > ? ? ? ? ? ? current = > self.stack[-1] > ??? ? ? if current == "": > ??? ??? return > ? ? ? ? ? ? try: > ? ? ? ? ? ? ? ? > current.append(value) > ? ? ? ? ? ? except > AttributeError: > 295:? ? ? ? ? ? current[name] > = value > > > Cheers! > > - n > > -- Dr. Nathan Edwards? ? ? ? ? > ? ? ? ? ? ? nje5 at georgetown.edu > Department of Biochemistry and Molecular & Cellular > Biology > ? ? ? ? ???Georgetown > University Medical Center > Room 1215, Harris Building? ? ? ? > ? Room 347, Basic Science > 3300 Whitehaven St, NW? ? ? ? ? > ? ? 3900 Reservoir Road, NW > Washington DC 20007? ? ? ? ? > ? ? ? ? ???Washington DC > 20007 > Phone: 202-687-7042? ? ? ? ? > ? ? ? ? ???Phone: > 202-687-1618 > Fax: 202-687-0057? ? ? ? ? ? > ? ? ? ? ? ???Fax: > 202-687-7186 > _______________________________________________ > Biopython mailing list? -? Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > From nje5 at georgetown.edu Fri Aug 27 00:13:29 2010 From: nje5 at georgetown.edu (Nathan J. Edwards) Date: Fri, 27 Aug 2010 00:13:29 -0400 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <108175.26561.qm@web62405.mail.re1.yahoo.com> References: <108175.26561.qm@web62405.mail.re1.yahoo.com> Message-ID: <4C773B69.3050308@georgetown.edu> On 8/26/2010 10:40 PM, Michiel de Hoon wrote: > The problem is with the XML returned by NCBI. Currently, the XML > returned by einfo contains elements that are not described > in the corresponding DTD > (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The > parser therefore doesn't know how to handle them. Could you write an > email to NCBI that einfo generates XML that is inconsistent with the > corresponding DTD? Sent. It would be nice (IWBN) if the parser threw an exception that indicated that the returned XML didn't validate...at least then the (very cryptic!) error message wouldn't look like a logic error in the parser. - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From nje5 at georgetown.edu Fri Aug 27 00:39:06 2010 From: nje5 at georgetown.edu (Nathan J. Edwards) Date: Fri, 27 Aug 2010 00:39:06 -0400 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C773B69.3050308@georgetown.edu> References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> Message-ID: <4C77416A.6030906@georgetown.edu> On 8/27/2010 12:13 AM, Nathan J. Edwards wrote: > > It would be nice (IWBN) if the parser threw an exception that indicated > that the returned XML didn't validate...at least then the (very > cryptic!) error message wouldn't look like a logic error in the parser. Actually, after wading though the Parser.py code some more, the bad element is clearly detected, and an attempt is made to ignore it (the empty string), which then subsequently leads to the TypeError exception in endElementHandler. Maybe the test and return of my first email is sufficient to deal with the empty strings inserted as part of the "ignore it" strategy. And, given the frequency with which NCBI seems to break these things, I _do_ prefer the "ignore it" strategy, if it works. :-) Cheers! - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From biopython at maubp.freeserve.co.uk Fri Aug 27 04:32:57 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:32:57 +0100 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C77416A.6030906@georgetown.edu> References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu> Message-ID: On Fri, Aug 27, 2010 at 5:39 AM, Nathan J. Edwards wrote: > On 8/27/2010 12:13 AM, Nathan J. Edwards wrote: >> >> It would be nice (IWBN) if the parser threw an exception that indicated >> that the returned XML didn't validate...at least then the (very >> cryptic!) error message wouldn't look like a logic error in the parser. > > Actually, after wading though the Parser.py code some more, the bad element > is clearly detected, and an attempt is made to ignore it (the empty string), > which then subsequently leads to the TypeError exception in > endElementHandler. I'd suggest issuing a warning for the bad element, rather than silently ignoring it. > Maybe the test and return of my first email is sufficient to deal with the > empty strings inserted as part of the "ignore it" strategy. > > And, given the frequency with which NCBI seems to break these things, > I _do_ prefer the "ignore it" strategy, if it works. :-) Michiel - does Nathan's fix make sense? We should probably save an example of this broken XML for a unit test... Nathan - have you notified the NCBI about this? I assume you would get an error putting the XML through a validator - if you haven't already done so that would be worthwhile. Or would you rather one of us contact them? Thanks, Peter From biopython at maubp.freeserve.co.uk Fri Aug 27 04:57:04 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:57:04 +0100 Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 > domains, among them most of the open-bio.org ones. ... I've > renewed biopython.org for a 2-year term, ... The site should be > back up soonish. Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Peter From vishal4linux2 at gmail.com Fri Aug 27 05:41:33 2010 From: vishal4linux2 at gmail.com (vishal bhardwa) Date: Fri, 27 Aug 2010 15:11:33 +0530 Subject: [Biopython] module pylab problem on ceton Message-ID: hello friends, how i can install pylab please give any solution i m useing CentOs operating system. thanks in advance vishal From biopython at maubp.freeserve.co.uk Fri Aug 27 05:58:51 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 10:58:51 +0100 Subject: [Biopython] module pylab problem on ceton In-Reply-To: References: Message-ID: On Fri, Aug 27, 2010 at 10:41 AM, vishal bhardwa wrote: > hello friends, > how i can install pylab please give any solution i m useing CentOs operating > system. This isn't really a Biopython question. Try: http://matplotlib.sourceforge.net/users/installing.html Peter From nje5 at georgetown.edu Fri Aug 27 12:10:49 2010 From: nje5 at georgetown.edu (Nathan Edwards) Date: Fri, 27 Aug 2010 12:10:49 -0400 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu> Message-ID: <4C77E389.7080006@georgetown.edu> > I'd suggest issuing a warning for the bad element, rather than silently > ignoring it. Except that I find the warning infrastructure pretty hard to use when I need to turn something off. Other alternatives providing a switch to choose between throwing an exception (probably the default) or silently coping. >> And, given the frequency with which NCBI seems to break these things, >> I _do_ prefer the "ignore it" strategy, if it works. :-) > > Nathan - have you notified the NCBI about this? I assume you would get > an error putting the XML through a validator - if you haven't already done > so that would be worthwhile. Or would you rather one of us contact them? Yes, NCBI has been notified and I just received a response that the developers have been notified. > I will bring this to our developers' attention. However, I will not > be able to provide your with any ETA of the correction/fix or other > comparable actions at this time. Visual inspection is sufficient to verify the element is not mentioned in the DTD, though I could fire up a validating parser I guess. Just did and it confirms the error. - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From mjldehoon at yahoo.com Sat Aug 28 03:47:25 2010 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Sat, 28 Aug 2010 00:47:25 -0700 (PDT) Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C77E389.7080006@georgetown.edu> Message-ID: <226633.67137.qm@web62407.mail.re1.yahoo.com> I think that for Biopython release 1.55, we should silently ignore this error using the fix proposed by Nathan. After the release is out, I suggest we add an optional argument "validate" to the read() and parse() function, defaulting to True. If validate is True, then read()/parse() raise an error if it finds elements in the XML that are not represented in the DTD. If validate is False, then such elements are silently ignored. This will require some other minor changes to the parser, so I'd like to do this after 1.55 is out. --Michiel. --- On Fri, 8/27/10, Nathan Edwards wrote: > From: Nathan Edwards > Subject: Re: [Biopython] Problem with Bio.Entrez... > To: "Peter" > Cc: "Michiel de Hoon" , biopython at lists.open-bio.org > Date: Friday, August 27, 2010, 12:10 PM > > > I'd suggest issuing a warning for the bad element, > rather than silently > > ignoring it. > > Except that I find the warning infrastructure pretty hard > to use when I need to turn something off. > > Other alternatives providing a switch to choose between > throwing an exception (probably the default) or silently > coping. > > >> And, given the frequency with which NCBI seems to > break these things, > >> I _do_ prefer the "ignore it" strategy, if it > works. :-) > > > > Nathan - have you notified the NCBI about this? I > assume you would get > > an error putting the XML through a validator - if you > haven't already done > > so that would be worthwhile. Or would you rather one > of us contact them? > > Yes, NCBI has been notified and I just received a response > that the developers have been notified. > > > I will bring this to our developers' attention. > However, I will not > > be able to provide your with any ETA of the > correction/fix or other > > comparable actions at this time. > > Visual inspection is sufficient to verify the element is > not mentioned in the DTD, though I could fire up a > validating parser I guess. Just did and it confirms the > error. > > - n > > -- Dr. Nathan Edwards? ? ? ? ? > ? ? ? ? ? ? nje5 at georgetown.edu > Department of Biochemistry and Molecular & Cellular > Biology > ? ? ? ? ???Georgetown > University Medical Center > Room 1215, Harris Building? ? ? ? > ? Room 347, Basic Science > 3300 Whitehaven St, NW? ? ? ? ? > ? ? 3900 Reservoir Road, NW > Washington DC 20007? ? ? ? ? > ? ? ? ? ???Washington DC > 20007 > Phone: 202-687-7042? ? ? ? ? > ? ? ? ? ???Phone: > 202-687-1618 > Fax: 202-687-0057? ? ? ? ? ? > ? ? ? ? ? ???Fax: > 202-687-7186 > From biopython at maubp.freeserve.co.uk Sat Aug 28 07:32:03 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 28 Aug 2010 12:32:03 +0100 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <226633.67137.qm@web62407.mail.re1.yahoo.com> References: <4C77E389.7080006@georgetown.edu> <226633.67137.qm@web62407.mail.re1.yahoo.com> Message-ID: On Sat, Aug 28, 2010 at 8:47 AM, Michiel de Hoon wrote: > I think that for Biopython release 1.55, we should silently ignore this > error using the fix proposed by Nathan. After the release is out, I > suggest we add an optional argument "validate" to the read() and > parse() function, defaulting to True. If validate is True, then read()/ > parse() raise an error if it finds elements in the XML that are not > represented in the DTD. If validate is False, then such elements > are silently ignored. This will require some other minor changes > to the parser, so I'd like to do this after 1.55 is out. > > --Michiel. Sounds good :) Peter From p.j.a.cock at googlemail.com Tue Aug 31 19:00:37 2010 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 1 Sep 2010 00:00:37 +0100 Subject: [Biopython] Biopython 1.55 released Message-ID: Dear Biopythoneers, After the beta earlier this month (thank you to everyone who helped test this), we?ve just released Biopython 1.55 . For full details see: http://news.open-bio.org/news/2010/08/biopython-1-55-released/ Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 12 people have contributed to this release, including 6 new people ? thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Cymon Cox * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Nathan Edwards (first contribution) * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download As usual, feedback is most welcome on the mailing lists (or bugzilla). Regards, Peter P.S. You can follow Biopython on Twitter, http://twitter.com/biopython From Achim.Treumann at NEPAF.com Sun Aug 1 01:53:17 2010 From: Achim.Treumann at NEPAF.com (Achim Treumann) Date: Sun, 1 Aug 2010 02:53:17 +0100 Subject: [Biopython] problem with SeqIO.index() and get_raw References: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local> Message-ID: <01798D2396253A449511F31F1CDE83550C3E6D@srv1.NEPAF.local> Hi Peter, Jordan andd others, many thanks for the fast replies. You are obviously right - installing 1.54 got me rolling. I now noticed that the tutorial I was working with was indeed 1.54 (should have checked that when I downloaded it separately from the distribution). When I was going through the tutorial I did not realise that the version I was working with was not 1.54... Don't think that it would be essential to put this into the FAQ - neither google nor searching this discussion list brought up other people who were struggling with this, I must have been the only one too thick to check version numbers :-) Thanks a lot again for your rapid help, Achim -----Original Message----- From: p.j.a.cock at googlemail.com on behalf of Peter Sent: Sat 31/07/2010 18:16 To: Achim Treumann Cc: biopython at lists.open-bio.org Subject: Re: [Biopython] problem with SeqIO.index() and get_raw On Sat, Jul 31, 2010 at 7:05 AM, Achim Treumann wrote: > Dear all, > > I am new to biopython and trying to familiarise myself with its utilities. > When I was trying to parse a swissprot.dat file to then copy the full > data back using the get_raw attribute, I got stuck (Biopython 1.53, > Python 2.6 on WinXP). > >... > > As I am typing, I realise that get_raw might only have been > implemented in Biopython 1.54... I will post this anyway, and if > upgrading sorts it, I will send a reply. Hi Achim, Well guessed. Yes, get_raw was added in Biopython 1.54, see http://news.open-bio.org/news/2010/05/biopython-release-154/ Are you reading the current tutorial on line (rather than the version shipped with Biopython 1.53)? It does mention this, although maybe it could be in the FAQ as well... would that help? Peter From rmb32 at cornell.edu Sun Aug 1 19:17:14 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sun, 01 Aug 2010 12:17:14 -0700 Subject: [Biopython] GMOD Evo Hackathon Open Call for Participation Message-ID: <4C55C83A.3060700@cornell.edu> We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From phosse1 at students.towson.edu Tue Aug 3 23:53:33 2010 From: phosse1 at students.towson.edu (Parsa Hosseini) Date: Tue, 3 Aug 2010 19:53:33 -0400 Subject: [Biopython] Biopython SUBA interface Message-ID: Hi everyone, I have some python cgi scripts which interface with the Arabidopsis thaliana SUBA database. I'd like to contribute such scripts (and hopefully much more). I was curious how I can go about submitting such code and/or if anyone would find such a script/interface of use? Thanks alot, -------------------------------------------- Parsa Hosseini Parsa.Hosseini at ars.usda.gov http://tiger.towson.edu/~phosse1/ 301-875-6525 From biopython at maubp.freeserve.co.uk Wed Aug 4 08:12:07 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 4 Aug 2010 09:12:07 +0100 Subject: [Biopython] Biopython SUBA interface In-Reply-To: References: Message-ID: On Wed, Aug 4, 2010 at 12:53 AM, Parsa Hosseini wrote: > Hi everyone, > I have some python cgi scripts which interface with the Arabidopsis > thaliana SUBA database. > I'd like to contribute such scripts (and hopefully much more). I was > curious how I can go about submitting such code and/or if anyone > would find such a script/interface of use? > Thanks alot, Hi Parsa, Are these stand alone scripts that you would use at the command line, or a Python module you can use in a Python script? Either way we could include them... I had a quick look at http://suba.plantenergy.uwa.edu.au/ and it isn't clear if they have an official API. Are you doing this by building the HTTP request and then parsing the HTML results? If so, that is worrying for two reasons. First, it is fragile and will need updates whenever the site makes changes to their layout (something that has happened to other HTML parsers in Biopython that have since been deprecated and removed). Secondly, in the absence of an official API are there any usage guidelines? The SUBA team may not be happy with people running scripts that could use up far more resources than several people using the website interface. As to would anyone find such a script/interface of use, well, personally probably not in my current work. But I'm sure there are people using Biopython working on plant genomes and Arabidopsis thaliana. Regards, Peter From biopython at maubp.freeserve.co.uk Wed Aug 11 15:14:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 11 Aug 2010 16:14:27 +0100 Subject: [Biopython] Using a dictionary rather than list for hierachy in Bio.SCOP.Cla Message-ID: Dear Biopythoneers - especially those using SCOP, Jeffrey Finkelstein has proposed a change to the Record class in Bio.SCOP.Cla to use a dictionary rather than a list for the hierarchy member to better match the SCOP specification, see his email quoted below and Bug 3109 for details: http://bugzilla.open-bio.org/show_bug.cgi?id=3109 This would be a backwards incompatible change, so feedback from anyone using Biopython's SCOP module would be important in deciding how to proceed. Comments please? Thank you, Peter On the dev list Jeffrey Finkelstein wrote: > I have submitted a bug report and a patch for a current feature of the > Bio.SCOP.Cla module that makes using it somewhat difficult. Specifically, > the Bio.Scop.Cla.Record class has a "hierarchy" member which is currently a > list, but should be a dictionary, according to the SCOP parseable > classification file format "specification" (it is an informal specification) > here: > http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html#scop-parseable-files. > > For a usage example, see the comments I have made at: > http://bugzilla.open-bio.org/show_bug.cgi?id=3109 > > I have CC'ed the original author of the module. Gavin (or anyone else), do > you have any objections to this change? > > Jeffrey See http://lists.open-bio.org/pipermail/biopython-dev/2010-August/008134.html From biopython at maubp.freeserve.co.uk Thu Aug 19 15:43:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 19 Aug 2010 16:43:56 +0100 Subject: [Biopython] Biopython 1.55 beta released Message-ID: Dear Biopythoneers, We?ve just released a beta of Biopython 1.55 for user testing, as announced on the news server (which has RSS and atom feeds) and on twitter: http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ http://twitter.com/biopython Since Biopython 1.54 was released three months ago, we?ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we?ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we?ve accidentally broken things ? which is why we?re doing this beta release. In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 10 people have contributed to this release (so far), including 5 new people - thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download Feedback is welcome through the mailing lists (or bugzilla), especially if you find something that doesn't work. Thank you, Peter From rmb32 at cornell.edu Thu Aug 19 17:09:45 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 19 Aug 2010 10:09:45 -0700 Subject: [Biopython] reminder: Aug 25 deadline for GMOD Hackathon application Message-ID: <4C6D6559.3080809@cornell.edu> Hi all, This is your one-week reminder: the deadline for open applications to the GMOD Evo hackathon is Wednesday, August 25th. Rob ======================================== We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From biopython at maubp.freeserve.co.uk Mon Aug 23 16:05:43 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 23 Aug 2010 17:05:43 +0100 Subject: [Biopython] Biopython 1.55 beta released In-Reply-To: References: Message-ID: On Thu, Aug 19, 2010 at 4:43 PM, Peter wrote: > Dear Biopythoneers, > > We?ve just released a beta of Biopython 1.55 for user testing, as > announced on the news server (which has RSS and atom feeds) and on > twitter: > http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ > http://twitter.com/biopython > > ... > > Feedback is welcome through the mailing lists (or bugzilla), > especially if you find something that doesn't work. Hi all, Is no news good news? So far there have been no problems reported. I've had a least one person report (off list) that the windows installers worked fine for them on Windows XP (32bit). Any other feedback on the beta? Thanks Peter From cgohlke at uci.edu Mon Aug 23 20:43:20 2010 From: cgohlke at uci.edu (Christoph Gohlke) Date: Mon, 23 Aug 2010 13:43:20 -0700 Subject: [Biopython] Biopython 1.55 beta released (Peter) In-Reply-To: References: Message-ID: <4C72DD68.20309@uci.edu> > Dear Biopythoneers, > > We?ve just released a beta of Biopython 1.55 for user testing, as > announced on the news server (which has RSS and atom feeds) and on > twitter: > http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ > http://twitter.com/biopython > > Since Biopython 1.54 was released three months ago, we?ve made a good > start on work for Python 3 support (via the 2to3 script), but as a > side effect of this we?ve had to update quite a lot of the older parts > of the library. Although the unit tests are all fine, there is a small > but real chance that we?ve accidentally broken things ? which is why > we?re doing this beta release. > > In terms of new features, the most noticeable highlight is that the > command line tool application wrapper classes are now executable, > which should make it much easier to call external tools. This is > described in the updated documentation. > http://biopython.org/DIST/docs/tutorial/Tutorial.html > http://biopython.org/DIST/docs/tutorial/Tutorial.pdf > > Note we are phasing out support for Python 2.4. We will continue to > support it for at least one further release (i.e. Biopython 1.56). > This could be delayed given feedback from our users (e.g. if this > proves to be a problem in combination with other libraries or a > popular Linux distribution). > > (At least) 10 people have contributed to this release (so far), > including 5 new people - thank you all: > > * Andres Colubri (first contribution) > * Carlos Rios Vera (first contribution) > * Claude Paroz (first contribution) > * Eric Talevich > * Frank Kauff > * Joao Rodrigues (first contribution) > * Konstantin Okonechnikov (first contribution) > * Michiel de Hoon > * Peter Cock > * Tiago Antao > > Source distributions and Windows installers are available from the > downloads page on the Biopython website: > http://www.biopython.org/wiki/Download > > Feedback is welcome through the mailing lists (or bugzilla), > especially if you find something that doesn't work. > > Thank you, > > Peter > Looks good. There are no test failures for the 32/64 bit msvc9 builds for Python 2.6/2.7 and numpy 1.4.1/1.5b2. -- Christoph From biopython at maubp.freeserve.co.uk Tue Aug 24 09:26:17 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 24 Aug 2010 10:26:17 +0100 Subject: [Biopython] Biopython 1.55 beta released (Peter) In-Reply-To: <4C72DD68.20309@uci.edu> References: <4C72DD68.20309@uci.edu> Message-ID: On Mon, Aug 23, 2010 at 9:43 PM, Christoph Gohlke wrote: > > Looks good. There are no test failures for the 32/64 bit msvc9 builds for > Python 2.6/2.7 and numpy 1.4.1/1.5b2. > Thank you - as far as I know you are the only person building Biopython on Windows 64 bit, so that is reassuring. Peter From schaefer at rostlab.org Tue Aug 24 13:37:19 2010 From: schaefer at rostlab.org (Christian Schaefer) Date: Tue, 24 Aug 2010 15:37:19 +0200 Subject: [Biopython] Contact Area Difference as an alternative to RMSD Message-ID: <4C73CB0F.7060100@rostlab.org> Hi, I'd be interested in the above alternative measure for structural difference as desribed in [1]. I know that there exists an implementation to make it useable via Python: It's a wrapper around icm-browser [2] implemented in the Biskit library [3]. However, it's a real pain to get the whole pipeline working and I haven't succeeded so far. So, does anybody know of an alternative implementation of CAD that is easy to use via python? Thanks, Chris [1] Abagyan RA, Totrov MM. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol. 1997 May 9;268(3):678-85. [2] http://www.molsoft.com/index.html [3] http://biskit.pasteur.fr/ -- Dipl.-Bioinf. Christian Schaefer Technical University Munich Department for Bioinformatics Faculty of Computer Science/I12 Boltzmannstr. 3 D-85748 Garching b. Muenchen Germany http://www.rostlab.org/~schaefer From vishal4linux2 at gmail.com Wed Aug 25 11:12:38 2010 From: vishal4linux2 at gmail.com (vishal bhardwa) Date: Wed, 25 Aug 2010 16:42:38 +0530 Subject: [Biopython] installing Biopython in Centos Message-ID: hello sir/mam how can i install biopython on Centos System Pls tell me any solution Vishal Bhardwaj Mb:-91-7696619429 From mitlox at op.pl Wed Aug 25 11:22:24 2010 From: mitlox at op.pl (xyz) Date: Wed, 25 Aug 2010 21:22:24 +1000 Subject: [Biopython] Writting fasta file Message-ID: <4C74FCF0.4070401@op.pl> Hello, the following code saves a multiple fasta file in a list and after reverse complement it writes the content back in a fasta file. in_handle = open(opts.inputFasta, "r") records = list(SeqIO.parse(in_handle, "fasta")) for record in records: record.seq = record.seq.reverse_complement() out_handle = open(opts.outputFasta, "w") SeqIO.write(records, out_handle, "fasta") How is it possible to do it without a list? Thank you in advance. From mitlox at op.pl Wed Aug 25 12:02:00 2010 From: mitlox at op.pl (xyz) Date: Wed, 25 Aug 2010 22:02:00 +1000 Subject: [Biopython] installing Biopython in Centos In-Reply-To: References: Message-ID: <4C750638.8090007@op.pl> Hi, I use Cent OS, but Python 2.6.5 is in my home directory installed and following both methods working fine for me: http://biopython.org/wiki/Download#Installation_Instructions http://biopython.org/wiki/Download#Easy_Install Cheers, On 25/08/10 21:12, vishal bhardwa wrote: > hello sir/mam > > how can i install biopython on Centos System Pls tell me any > solution > > > > > > Vishal Bhardwaj > Mb:-91-7696619429 > _______________________________________________ > Biopython mailing list - Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > > From biopython at maubp.freeserve.co.uk Wed Aug 25 12:59:58 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 25 Aug 2010 13:59:58 +0100 Subject: [Biopython] installing Biopython in Centos In-Reply-To: References: Message-ID: On Wed, Aug 25, 2010 at 12:12 PM, vishal bhardwa wrote: > hello sir/mam > > ? ? ? ? how can i install biopython on Centos System Pls tell me any > solution > > Vishal Bhardwaj > Mb:-91-7696619429 Hello Vishal, CentOS currently comes with Python 2.4, so you should be able to use that and install Biopython from source as normal. However, Python 2.4 is now very out of date so many packages don't support it anymore. It lacks a few useful modules like SQLite3 support and ElementTree for XML parser. It is also noticeable slower than more recent releases, but that may not be an issue for you. NumPy still supports Python 2.4, and Biopython still supports Python 2.4, but we plan to drop support for Python 2.4 after Biopython 1.56 is released (which will be some time later this year). We have servers running CentOS release 5.4 (Final) and CentOS 5.5 (final) where the administrator has installed Python 2.6 at /usr/local/bin/python2.6 or Python 2.7 at /usr/local/bin/python2.7 and Biopython works fine there. It would be worth considering installing Python 2.6 or 2.7. Ask your systems administrator if they can do this for you, or do it yourself under your user directory as "xyz" suggested. Peter From biopython at maubp.freeserve.co.uk Wed Aug 25 13:08:41 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 25 Aug 2010 14:08:41 +0100 Subject: [Biopython] Writting fasta file In-Reply-To: <4C74FCF0.4070401@op.pl> References: <4C74FCF0.4070401@op.pl> Message-ID: On Wed, Aug 25, 2010 at 12:22 PM, xyz wrote: > Hello, > the following code saves a multiple fasta file in a list and after reverse > complement it writes the content back in a fasta file. > > ?in_handle = open(opts.inputFasta, "r") > ?records = list(SeqIO.parse(in_handle, "fasta")) > > ?for record in records: > ? ? ?record.seq = record.seq.reverse_complement() > > ?out_handle = open(opts.outputFasta, "w") > ?SeqIO.write(records, out_handle, "fasta") > > How is it possible to do it without a list? > > Thank you in advance. Hi "xyz", Did you try looking in the tutorial? i.e. http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement You could modify your code to use a generator expression like this: def make_rc(record): """Modifies a SeqRecord in place, and returns it.""" record.seq = record.seq.reverse_complement() return record records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) SeqIO.write(records, out_opts.outputFasta, "fasta") I also changed it to pass filenames directly to SeqIO - its shorter ;) See also this thread about adding a reverse complement method to the SeqRecord which would make this easier: http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html Peter From mjldehoon at yahoo.com Wed Aug 25 13:52:58 2010 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 25 Aug 2010 06:52:58 -0700 (PDT) Subject: [Biopython] Deprecated code to be removed from Biopython Message-ID: <556514.21952.qm@web62405.mail.re1.yahoo.com> Dear all, Below are the bits of code in Biopython that are currently deprecated (with a DeprecationWarning). These have been deprecated since Biopython 1.51, and we are considering to remove them completely for the final release of Biopython 1.55. Any objections? Is anybody still using any of this code? Thanks, --Michiel. Bio.Align.FormatConvert Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter Bio.Entrez.efetch: rettype="genbank" option Bio.Fasta Bio.SCOP.Dom.Parser Bio.SwissProt.SProt Bio.Transcribe Bio.Translate BioSQL.BioSeqDatabase.open_database: driver="psycopg" option From ajperry at pansapiens.com Thu Aug 26 04:03:46 2010 From: ajperry at pansapiens.com (Andrew Perry) Date: Thu, 26 Aug 2010 14:03:46 +1000 Subject: [Biopython] Deprecated code to be removed from Biopython In-Reply-To: <556514.21952.qm@web62405.mail.re1.yahoo.com> References: <556514.21952.qm@web62405.mail.re1.yahoo.com> Message-ID: On 25 August 2010 23:52, Michiel de Hoon wrote: > Dear all, > > Below are the bits of code in Biopython that are currently deprecated (with > a DeprecationWarning). These have been deprecated since Biopython 1.51, and > we are considering to remove them completely for the final release of > Biopython 1.55. Any objections? Is anybody still using any of this code? > > Thanks, > --Michiel. > > Bio.Align.FormatConvert > Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter > Bio.Entrez.efetch: rettype="genbank" option > Bio.Fasta > Bio.SCOP.Dom.Parser > Bio.SwissProt.SProt > Bio.Transcribe > Bio.Translate > BioSQL.BioSeqDatabase.open_database: driver="psycopg" option > > No objections here. I did a quick grep over some of my code from the last two or three years - while I'm still using things like Bio.Align.FormatConvert (probably because I was cut and pasting from even older code), and Bio.SwissProt.SProt in some even older scripts, a quick look at the API documentation for these deprecated parts provides clear and simple pointers on how to migrate, so I'm happy. Good work on the docs in this respect ! Andrew Perry From biopython at maubp.freeserve.co.uk Thu Aug 26 10:57:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 11:57:27 +0100 Subject: [Biopython] Problem with biopython.org domain Message-ID: Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter From jfi.mamede at gmail.com Thu Aug 26 11:02:30 2010 From: jfi.mamede at gmail.com (=?ISO-8859-1?Q?Jo=E3o_Mamede?=) Date: Thu, 26 Aug 2010 13:02:30 +0200 Subject: [Biopython] Something happened to the domain? Message-ID: <4C7649C6.1080503@gmail.com> I was trying to see the new changes in biopython in the website, however when I type biopython.org it asks me if I want to rent the domain. What's the direct ip if the machine is up? Thanks From biopython at maubp.freeserve.co.uk Thu Aug 26 11:15:35 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 12:15:35 +0100 Subject: [Biopython] Something happened to the domain? In-Reply-To: <4C7649C6.1080503@gmail.com> References: <4C7649C6.1080503@gmail.com> Message-ID: On Thu, Aug 26, 2010 at 12:02 PM, Jo?o Mamede wrote: > ?I was trying to see the new changes in biopython in the website, however > when I type biopython.org it asks me if I want to rent the domain. > What's the direct ip if the machine is up? > > Thanks Hi Jo?o, I sent out an email shortly before your query - hopefully you've received it now: http://lists.open-bio.org/pipermail/biopython/2010-August/006712.html Peter From dag at sonsorol.org Thu Aug 26 11:26:57 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 26 Aug 2010 07:26:57 -0400 Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: References: Message-ID: <4C764F81.1060100@sonsorol.org> I manage or am the admin/technical/billing account holder for 24 domains, among them most of the open-bio.org ones. Biopython.org is one that I do not own. Actually since NetSol is offering to let me change DNS maybe I'm the technical contact - have to wait and see on this. Normally for domains I control netsol starts email nagging me constantly - never got emails about this one. However, Networksolutions allows *anyone* with a payment method to renew any domain for any reason. I've renewed biopython.org for a 2-year term, paying out of pocket like I do for all OBF domains so our $$ stays in our bank account. > Order Confirmation > > Order Number: 375229424 > Today's Charges: $65.98 > Future Charges: $0.00 > Credit Card: xxxxxxxxxxx1002 The site should be back up soonish. I can't change the DNS entry that points the website to the expired splash page until netsol processes the renewal. Upcoming domain expiration dates: biomoby.org will expire Oct 1 bior.org will expire Nov 5 biosoap.org will expire Oct 9 -Chris Peter wrote: > Hi all, > > We appear to have a temporary problem with our biopython.org domain, > which I trust the OBF admin team will address shortly. > > As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page > and http://biopython.open-bio.org/DIST/ for the downloads. > > Source code is hosted separately on github, > http://github.com/biopython/biopython/ > > Apologies, > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From mitlox at op.pl Thu Aug 26 11:27:31 2010 From: mitlox at op.pl (xyz) Date: Thu, 26 Aug 2010 21:27:31 +1000 Subject: [Biopython] Writting fasta file In-Reply-To: References: <4C74FCF0.4070401@op.pl> Message-ID: <4C764FA3.6080805@op.pl> On 25/08/10 23:08, Peter wrote: > > Hi "xyz", > > Did you try looking in the tutorial? i.e. > http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement > > You could modify your code to use a generator expression like this: > > def make_rc(record): > """Modifies a SeqRecord in place, and returns it.""" > record.seq = record.seq.reverse_complement() > return record > records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) > SeqIO.write(records, out_opts.outputFasta, "fasta") > > I also changed it to pass filenames directly to SeqIO - its shorter ;) > > See also this thread about adding a reverse complement > method to the SeqRecord which would make this easier: > http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html > > Peter > Thank you for your code it looks much better than mine. In order to save memory is it possible to write each record ie. one by one with SeqIO.write instead of all records at once? From biopython at maubp.freeserve.co.uk Thu Aug 26 11:59:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 12:59:56 +0100 Subject: [Biopython] Writting fasta file In-Reply-To: <4C764FA3.6080805@op.pl> References: <4C74FCF0.4070401@op.pl> <4C764FA3.6080805@op.pl> Message-ID: On Thu, Aug 26, 2010 at 12:27 PM, xyz wrote: > On 25/08/10 23:08, Peter wrote: >> >> Hi "xyz", >> >> Did you try looking in the tutorial? i.e. >> >> http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement >> >> You could modify your code to use a generator expression like this: >> >> def make_rc(record): >> ? ? """Modifies a SeqRecord in place, and returns it.""" >> ? ? record.seq = record.seq.reverse_complement() >> ? ? return record >> records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) >> SeqIO.write(records, out_opts.outputFasta, "fasta") >> >> I also changed it to pass filenames directly to SeqIO - its shorter ;) > > Thank you for your code it looks much better than mine. > > In order to save memory is it possible to write each record ie. one by one > with SeqIO.write instead of all records at once? The code is already doing it one by one. It uses a generator expression (rather than a list or list comprehension which would put all the records into memory at once) to make the reverse complemented records: For writing FASTA files (and most other formats), SeqIO.write() only needs to look at one record at a time, and won't load them all into memory. Peter From chapmanb at 50mail.com Thu Aug 26 11:55:17 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 26 Aug 2010 07:55:17 -0400 Subject: [Biopython] Writting fasta file In-Reply-To: <4C764FA3.6080805@op.pl> References: <4C74FCF0.4070401@op.pl> <4C764FA3.6080805@op.pl> Message-ID: <20100826115517.GW23299@sobchak.mgh.harvard.edu> Hello; > >Did you try looking in the tutorial? i.e. > >http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-reverse-complement > > > >You could modify your code to use a generator expression like this: > > > >def make_rc(record): > > """Modifies a SeqRecord in place, and returns it.""" > > record.seq = record.seq.reverse_complement() > > return record > >records = (make_rc(r) for r in SeqIO.parse(in_opts.inputFasta, "fasta")) > >SeqIO.write(records, out_opts.outputFasta, "fasta") [...] > In order to save memory is it possible to write each record ie. one > by one with SeqIO.write instead of all records at once? That's what Peter's code does. The write function pulls one record at a time from the records generator. In addition to the Biopython documentation, Andrew has a nice tutorial which goes into the details of generators: http://www.dalkescientific.com/writings/NBN/generators.html Brad From biopython at maubp.freeserve.co.uk Thu Aug 26 12:03:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 13:03:48 +0100 Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 domains, > among them most of the open-bio.org ones. > > Biopython.org is one that I do not own. Actually since NetSol is offering to > let me change DNS maybe I'm the technical contact - have to wait and see on > this. Normally for domains I control netsol starts email nagging me > constantly - never got emails about this one. > > > However, Networksolutions allows *anyone* with a payment method to renew any > domain for any reason. > > I've renewed biopython.org for a 2-year term, paying out of pocket like I do > for all OBF domains so our $$ stays in our bank account. > > >> Order Confirmation >> >> Order Number: 375229424 >> Today's Charges: $65.98 >> Future Charges: $0.00 >> Credit Card: xxxxxxxxxxx1002 > > The site should be back up soonish. I can't change the DNS entry that points > the website to the expired splash page until netsol processes the renewal. > > Upcoming domain expiration dates: > > biomoby.org will expire Oct 1 > bior.org will expire Nov 5 > biosoap.org will expire Oct 9 > > > -Chris Thanks Chris :) Will you be able to update the domain's contact details to be consistent with the other Bio* domains? Peter From vishal4linux2 at gmail.com Thu Aug 26 12:16:20 2010 From: vishal4linux2 at gmail.com (vishal bhardwa) Date: Thu, 26 Aug 2010 05:16:20 -0700 Subject: [Biopython] vishal bhardwa wants to chat Message-ID: ----------------------------------------------------------------------- vishal bhardwa wants to stay in better touch using some of Google's coolest new products. If you already have Gmail or Google Talk, visit: http://mail.google.com/mail/b-fa78ca1c25-6ed1ae4af1-rxWDot9g7gySnmbrqygKhSfE2Ro You'll need to click this link to be able to chat with vishal bhardwa. To get Gmail - a free email account from Google with over 2,800 megabytes of storage - and chat with vishal bhardwa, visit: http://mail.google.com/mail/a-fa78ca1c25-6ed1ae4af1-rxWDot9g7gySnmbrqygKhSfE2Ro Gmail offers: - Instant messaging right inside Gmail - Powerful spam protection - Built-in search for finding your messages and a helpful way of organizing emails into "conversations" - No pop-up ads or untargeted banners - just text ads and related information that are relevant to the content of your messages All this, and its yours for free. But wait, there's more! By opening a Gmail account, you also get access to Google Talk, Google's instant messaging service: http://www.google.com/talk/ Google Talk offers: - Web-based chat that you can use anywhere, without a download - A contact list that's synchronized with your Gmail account - Free, high quality PC-to-PC voice calls when you download the Google Talk client We're working hard to add new features and make improvements, so we might also ask for your comments and suggestions periodically. We appreciate your help in making our products even better! Thanks, The Google Team To learn more about Gmail and Google Talk, visit: http://mail.google.com/mail/help/about.html http://www.google.com/talk/about.html (If clicking the URLs in this message does not work, copy and paste them into the address bar of your browser). From biopython at maubp.freeserve.co.uk Thu Aug 26 12:28:18 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 13:28:18 +0100 Subject: [Biopython] vishal bhardwa wants to chat In-Reply-To: References: Message-ID: On Thu, Aug 26, 2010 at 1:16 PM, vishal bhardwa wrote: > ----------------------------------------------------------------------- > > vishal bhardwa wants to stay in better touch using some of Google's coolest new > products. > > If you already have Gmail or Google Talk, visit ... Hi all, Vishal and other - please try not to sending these kinds of product or service adverts to mailing lists. Thank you, Peter From nje5 at georgetown.edu Fri Aug 27 01:43:08 2010 From: nje5 at georgetown.edu (Nathan J. Edwards) Date: Thu, 26 Aug 2010 21:43:08 -0400 Subject: [Biopython] Problem with Bio.Entrez... Message-ID: <4C77182C.40007@georgetown.edu> Seems to be a problem with Entrez XML parsing: from Bio import Entrez Entrez.email = 'xxxyy at georgetown.edu' handle = Entrez.einfo(db='pubmed') result = Entrez.read(handle) results in: Traceback (most recent call last): File "C:/Documents and Settings/Nathan/My Documents/BCHB524/testing.py", line 5, in result = Entrez.read(handle) File "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py", line 261, in read record = handler.read(handle) File "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 150, in read self.parser.ParseFile(handle) File "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 295, in endElementHandler current[name] = value TypeError: 'str' object does not support item assignment error is in Parser.endElementHandler: current = self.stack[-1] try: current.append(value) except AttributeError: 295: current[name] = value because current is the empty string "". The problem is probably that the empty string shouldn't be on the stack, given the logic here and elsewhere, but a simple test for the empty string does get things working again. current = self.stack[-1] if current == "": return try: current.append(value) except AttributeError: 295: current[name] = value Cheers! - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From mjldehoon at yahoo.com Fri Aug 27 02:40:52 2010 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Thu, 26 Aug 2010 19:40:52 -0700 (PDT) Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C77182C.40007@georgetown.edu> Message-ID: <108175.26561.qm@web62405.mail.re1.yahoo.com> The problem is with the XML returned by NCBI. Currently, the XML returned by einfo contains elements that are not described in the corresponding DTD (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The parser therefore doesn't know how to handle them. Could you write an email to NCBI that einfo generates XML that is inconsistent with the corresponding DTD? Best, --Michiel. --- On Thu, 8/26/10, Nathan J. Edwards wrote: > From: Nathan J. Edwards > Subject: [Biopython] Problem with Bio.Entrez... > To: biopython at lists.open-bio.org > Date: Thursday, August 26, 2010, 9:43 PM > > Seems to be a problem with Entrez XML parsing: > > from Bio import Entrez > Entrez.email = 'xxxyy at georgetown.edu' > > handle = Entrez.einfo(db='pubmed') > result = Entrez.read(handle) > > results in: > > Traceback (most recent call last): > ? File "C:/Documents and Settings/Nathan/My > Documents/BCHB524/testing.py", line 5, in > ? ? result = Entrez.read(handle) > ? File > "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py", > line 261, in read > ? ? record = handler.read(handle) > ? File > "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", > line 150, in read > ? ? self.parser.ParseFile(handle) > ? File > "C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", > line 295, in endElementHandler > ? ? current[name] = value > TypeError: 'str' object does not support item assignment > > error is in Parser.endElementHandler: > > ? ? ? ? ? ? current = > self.stack[-1] > ? ? ? ? ? ? try: > ? ? ? ? ? ? ? ? > current.append(value) > ? ? ? ? ? ? except > AttributeError: > 295:? ? ? ? ? ? current[name] > = value > > because current is the empty string "". > > The problem is probably that the empty string shouldn't be > on the stack, given the logic here and elsewhere, but a > simple test for the empty string does get things working > again. > > ? ? ? ? ? ? current = > self.stack[-1] > ??? ? ? if current == "": > ??? ??? return > ? ? ? ? ? ? try: > ? ? ? ? ? ? ? ? > current.append(value) > ? ? ? ? ? ? except > AttributeError: > 295:? ? ? ? ? ? current[name] > = value > > > Cheers! > > - n > > -- Dr. Nathan Edwards? ? ? ? ? > ? ? ? ? ? ? nje5 at georgetown.edu > Department of Biochemistry and Molecular & Cellular > Biology > ? ? ? ? ???Georgetown > University Medical Center > Room 1215, Harris Building? ? ? ? > ? Room 347, Basic Science > 3300 Whitehaven St, NW? ? ? ? ? > ? ? 3900 Reservoir Road, NW > Washington DC 20007? ? ? ? ? > ? ? ? ? ???Washington DC > 20007 > Phone: 202-687-7042? ? ? ? ? > ? ? ? ? ???Phone: > 202-687-1618 > Fax: 202-687-0057? ? ? ? ? ? > ? ? ? ? ? ???Fax: > 202-687-7186 > _______________________________________________ > Biopython mailing list? -? Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > From nje5 at georgetown.edu Fri Aug 27 04:13:29 2010 From: nje5 at georgetown.edu (Nathan J. Edwards) Date: Fri, 27 Aug 2010 00:13:29 -0400 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <108175.26561.qm@web62405.mail.re1.yahoo.com> References: <108175.26561.qm@web62405.mail.re1.yahoo.com> Message-ID: <4C773B69.3050308@georgetown.edu> On 8/26/2010 10:40 PM, Michiel de Hoon wrote: > The problem is with the XML returned by NCBI. Currently, the XML > returned by einfo contains elements that are not described > in the corresponding DTD > (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The > parser therefore doesn't know how to handle them. Could you write an > email to NCBI that einfo generates XML that is inconsistent with the > corresponding DTD? Sent. It would be nice (IWBN) if the parser threw an exception that indicated that the returned XML didn't validate...at least then the (very cryptic!) error message wouldn't look like a logic error in the parser. - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From nje5 at georgetown.edu Fri Aug 27 04:39:06 2010 From: nje5 at georgetown.edu (Nathan J. Edwards) Date: Fri, 27 Aug 2010 00:39:06 -0400 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C773B69.3050308@georgetown.edu> References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> Message-ID: <4C77416A.6030906@georgetown.edu> On 8/27/2010 12:13 AM, Nathan J. Edwards wrote: > > It would be nice (IWBN) if the parser threw an exception that indicated > that the returned XML didn't validate...at least then the (very > cryptic!) error message wouldn't look like a logic error in the parser. Actually, after wading though the Parser.py code some more, the bad element is clearly detected, and an attempt is made to ignore it (the empty string), which then subsequently leads to the TypeError exception in endElementHandler. Maybe the test and return of my first email is sufficient to deal with the empty strings inserted as part of the "ignore it" strategy. And, given the frequency with which NCBI seems to break these things, I _do_ prefer the "ignore it" strategy, if it works. :-) Cheers! - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From biopython at maubp.freeserve.co.uk Fri Aug 27 08:32:57 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:32:57 +0100 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C77416A.6030906@georgetown.edu> References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu> Message-ID: On Fri, Aug 27, 2010 at 5:39 AM, Nathan J. Edwards wrote: > On 8/27/2010 12:13 AM, Nathan J. Edwards wrote: >> >> It would be nice (IWBN) if the parser threw an exception that indicated >> that the returned XML didn't validate...at least then the (very >> cryptic!) error message wouldn't look like a logic error in the parser. > > Actually, after wading though the Parser.py code some more, the bad element > is clearly detected, and an attempt is made to ignore it (the empty string), > which then subsequently leads to the TypeError exception in > endElementHandler. I'd suggest issuing a warning for the bad element, rather than silently ignoring it. > Maybe the test and return of my first email is sufficient to deal with the > empty strings inserted as part of the "ignore it" strategy. > > And, given the frequency with which NCBI seems to break these things, > I _do_ prefer the "ignore it" strategy, if it works. :-) Michiel - does Nathan's fix make sense? We should probably save an example of this broken XML for a unit test... Nathan - have you notified the NCBI about this? I assume you would get an error putting the XML through a validator - if you haven't already done so that would be worthwhile. Or would you rather one of us contact them? Thanks, Peter From biopython at maubp.freeserve.co.uk Fri Aug 27 08:57:04 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:57:04 +0100 Subject: [Biopython] [Open-bio-l] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 > domains, among them most of the open-bio.org ones. ... I've > renewed biopython.org for a 2-year term, ... The site should be > back up soonish. Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Peter From vishal4linux2 at gmail.com Fri Aug 27 09:41:33 2010 From: vishal4linux2 at gmail.com (vishal bhardwa) Date: Fri, 27 Aug 2010 15:11:33 +0530 Subject: [Biopython] module pylab problem on ceton Message-ID: hello friends, how i can install pylab please give any solution i m useing CentOs operating system. thanks in advance vishal From biopython at maubp.freeserve.co.uk Fri Aug 27 09:58:51 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 10:58:51 +0100 Subject: [Biopython] module pylab problem on ceton In-Reply-To: References: Message-ID: On Fri, Aug 27, 2010 at 10:41 AM, vishal bhardwa wrote: > hello friends, > how i can install pylab please give any solution i m useing CentOs operating > system. This isn't really a Biopython question. Try: http://matplotlib.sourceforge.net/users/installing.html Peter From nje5 at georgetown.edu Fri Aug 27 16:10:49 2010 From: nje5 at georgetown.edu (Nathan Edwards) Date: Fri, 27 Aug 2010 12:10:49 -0400 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: References: <108175.26561.qm@web62405.mail.re1.yahoo.com> <4C773B69.3050308@georgetown.edu> <4C77416A.6030906@georgetown.edu> Message-ID: <4C77E389.7080006@georgetown.edu> > I'd suggest issuing a warning for the bad element, rather than silently > ignoring it. Except that I find the warning infrastructure pretty hard to use when I need to turn something off. Other alternatives providing a switch to choose between throwing an exception (probably the default) or silently coping. >> And, given the frequency with which NCBI seems to break these things, >> I _do_ prefer the "ignore it" strategy, if it works. :-) > > Nathan - have you notified the NCBI about this? I assume you would get > an error putting the XML through a validator - if you haven't already done > so that would be worthwhile. Or would you rather one of us contact them? Yes, NCBI has been notified and I just received a response that the developers have been notified. > I will bring this to our developers' attention. However, I will not > be able to provide your with any ETA of the correction/fix or other > comparable actions at this time. Visual inspection is sufficient to verify the element is not mentioned in the DTD, though I could fire up a validating parser I guess. Just did and it confirms the error. - n -- Dr. Nathan Edwards nje5 at georgetown.edu Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Room 1215, Harris Building Room 347, Basic Science 3300 Whitehaven St, NW 3900 Reservoir Road, NW Washington DC 20007 Washington DC 20007 Phone: 202-687-7042 Phone: 202-687-1618 Fax: 202-687-0057 Fax: 202-687-7186 From mjldehoon at yahoo.com Sat Aug 28 07:47:25 2010 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Sat, 28 Aug 2010 00:47:25 -0700 (PDT) Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <4C77E389.7080006@georgetown.edu> Message-ID: <226633.67137.qm@web62407.mail.re1.yahoo.com> I think that for Biopython release 1.55, we should silently ignore this error using the fix proposed by Nathan. After the release is out, I suggest we add an optional argument "validate" to the read() and parse() function, defaulting to True. If validate is True, then read()/parse() raise an error if it finds elements in the XML that are not represented in the DTD. If validate is False, then such elements are silently ignored. This will require some other minor changes to the parser, so I'd like to do this after 1.55 is out. --Michiel. --- On Fri, 8/27/10, Nathan Edwards wrote: > From: Nathan Edwards > Subject: Re: [Biopython] Problem with Bio.Entrez... > To: "Peter" > Cc: "Michiel de Hoon" , biopython at lists.open-bio.org > Date: Friday, August 27, 2010, 12:10 PM > > > I'd suggest issuing a warning for the bad element, > rather than silently > > ignoring it. > > Except that I find the warning infrastructure pretty hard > to use when I need to turn something off. > > Other alternatives providing a switch to choose between > throwing an exception (probably the default) or silently > coping. > > >> And, given the frequency with which NCBI seems to > break these things, > >> I _do_ prefer the "ignore it" strategy, if it > works. :-) > > > > Nathan - have you notified the NCBI about this? I > assume you would get > > an error putting the XML through a validator - if you > haven't already done > > so that would be worthwhile. Or would you rather one > of us contact them? > > Yes, NCBI has been notified and I just received a response > that the developers have been notified. > > > I will bring this to our developers' attention. > However, I will not > > be able to provide your with any ETA of the > correction/fix or other > > comparable actions at this time. > > Visual inspection is sufficient to verify the element is > not mentioned in the DTD, though I could fire up a > validating parser I guess. Just did and it confirms the > error. > > - n > > -- Dr. Nathan Edwards? ? ? ? ? > ? ? ? ? ? ? nje5 at georgetown.edu > Department of Biochemistry and Molecular & Cellular > Biology > ? ? ? ? ???Georgetown > University Medical Center > Room 1215, Harris Building? ? ? ? > ? Room 347, Basic Science > 3300 Whitehaven St, NW? ? ? ? ? > ? ? 3900 Reservoir Road, NW > Washington DC 20007? ? ? ? ? > ? ? ? ? ???Washington DC > 20007 > Phone: 202-687-7042? ? ? ? ? > ? ? ? ? ???Phone: > 202-687-1618 > Fax: 202-687-0057? ? ? ? ? ? > ? ? ? ? ? ???Fax: > 202-687-7186 > From biopython at maubp.freeserve.co.uk Sat Aug 28 11:32:03 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 28 Aug 2010 12:32:03 +0100 Subject: [Biopython] Problem with Bio.Entrez... In-Reply-To: <226633.67137.qm@web62407.mail.re1.yahoo.com> References: <4C77E389.7080006@georgetown.edu> <226633.67137.qm@web62407.mail.re1.yahoo.com> Message-ID: On Sat, Aug 28, 2010 at 8:47 AM, Michiel de Hoon wrote: > I think that for Biopython release 1.55, we should silently ignore this > error using the fix proposed by Nathan. After the release is out, I > suggest we add an optional argument "validate" to the read() and > parse() function, defaulting to True. If validate is True, then read()/ > parse() raise an error if it finds elements in the XML that are not > represented in the DTD. If validate is False, then such elements > are silently ignored. This will require some other minor changes > to the parser, so I'd like to do this after 1.55 is out. > > --Michiel. Sounds good :) Peter From p.j.a.cock at googlemail.com Tue Aug 31 23:00:37 2010 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 1 Sep 2010 00:00:37 +0100 Subject: [Biopython] Biopython 1.55 released Message-ID: Dear Biopythoneers, After the beta earlier this month (thank you to everyone who helped test this), we?ve just released Biopython 1.55 . For full details see: http://news.open-bio.org/news/2010/08/biopython-1-55-released/ Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 12 people have contributed to this release, including 6 new people ? thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Cymon Cox * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Nathan Edwards (first contribution) * Peter Cock * Tiago Antao Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download As usual, feedback is most welcome on the mailing lists (or bugzilla). Regards, Peter P.S. You can follow Biopython on Twitter, http://twitter.com/biopython