From bugzilla-daemon at portal.open-bio.org Tue Sep 2 09:06:51 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 2 Sep 2008 09:06:51 -0400 Subject: [Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors In-Reply-To: Message-ID: <200809021306.m82D6p9i021009@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2543 ------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-02 09:06 EST ------- Hi Frank, Did you get a chance to look at that code for named ancestors? Thanks Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Sep 2 10:05:17 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 2 Sep 2008 10:05:17 -0400 Subject: [Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors In-Reply-To: Message-ID: <200809021405.m82E5HRM025041@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2543 ------- Comment #4 from cymon.cox at gmail.com 2008-09-02 10:05 EST ------- Hi Peter, > Can I ask if you've actually come across trees with names ancestor nodes in > "real life"? That would make this bug more important. If so, the name of the > tool would be interesting, P4 (http://code.google.com/p/p4-phylogenetics/) is the only one I'm aware of. As Frank implies the labels at nodes arent necessarily names of ancestors but rather are just labels that can be any text. In P4 they are they are just an string attribute of the node object. P4 uses them primarily to aid tree drawing. Support indices in phylogenetics are properties of branches and this is fine in a unrooted tree context. But most systematists want to orientate the tree, ie. root it informally, and refer to a particular node having the support value of its subtending branch. Its therefore useful to transfer the branch support values to node labels before drawing the tree. > an example tree file would be great to add to > Biopython as a test case. How about this: +--------------3:t9 +------2:B | | +----------------5:t8 | +-----4:C +-----1:A +---------------6:t4 | | | +---------------7:t6 | |------------------8:t2 0 | +------------11:t0 | +-----10:E | | +-----------------12:t7 | | +-----9:D +------15:t5 | +------14:G +-----13:F +-----------------16:t3 | +--------17:t1 """ #NEXUS begin taxa; dimensions ntax=10; taxlabels t0 t1 t2 t3 t4 t5 t6 t7 t8 t9; end; begin trees; tree random = [&U] (((t9:0.385832, (t8:0.445135, t4:0.41401)C:0.024032)B:0.041436, t6:0.392496)A:0.0291131, t2:0.497673, ((t0:0.301171, t7:0.482152)E:0.0268148, ((t5:0.0984167, t3:0.488578)G:0.0349662, t1:0.130208)F:0.0318288)D:0.0273876); end; """ (Hi Frank) Cheers, Cymon. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Sep 2 11:44:11 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 2 Sep 2008 11:44:11 -0400 Subject: [Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors In-Reply-To: Message-ID: <200809021544.m82FiBej030561@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2543 ------- Comment #5 from fkauff at biologie.uni-kl.de 2008-09-02 11:44 EST ------- (In reply to comment #3) Hi Peter, haven't done anything yet. The previously mentioned code works different (assigning values to nodes within a [&...] comment), rather than names to nodes. Assigning names to nodes can be very useful, but as Cymon mention, P4 seems to be the only program that can handle them. In my opinion, naming nodes is a feature, and I would not regard the lack of this feature as a bug. But I'll have a look at the code and see how easy this can be changed. It would actually be nice if P4 and Bio.Nexus, both being python programs, could read each other's trees. (Hi Cymon :-) ) Frank > Hi Frank, > > Did you get a chance to look at that code for named ancestors? > > Thanks > > Peter > -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From biopython at maubp.freeserve.co.uk Tue Sep 2 11:49:09 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 2 Sep 2008 16:49:09 +0100 Subject: [Biopython-dev] Preparing for Biopython 1.48 Message-ID: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> Dear all, Is there anything we need to address before starting to prepare Biopython 1.48? This is likely to be the final Numeric only release of Biopython, with the following release hopefully supporting both Numeric and numpy in some way. (As an aside, once we support numpy, having scipy as an optional dependency for the statistics Tiago wanted to use in Bio.PopGen does seem less onerous.) Regarding potentially deprecating Bio.Mindy and Martel, I propose we do this in the following release (i.e. after Biopython 1.48). We can then drop the mxTextTools dependency completely. While I would like to address some of the enhancements (esp Bug 2530) these can wait. Ignoring the enhancements, there are several "small" issues on bugzilla that could be dealt with, but nothing that I think warrants delaying the release. One question: Currently Bio.SeqIO in CVS has partial support for writing GenBank files (basically the sequence and minimal annotation - no references, no features). I don't want to rush something out without proper testing, so do people think it would be better to ship with this partial support, or temporarily disable it (a one line change in Bio/SeqIO/__init__.py to the _FormatToWriter dictionary, and probably refreshing the expected unit test output). Comments and suggestions welcome! Thanks, Peter From tiagoantao at gmail.com Tue Sep 2 14:25:31 2008 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 2 Sep 2008 19:25:31 +0100 Subject: [Biopython-dev] Preparing for Biopython 1.48 In-Reply-To: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> References: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> Message-ID: <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> Hi All, On Tue, Sep 2, 2008 at 4:49 PM, Peter wrote: > (As an aside, once we support numpy, having scipy as an optional > dependency for the statistics Tiago wanted to use in Bio.PopGen does > seem less onerous.) > First, my apologies for not reporting back from BOSC,but I was in a conference/professional visit spree for the last 3 months, returned last most. Basically it was not OK: I arrived there from a previous conference and did the presentation without little sleep, it was probably the sloppiest presentation in my whole life. My sincere apologies. On a better front, I have a lot of new content for Bio.PopGen, a few remarks: 1. No documentation and testing done, so I will skip adding content to 1.48. But I will surely add to 1.49. 2. None of the new content relies on scipy (as there was no agreement on that), but being able to use scipy would make things much easier. Most of anything that can be called "population genetics" is nothing more than statistics (statistics were invented because of population genetics). So a change in policy would be welcomed (and would make Bio.PopGen really useful for a wide audience - currently it has only niche users). In another front, we published a paper using content from Bio.PopGen 1.44 http://www.biomedcentral.com/1471-2105/9/323 Regards, Tiago From biopython at maubp.freeserve.co.uk Tue Sep 2 15:05:31 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 2 Sep 2008 20:05:31 +0100 Subject: [Biopython-dev] Preparing for Biopython 1.48 In-Reply-To: References: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> Message-ID: <320fb6e00809021205v4ec1a8f3wa3997881ad1e7d07@mail.gmail.com> Tiago wrote: >> First, my apologies for not reporting back from BOSC,but I was in a >> conference/professional visit spree for the last 3 months, returned last >> most. Basically it was not OK: I arrived there from a previous conference >> and did the presentation without little sleep, it was probably the >> sloppiest presentation in my whole life. My sincere apologies. I hardly dared ask how you felt at the end of your almost round the world trip ;) Jared wrote: > Despite Tiago's self-criticism I thought his BOSC presentation was fine and > up to par with the rest of them. > > jared That sounds much more positive :) This reminds me that I could/should make a PDF version of the BOSC 2008 slides to go online here: http://biopython.org/wiki/Documentation#Presentations >> On a better front, I have a lot of new content for Bio.PopGen, a few >> remarks: >> 1. No documentation and testing done, so I will skip adding content to >> 1.48. But I will surely add to 1.49. That sounds sensible, and another reason to get Biopython 1.48 out soon. Depending how my day goes tomorrow, I could try then. >> 2. None of the new content relies on scipy (as there was no agreement on >> that), but being able to use scipy would make things much easier. Most of >> anything that can be called "population genetics" is nothing more than >> statistics (statistics were invented because of population genetics). So a >> change in policy would be welcomed (and would make Bio.PopGen really >> useful for a wide audience - currently it has only niche users). Let's get the move from Numeric to NumPy done after Biopython 1.48, and re-open the possible SciPy dependency question then. >> In another front, we published a paper using content from Bio.PopGen 1.44 >> http://www.biomedcentral.com/1471-2105/9/323 Excellent, Peter From jflatow at northwestern.edu Tue Sep 2 14:42:52 2008 From: jflatow at northwestern.edu (Jared Flatow) Date: Tue, 2 Sep 2008 13:42:52 -0500 Subject: [Biopython-dev] Preparing for Biopython 1.48 In-Reply-To: <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> References: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> Message-ID: Despite Tiago's self-criticism I thought his BOSC presentation was fine and up to par with the rest of them. jared On Sep 2, 2008, at 1:25 PM, Tiago Ant?o wrote: > Hi All, > > On Tue, Sep 2, 2008 at 4:49 PM, Peter > wrote: > >> (As an aside, once we support numpy, having scipy as an optional >> dependency for the statistics Tiago wanted to use in Bio.PopGen does >> seem less onerous.) >> > > First, my apologies for not reporting back from BOSC,but I was in a > conference/professional visit spree for the last 3 months, returned > last > most. Basically it was not OK: I arrived there from a previous > conference > and did the presentation without little sleep, it was probably the > sloppiest > presentation in my whole life. My sincere apologies. > > On a better front, I have a lot of new content for Bio.PopGen, a few > remarks: > 1. No documentation and testing done, so I will skip adding content > to 1.48. > But I will surely add to 1.49. > 2. None of the new content relies on scipy (as there was no > agreement on > that), but being able to use scipy would make things much easier. > Most of > anything that can be called "population genetics" is nothing more than > statistics (statistics were invented because of population > genetics). So a > change in policy would be welcomed (and would make Bio.PopGen really > useful > for a wide audience - currently it has only niche users). > > > In another front, we published a paper using content from Bio.PopGen > 1.44 > http://www.biomedcentral.com/1471-2105/9/323 > > Regards, > Tiago > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > From tiagoantao at gmail.com Tue Sep 2 15:29:55 2008 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 2 Sep 2008 20:29:55 +0100 Subject: [Biopython-dev] Preparing for Biopython 1.48 In-Reply-To: <320fb6e00809021205v4ec1a8f3wa3997881ad1e7d07@mail.gmail.com> References: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> <320fb6e00809021205v4ec1a8f3wa3997881ad1e7d07@mail.gmail.com> Message-ID: <6d941f120809021229u389d1550re8bb7ec4ad3fc5b@mail.gmail.com> On Tue, Sep 2, 2008 at 8:05 PM, Peter wrote: > This reminds me that I could/should make a PDF version of the BOSC > 2008 slides to go online here: > http://biopython.org/wiki/Documentation#Presentations > http://www.slideshare.net/tiago/bosc-2008-biopython Is there for a month, by I completely forgot to inform. Tiago From bugzilla-daemon at portal.open-bio.org Wed Sep 3 12:46:30 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 3 Sep 2008 12:46:30 -0400 Subject: [Biopython-dev] [Bug 2578] New: The GenBank SeqRecord parser does not record module type or if circular Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2578 Summary: The GenBank SeqRecord parser does not record module type or if circular Product: Biopython Version: 1.47 Platform: All OS/Version: All Status: NEW Severity: minor Priority: P2 Component: Main Distribution AssignedTo: biopython-dev at biopython.org ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk Filing this bug after discussion on the mailing list, where the issue was raised by Chris Lasher: http://lists.open-bio.org/pipermail/biopython/2008-September/004474.html http://lists.open-bio.org/pipermail/biopython/2008-September/004475.html http://lists.open-bio.org/pipermail/biopython/2008-September/004476.html The LOCUS line at the start of a GenBank record can record the molecule type (DNA, RNA, mRNA, protein etc) and also if the sequence is linear or circular, e.g. LOCUS NC_002678 7036071 bp DNA circular BCT 22-JUL-2008 Currently Bio.SeqIO (and Bio.GenBank.FeatureParser if called directly) do not record these two bits of information in the SeqRecord. Bio.SeqIO uses the Bio.GenBank.FeatureParser, which gets passed this information from the Scanner via the residue_type event. This is a combined lump of data containing both the sequence type (DNA, RNA etc) and if it is linear or circular. It is currently only used to determine the Seq alphabet, and has never been recorded. So in addition to not recording if the LOCUS line said the sequence was circular, if the LOCUS line contained cDNA, mRNA, ... this fine detail is also currently lost in the SeqRecord representation. On the other hand, the Bio.GenBank.RecordParser stores all this as the record's residue_type property (a single combined field, presumably reflecting the layout of early GenBank files). It would be a logical improvement to record the sequence data (molecule type and if circular) in the SeqRecord's annotations dictionary - perhaps as two fields but we'd need to check if that would be straight forward for EMBL files too. Alternatively, if Biopython included a native CircularSeq object, we could use that explicitly when the sequence is declared as circular. This might be considered a little surprising though. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 3 12:54:35 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 3 Sep 2008 12:54:35 -0400 Subject: [Biopython-dev] [Bug 2578] The GenBank SeqRecord parser does not record module type or if circular In-Reply-To: Message-ID: <200809031654.m83GsZ5G017770@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2578 ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-03 12:54 EST ------- Note that after any change made to record this information, the preliminary GenBank writing support for Bio.SeqIO should also be updated - see Bug 2294. It would also be sensible to see how BioPerl, BioJava etc store this information within BioSQL so that if possible we can do it the same way. I'm assuming this is just a case of picking the same text (term table key) for our annotations dictionary key. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 3 12:55:38 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 3 Sep 2008 12:55:38 -0400 Subject: [Biopython-dev] [Bug 2578] The GenBank SeqRecord parser does not record molecule type or if circular In-Reply-To: Message-ID: <200809031655.m83GtcPl017915@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2578 biopython-bugzilla at maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Summary|The GenBank SeqRecord parser|The GenBank SeqRecord parser |does not record module type |does not record molecule |or if circular |type or if circular ------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-03 12:55 EST ------- Fixed the typo in "molecule" for the bug title. Whoops. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From biopython at maubp.freeserve.co.uk Thu Sep 4 14:36:44 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 4 Sep 2008 19:36:44 +0100 Subject: [Biopython-dev] Preparing for Biopython 1.48 In-Reply-To: <6d941f120809021229u389d1550re8bb7ec4ad3fc5b@mail.gmail.com> References: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> <320fb6e00809021205v4ec1a8f3wa3997881ad1e7d07@mail.gmail.com> <6d941f120809021229u389d1550re8bb7ec4ad3fc5b@mail.gmail.com> Message-ID: <320fb6e00809041136q4c01360ane4b0efcc58a68b8a@mail.gmail.com> On Tue, Sep 2, 2008 at 8:29 PM, Tiago Ant?o wrote: > On Tue, Sep 2, 2008 at 8:05 PM, Peter wrote: > >> This reminds me that I could/should make a PDF version of the BOSC >> 2008 slides to go online here: >> http://biopython.org/wiki/Documentation#Presentations >> > > http://www.slideshare.net/tiago/bosc-2008-biopython > Is there for a month, by I completely forgot to inform. I spotted the slide share thing (it surprised me last year) and added that to the wiki page already. On to practical matters, I've just done a clean check out on Linux and run the test suite, everything passes except these ones with external dependencies: test_GFF ... skipping. Environment is not configured for this test (not important if you do not plan to use Bio.GFF). test_PopGen_FDist ... skipping. Fdist not found (not a problem if you do not intend to use it). test_PopGen_SimCoal ... skipping. SimCoal not found (not a problem if you do not intend to use it). test_Wise ... skipping. sh: dnal: command not found test_psw ... skipping. sh: dnal: command not found I've never installed any of the PopGen tools - I presume these tests are still OK on your machine(s) Tiago? I've also never installed dnal, or setup whatever test_GFF wants. Could anyone confirm these are OK? I have run the BioSQL tests though. Peter From tiagoantao at gmail.com Fri Sep 5 06:05:26 2008 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Fri, 5 Sep 2008 11:05:26 +0100 Subject: [Biopython-dev] Preparing for Biopython 1.48 In-Reply-To: <320fb6e00809041136q4c01360ane4b0efcc58a68b8a@mail.gmail.com> References: <320fb6e00809020849i7c480997g810ffbc523143f47@mail.gmail.com> <6d941f120809021125u7188d67l2612fd0f09277abc@mail.gmail.com> <320fb6e00809021205v4ec1a8f3wa3997881ad1e7d07@mail.gmail.com> <6d941f120809021229u389d1550re8bb7ec4ad3fc5b@mail.gmail.com> <320fb6e00809041136q4c01360ane4b0efcc58a68b8a@mail.gmail.com> Message-ID: <6d941f120809050305v7f991fe0jcfdfc650936e7348@mail.gmail.com> On Thu, Sep 4, 2008 at 7:36 PM, Peter wrote: > I've never installed any of the PopGen tools - I presume these tests > are still OK on your machine(s) Tiago? > > All tests are OK here (Linux x86). From biopython at maubp.freeserve.co.uk Fri Sep 5 06:43:27 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 5 Sep 2008 11:43:27 +0100 Subject: [Biopython-dev] CVS freeze for Biopython 1.48 Message-ID: <320fb6e00809050343y598c436fi9aa65ec272f1492d@mail.gmail.com> Dear all, I'm going to try and put together Biopython 1.48 this afternoon, so could you all not commit any changes until further notice please. I'll be doing the source code releases (and possibly a Windows installer for Python 2.3 tonight if my old laptop still has all the MS compilers working), but there will then be a slight delay while we get the (other) Windows installers done. Thank you, Peter From biopython at maubp.freeserve.co.uk Fri Sep 5 19:19:13 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 6 Sep 2008 00:19:13 +0100 Subject: [Biopython-dev] Nexus issue on Windows with Python 2.3 Message-ID: <320fb6e00809051619v762ee276ld0d44a300403bfeb@mail.gmail.com> Can anyone using Windows and/or Python 2.3 try running the test suite? I'm seeing a problem with test_SeqIO.py and test_AlignIO.py when they call Bio.Nexus to construct a particular Nexus object (using seqences originally read in from Tests/Nexus/test_Nexus_input.nex for what its worth). This triggers: TypeError: zip() requires at least one sequence On Linux with Python 2.4, and Mac OS X with Python 2.5 these two tests both passed for me. Peter From biopython at maubp.freeserve.co.uk Sat Sep 6 05:06:20 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 6 Sep 2008 10:06:20 +0100 Subject: [Biopython-dev] Nexus issue on Windows with Python 2.3 In-Reply-To: <320fb6e00809051619v762ee276ld0d44a300403bfeb@mail.gmail.com> References: <320fb6e00809051619v762ee276ld0d44a300403bfeb@mail.gmail.com> Message-ID: <320fb6e00809060206q88a44cblb1188380ae921dde@mail.gmail.com> On Sat, Sep 6, 2008 at 12:19 AM, Peter wrote: > Can anyone using Windows and/or Python 2.3 try running the test suite? > > I'm seeing a problem with test_SeqIO.py and test_AlignIO.py when they > call Bio.Nexus to construct a particular Nexus object (using seqences > originally read in from Tests/Nexus/test_Nexus_input.nex for what its > worth). This triggers: > > TypeError: zip() requires at least one sequence > > On Linux with Python 2.4, and Mac OS X with Python 2.5 these two tests > both passed for me. This was a python 2.3 problem, the Nexus code (Bio/Nexus/Nexus.py line 1633) was using a Python 2.4+ only feature, see http://docs.python.org/lib/built-in-funcs.html sitesm=zip(*[self.matrix[t].tostring() for t in self.taxlabels]) I've added a check in CVS for an empty list of taxlabels (with a comment about python 2.3). Peter From biopython at maubp.freeserve.co.uk Sat Sep 6 06:04:08 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 6 Sep 2008 11:04:08 +0100 Subject: [Biopython-dev] New line issues in the source zip or tarballs Message-ID: <320fb6e00809060304h429f1085r301170aa93d4eb73@mail.gmail.com> I've run into a little issue on Windows while preparing Biopython 1.48, If you check out the latest code from CVS on Windows, then assuming the CVS client is setup correctly, all the python files and plain text input files get DOS/Windows newlines. Running the test suite looks OK (there are a few little known issues l've previously mentioned). However, having built a release on Linux, it seems both the tarball and the zip file contain the text files using Unix newlines. I can build Biopython on Windows from the zip file (Unix newlines are not a problem for running the python code), but it does break a few of the unit tests (test_SCOP_Cla.py and test_SCOP_Raf.py and test_PopGen_SimCoal_nodepend.py). This is only an issue for the minority of Windows users who will actually run the test suite. Most will just use the click-and-run installers which don't include the tests, and I expect anyone trying to build Biopython on Windows will probably use CVS. So we could just ignore this for the time being... One solution would be to try and tweak the source code distributions so the tarball uses linux line endings, while the zip file uses DOS/Windows. This does seem nasty. Or, we can try and tweak the failing unit tests to cope with their input files in either format. In the case of test_PopGen_SimCoal_nodepend.py the failure is expecting simple.par and simple_100_30.par to be exactly the same size (in class TemplateTest, line 47). This is not true going to be true when the input file uses Unix new lines but the generated file uses Windows new lines. Perhaps using a simple bit of code to load the files line by line and compare them would work here? Peter From fkauff at biologie.uni-kl.de Mon Sep 8 03:34:32 2008 From: fkauff at biologie.uni-kl.de (Frank Kauff) Date: Mon, 08 Sep 2008 09:34:32 +0200 Subject: [Biopython-dev] Nexus issue on Windows with Python 2.3 In-Reply-To: <320fb6e00809060206q88a44cblb1188380ae921dde@mail.gmail.com> References: <320fb6e00809051619v762ee276ld0d44a300403bfeb@mail.gmail.com> <320fb6e00809060206q88a44cblb1188380ae921dde@mail.gmail.com> Message-ID: <48C4D588.701@biologie.uni-kl.de> Peter wrote: > On Sat, Sep 6, 2008 at 12:19 AM, Peter wrote: > >> Can anyone using Windows and/or Python 2.3 try running the test suite? >> >> I'm seeing a problem with test_SeqIO.py and test_AlignIO.py when they >> call Bio.Nexus to construct a particular Nexus object (using seqences >> originally read in from Tests/Nexus/test_Nexus_input.nex for what its >> worth). This triggers: >> >> TypeError: zip() requires at least one sequence >> >> On Linux with Python 2.4, and Mac OS X with Python 2.5 these two tests >> both passed for me. >> > > This was a python 2.3 problem, the Nexus code (Bio/Nexus/Nexus.py line > 1633) was using a Python 2.4+ only feature, see > http://docs.python.org/lib/built-in-funcs.html > > sitesm=zip(*[self.matrix[t].tostring() for t in self.taxlabels]) > > I've added a check in CVS for an empty list of taxlabels (with a > comment about python 2.3). > > Good catch. Thanks Peter for fixing it. > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev > > -- J-Prof. Dr. Frank Kauff Molecular Phylogenetics FB Biologie, 13/276 TU Kaiserslautern Postfach 3049 67653 Kaiserslautern Tel. +49 (0)631 205-2562 Fax. +49 (0)631 205-2998 email: fkauff at biologie.uni-kl.de skype: frank.kauff From p.j.a.cock at googlemail.com Mon Sep 8 05:41:33 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 8 Sep 2008 10:41:33 +0100 Subject: [Biopython-dev] test_SVDSuperimposer.py Message-ID: <320fb6e00809080241x3db79410lf54dd1612e5e04cc@mail.gmail.com> Hi all, I've noticed test_SVDSuperimposer.py seems to stall/run for ever on one of the Linux machines I have run it one. However, on my main Linux machine it is fine, and on Mac OS X. Has anyone else noticed this? Maybe there is some common thread (e.g. version of Numeric or something). Peter From p.j.a.cock at googlemail.com Mon Sep 8 06:43:17 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 8 Sep 2008 11:43:17 +0100 Subject: [Biopython-dev] test_SVDSuperimposer.py In-Reply-To: <364233.84511.qm@web62401.mail.re1.yahoo.com> References: <320fb6e00809080241x3db79410lf54dd1612e5e04cc@mail.gmail.com> <364233.84511.qm@web62401.mail.re1.yahoo.com> Message-ID: <320fb6e00809080343t78e068een8e50d0237d9852c8@mail.gmail.com> On Mon, Sep 8, 2008 at 11:36 AM, Michiel de Hoon wrote: > When installing Numerical Python, run > > python setup.py config > > before build, install. > (assuming you are using Numerical Python version 24.2). > > --Michiel. I've checked and it is version 24.2 that is installed on the machine in question. I'm not sure if this was installed from source or via the yum package manager, but Numeric seems to work. $ python Python 2.5 (r25:51908, Nov 23 2006, 18:40:28) [GCC 4.1.1 20061011 (Red Hat 4.1.1-30)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> Numeric.__version__ '24.2' I imagine if there was something seriously wrong with this Numeric installation it would have shown up in other unit tests. So it looks like the version of Numeric isn't the issue. Any other ideas? I take it you've never had a problem with test_SVDSuperimposer.py getting stuck? Thanks, Peter From mjldehoon at yahoo.com Mon Sep 8 06:36:44 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Mon, 8 Sep 2008 03:36:44 -0700 (PDT) Subject: [Biopython-dev] test_SVDSuperimposer.py In-Reply-To: <320fb6e00809080241x3db79410lf54dd1612e5e04cc@mail.gmail.com> Message-ID: <364233.84511.qm@web62401.mail.re1.yahoo.com> When installing Numerical Python, run python setup.py config before build, install. (assuming you are using Numerical Python version 24.2). --Michiel. --- On Mon, 9/8/08, Peter Cock wrote: > From: Peter Cock > Subject: [Biopython-dev] test_SVDSuperimposer.py > To: "BioPython-Dev Mailing List" > Date: Monday, September 8, 2008, 5:41 AM > Hi all, > > I've noticed test_SVDSuperimposer.py seems to stall/run > for ever on > one of the Linux machines I have run it one. However, on > my main > Linux machine it is fine, and on Mac OS X. Has anyone else > noticed > this? Maybe there is some common thread (e.g. version of > Numeric or > something). > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From biopython at maubp.freeserve.co.uk Mon Sep 8 07:20:57 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 8 Sep 2008 12:20:57 +0100 Subject: [Biopython-dev] CVS freeze for Biopython 1.48 In-Reply-To: <320fb6e00809050343y598c436fi9aa65ec272f1492d@mail.gmail.com> References: <320fb6e00809050343y598c436fi9aa65ec272f1492d@mail.gmail.com> Message-ID: <320fb6e00809080420y5f456ab4uc4ec42d845c25f1a@mail.gmail.com> On Fri, Sep 5, 2008 at 11:43 AM, Peter wrote: > Dear all, > > I'm going to try and put together Biopython 1.48 this afternoon, so > could you all not commit any changes until further notice please. This took longer than planned. I have now tagged CVS and uploaded the tar-ball and zip file for Biopython 1.48 to http://biopython.org/DIST/ as usual. Before we make the public announcement (email, news server, and wiki pages), having one or two people try downloading these, installing from source and running the unit tests would be great. Little things (like documentation improvements!) can go into CVS now, but could you all refrain from any major changes (like Numeric/numpy, additional deprecations or removals) until the release has been public for a few days without issue? Just in case we have to tweak things, this would make dealing with CVS easier. Thanks. > I'll be doing the source code releases (and possibly a Windows > installer for Python 2.3 tonight if my old laptop still has all the MS > compilers working), but there will then be a slight delay while we get > the (other) Windows installers done. I may be able to do the Python 2.3 Windows installer tonight - we'll see. For future reference, hevea 1.08 which my linux box had installed doesn't work nicely on the tutorial (the title page information goes missing), but hevea 1.10 is fine. http://biopython.org/DIST/docs/tutorial/Tutorial.pdf http://biopython.org/DIST/docs/tutorial/Tutorial.html Also, we're currently using epydoc version 3.0.1 for the API documentation: http://biopython.org/DIST/docs/api/ I did check in a few more module level docstrings so this does look a bit more complete than in Biopython 1.47. There is still room for improvement, for example Bio.SeqUtils needs some love. Also many of the deprecated modules don't say they are deprecated in the module level docstring which I think is good thing to do. Any views on this? Thanks, Peter From tiagoantao at gmail.com Mon Sep 8 07:42:51 2008 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Mon, 8 Sep 2008 12:42:51 +0100 Subject: [Biopython-dev] New line issues in the source zip or tarballs In-Reply-To: <320fb6e00809060304h429f1085r301170aa93d4eb73@mail.gmail.com> References: <320fb6e00809060304h429f1085r301170aa93d4eb73@mail.gmail.com> Message-ID: <6d941f120809080442r1797666eu70e35c60353c5462@mail.gmail.com> Hi, On Sat, Sep 6, 2008 at 11:04 AM, Peter wrote: > In the case of test_PopGen_SimCoal_nodepend.py the failure is > expecting simple.par and simple_100_30.par to be exactly the same size > (in class TemplateTest, line 47). This is not true going to be true > when the input file uses Unix new lines but the generated file uses > Windows new lines. Perhaps using a simple bit of code to load the > files line by line and compare them would work here? > I am currently at a workshop (I belong to the organization committee, so I don't have much time), but I will try to sort this in the next couple of days. Tiago From biopython at maubp.freeserve.co.uk Mon Sep 8 08:14:09 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 8 Sep 2008 13:14:09 +0100 Subject: [Biopython-dev] New line issues in the source zip or tarballs In-Reply-To: <6d941f120809080442r1797666eu70e35c60353c5462@mail.gmail.com> References: <320fb6e00809060304h429f1085r301170aa93d4eb73@mail.gmail.com> <6d941f120809080442r1797666eu70e35c60353c5462@mail.gmail.com> Message-ID: <320fb6e00809080514u5df6d9dej144c783076cbe467@mail.gmail.com> Tiago wrote: > Peter wrote: >> In the case of test_PopGen_SimCoal_nodepend.py the failure is >> expecting simple.par and simple_100_30.par to be exactly the same size >> (in class TemplateTest, line 47). This is not true going to be true >> when the input file uses Unix new lines but the generated file uses >> Windows new lines. Perhaps using a simple bit of code to load the >> files line by line and compare them would work here? > > I am currently at a workshop (I belong to the organization committee, so I > don't have much time), but I will try to sort this in the next couple of > days. Hi Tiago, This issue new line issue has probably been there since Biopython 1.45 without anyone else spotting it, so I don't see fixing it as urgent. Hopefully we can resolve this for the next release instead. I hope your workshop goes well, Peter From mjldehoon at yahoo.com Mon Sep 8 08:11:56 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Mon, 8 Sep 2008 05:11:56 -0700 (PDT) Subject: [Biopython-dev] test_SVDSuperimposer.py In-Reply-To: <320fb6e00809080343t78e068een8e50d0237d9852c8@mail.gmail.com> Message-ID: <339043.58717.qm@web62407.mail.re1.yahoo.com> Try if the eigenvalues function in Numerical Python works. If it hangs, you'll know the problem is in Numerical Python. --Michiel --- On Mon, 9/8/08, Peter Cock wrote: > From: Peter Cock > Subject: Re: [Biopython-dev] test_SVDSuperimposer.py > To: mjldehoon at yahoo.com > Cc: "BioPython-Dev Mailing List" > Date: Monday, September 8, 2008, 6:43 AM > On Mon, Sep 8, 2008 at 11:36 AM, Michiel de Hoon > wrote: > > When installing Numerical Python, run > > > > python setup.py config > > > > before build, install. > > (assuming you are using Numerical Python version > 24.2). > > > > --Michiel. > > I've checked and it is version 24.2 that is installed > on the machine > in question. I'm not sure if this was installed from > source or via > the yum package manager, but Numeric seems to work. > > $ python > Python 2.5 (r25:51908, Nov 23 2006, 18:40:28) > [GCC 4.1.1 20061011 (Red Hat 4.1.1-30)] on linux2 > Type "help", "copyright", > "credits" or "license" for more > information. > >>> import Numeric > >>> Numeric.__version__ > '24.2' > > I imagine if there was something seriously wrong with this > Numeric > installation it would have shown up in other unit tests. > So it looks > like the version of Numeric isn't the issue. Any other > ideas? > > I take it you've never had a problem with > test_SVDSuperimposer.py getting stuck? > > Thanks, > > Peter From p.j.a.cock at googlemail.com Mon Sep 8 08:24:01 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 8 Sep 2008 13:24:01 +0100 Subject: [Biopython-dev] test_SVDSuperimposer.py In-Reply-To: <339043.58717.qm@web62407.mail.re1.yahoo.com> References: <320fb6e00809080343t78e068een8e50d0237d9852c8@mail.gmail.com> <339043.58717.qm@web62407.mail.re1.yahoo.com> Message-ID: <320fb6e00809080524i1f75c601p2a7191b6207bd2e@mail.gmail.com> On Mon, Sep 8, 2008 at 1:11 PM, Michiel de Hoon wrote: > Try if the eigenvalues function in Numerical Python works. If it hangs, you'll know the problem is in Numerical Python. Good thinking - it does indeed hang on the machine in question, $ python Python 2.5 (r25:51908, Nov 23 2006, 18:40:28) [GCC 4.1.1 20061011 (Red Hat 4.1.1-30)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric, LinearAlgebra >>> Numeric.__version__ '24.2' >>> data = Numeric.array([[1,2,3],[4,5,6],[7,8,9]]) >>> LinearAlgebra.eigenvalues(data) [hangs here] This works fine on another Linux box, $ python Python 2.4.3 (#1, Jun 27 2006, 16:32:39) [GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric, LinearAlgebra >>> Numeric.__version__ '24.2' >>> data = Numeric.array([[1,2,3],[4,5,6],[7,8,9]]) >>> LinearAlgebra.eigenvalues(data) array([ 1.61168440e+01, -1.11684397e+00, -1.30367773e-15]) And this example also works on the Mac: $ python Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric, LinearAlgebra >>> Numeric.__version__ '24.2' >>> data = Numeric.array([[1,2,3],[4,5,6],[7,8,9]]) >>> LinearAlgebra.eigenvalues(data) array([ 1.61168440e+01, -1.11684397e+00, -1.30367773e-15]) So we can probably rule out a problem with Biopython in test_SVDSuperimposer.py which is good, but I should probably try and work out what is wrong with Numeric on this particular machine... Thanks for your advice, Peter From mjldehoon at yahoo.com Mon Sep 8 08:56:37 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Mon, 8 Sep 2008 05:56:37 -0700 (PDT) Subject: [Biopython-dev] test_SVDSuperimposer.py In-Reply-To: <320fb6e00809080524i1f75c601p2a7191b6207bd2e@mail.gmail.com> Message-ID: <622098.12504.qm@web62404.mail.re1.yahoo.com> > So we can probably rule out a problem with Biopython in > test_SVDSuperimposer.py which is good, but I should > probably try and > work out what is wrong with Numeric on this particular > machine... > Have a look at this: http://projects.scipy.org/pipermail/numpy-discussion/2004-January/015074.html --Michiel. From quwubin at gmail.com Mon Sep 8 09:59:57 2008 From: quwubin at gmail.com (Wubin Qu) Date: Mon, 8 Sep 2008 21:59:57 +0800 Subject: [Biopython-dev] BioPythonGUI: Graphical User Interface for BioPython Message-ID: Hi all, I started a new project named BioPythonGUI for a few of days. The following is the 'About' page from BioPythonGUI project. BioPythonGUI is a Graphical User Interface of BioPython. BioPython is a widely used python module set in bioinformatics. It help researchers: - Parsing files in di fferent database formats - Interfaces into programs like Blast, Entrez and PubMed - A sequence class (can transcribe, translate, invert, etc) - Code for handling alignments of sequences - Clustering algorithms - etc. However, it's not everyone can use the BioPython, especially ones who do not know much about the programming. How can you expect a professor who never known about any programming to use BioPython to parse the BLAST report file? This is the problem which the BioPythonGUI would solve. I started the project with the goal "Everyone can use BioPython with BioPythonGUI". Until now, there are two modules SeqGUI and BlastGUI are available in BioPythonGUI. I would greatly appreciate if you use BioPythonGUI and send me the feedback. Please see the developer's blog for details. Project Blog: http://biopythongui.blogspot.com/ Download: https://sites.google.com/site/biopythongui/download Screenshots: http://picasaweb.google.com/quwubin/BioPythonGUI02# ______________________________ Best regards, Wubin Qu From p.j.a.cock at googlemail.com Mon Sep 8 10:12:15 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 8 Sep 2008 15:12:15 +0100 Subject: [Biopython-dev] [BioPython] BioPythonGUI: Graphical User Interface for BioPython In-Reply-To: References: Message-ID: <320fb6e00809080712v6c33d42fheb982f52e62e6e95@mail.gmail.com> On Mon, Sep 8, 2008 at 2:43 PM, Wubin Qu wrote: > Hi all, > > I started a new project named BioPythonGUI for a few of days. Hello Wubin Qu, > BioPythonGUI is a Graphical User Interface of BioPython. I'm uncomfortable about the name BioPythonGUI, as this to me implies it is part of Biopython (whereas is it currently just a third party project built on top of Biopython). What do other people think? > However, it's not everyone can use the BioPython, especially ones who do not > know much about the programming. How can you expect a professor who never > known about any programming to use BioPython to parse the BLAST report file? > This is the problem which the BioPythonGUI would solve. I started the > project with the goal "Everyone can use BioPython with BioPythonGUI". I don't really understand your goal. How would a non-programming professor use your program to parse a BLAST report file? The NCBI already try and make the HTML and plain text output useful to non-programmers and from looking at the screenshots I don't see how your tool would help. > Until now, there are two modules SeqGUI and BlastGUI are available in > BioPythonGUI. I would greatly appreciate if you use BioPythonGUI and send me > the feedback. I see your module SeqGUI builds on the SeqGui.py in BioPython (in the scripts directory). It might make sense to include your improvements to this code as part of Biopython. I haven't looked at your code yet, so I don't know how much you've changed things. It is nice to be able to be able to translate, transcribe, reverse complement etc in a GUI, but personally I don't see the point or writing a little application just for this. Also, there are probably many many existing tools out there that already offer this functionality. However, I am happy writing code, so I am not in your target audience. Regarding your BlastGUI idea, I can see that a GUI for standalone blast is nicer than the command line for some people. However, I don't see how this is more useful than running a local blast web server (something the NCBI already provides). Sorry for being so negative, Peter From quwubin at gmail.com Mon Sep 8 10:38:27 2008 From: quwubin at gmail.com (Wubin Qu) Date: Mon, 8 Sep 2008 22:38:27 +0800 Subject: [Biopython-dev] [BioPython] BioPythonGUI: Graphical User Interface for BioPython In-Reply-To: <320fb6e00809080712v6c33d42fheb982f52e62e6e95@mail.gmail.com> References: <320fb6e00809080712v6c33d42fheb982f52e62e6e95@mail.gmail.com> Message-ID: Hi Peter, Thans for your reply. My goal is simple: Programs with GUI are easily to use. BioPython with GUI will facilitate people. The next module is: BlastParserGUI. I think it will be useful. Yes, SeqGUI is built on SeqGui.py. And I learn a lot from SeqGui.py. It inspires me to build other modules. I mentioned this here . ______________________________ Best regards, Wubin Qu 2008/9/8 Peter Cock > On Mon, Sep 8, 2008 at 2:43 PM, Wubin Qu wrote: > > Hi all, > > > > I started a new project named BioPythonGUI for a few of days. > > Hello Wubin Qu, > > > BioPythonGUI is a Graphical User Interface of BioPython. > > I'm uncomfortable about the name BioPythonGUI, as this to me implies > it is part of Biopython (whereas is it currently just a third party > project built on top of Biopython). What do other people think? > > > However, it's not everyone can use the BioPython, especially ones who do > not > > know much about the programming. How can you expect a professor who never > > known about any programming to use BioPython to parse the BLAST report > file? > > This is the problem which the BioPythonGUI would solve. I started the > > project with the goal "Everyone can use BioPython with BioPythonGUI". > > I don't really understand your goal. How would a non-programming > professor use your program to parse a BLAST report file? The NCBI > already try and make the HTML and plain text output useful to > non-programmers and from looking at the screenshots I don't see how > your tool would help. > > > Until now, there are two modules SeqGUI and BlastGUI are available in > > BioPythonGUI. I would greatly appreciate if you use BioPythonGUI and send > me > > the feedback. > > I see your module SeqGUI builds on the SeqGui.py in BioPython (in the > scripts directory). It might make sense to include your improvements > to this code as part of Biopython. I haven't looked at your code yet, > so I don't know how much you've changed things. > > It is nice to be able to be able to translate, transcribe, reverse > complement etc in a GUI, but personally I don't see the point or > writing a little application just for this. Also, there are probably > many many existing tools out there that already offer this > functionality. However, I am happy writing code, so I am not in your > target audience. > > Regarding your BlastGUI idea, I can see that a GUI for standalone > blast is nicer than the command line for some people. However, I > don't see how this is more useful than running a local blast web > server (something the NCBI already provides). > > Sorry for being so negative, > > Peter > From biopython at maubp.freeserve.co.uk Tue Sep 9 06:14:11 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 9 Sep 2008 11:14:11 +0100 Subject: [Biopython-dev] Biopython 1.48 released Message-ID: <320fb6e00809090314s722f404bqda71d7d9f97360e7@mail.gmail.com> We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete). The following additional file formats are now supported in Bio.SeqIO and Bio.AlignIO: * reading and writing "tab" format (simple tab separated) * writing "nexus" files * reading "pir" files (NBRF/PIR) * basic support for writing "genbank" files (GenBank plain text) This release also fixes some problems reading Clustal alignments (introduced in Biopython 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers. The SeqRecord and Alignment objects have a new method to get the object as a string in a given file format (handled via Bio.SeqIO and Bio.AlignIO). Bio.PubMed and the online code in Bio.GenBank are now considered obsolete, and we intend to deprecate them after the next release. For accessing PubMed and GenBank, please use Bio.Entrez instead. Martel and Bio.Mindy are now considered to be obsolete, and are likely to be deprecated and removed in a future release, at which point we will drop the optional dependency on mxTextTools. Bio.Fasta is also considered to be obsolete, please use Bio.SeqIO instead. We do intend to deprecate this module eventually, however, for several years this was the primary FASTA parsing module in Biopython and is likely to be in use in many existing scripts. In addition a number of other modules have been deprecated, including: Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics - see the DEPRECATED file for full details. Source distributions are available from the Biopython website at http://biopython.org, and Windows installers will be added shortly. My thanks to all bug reporters, code contributors and others who made this new release possible. Peter, on behalf of the Biopython developers P.S. This message will be forwarded to the Biopython anoucement mailing list shortly. For those of you who prefer news readers to email lists, have a look at the OBF news server: http://news.open-bio.org/news/2008/09/biopython-release-148/ where there are Biopython news feeds available: http://news.open-bio.org/news/category/obf-projects/biopython/feed/rdf http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss2 http://news.open-bio.org/news/category/obf-projects/biopython/feed/atom From mhampton at d.umn.edu Tue Sep 9 10:21:15 2008 From: mhampton at d.umn.edu (Marshall Hampton) Date: Tue, 9 Sep 2008 09:21:15 -0500 (CDT) Subject: [Biopython-dev] BioPythonGUI: Graphical User Interface for BioPython Message-ID: Hi, I think I'd mentioned this before on this list, but the BioPythonGUI post made me think I should again: people interested in GUIs and visualization with biopython should check out the Sage project: www.sagemath.org. I help maintain the inclusion of biopython in Sage as an optional package. Sage is a python-based computational platform that unites a great deal of mathematical software, and uses a web browser as its GUI. This makes sharing code very easy. I teach a bioinformatics course using Sage and biopython, which has been working very well. I wrote a brief introduction that gives some idea of what is possible with the Sage/biopython combination: http://openwetware.org/wiki/Open_writing_projects/Sage_and_cython_a_brief_introduction ...and the Sage wiki @interact examples might also give some ideas: http://wiki.sagemath.org/interact Cheers, Marshall Hampton University of Minnesota, Duluth PS. Sorry if this gets sent twice, I think I messed up the list address the first time. From mhampton at d.umn.edu Tue Sep 9 10:14:27 2008 From: mhampton at d.umn.edu (Marshall Hampton) Date: Tue, 9 Sep 2008 09:14:27 -0500 (CDT) Subject: [Biopython-dev] BioPythonGUI: Graphical User Interface for BioPython Message-ID: Hi, I think I'd mentioned this before on this list, but the BioPythonGUI post made me think I should again: people interested in GUIs and visualization with biopython should check out the Sage project: www.sagemath.org. I help maintain the inclusion of biopython in Sage as an optional package. Sage is a python-based computational platform that unites a great deal of mathematical software, and uses a web browser as its GUI. This makes sharing code very easy. I teach a bioinformatics course using Sage and biopython, which has been working very well. I wrote a brief introduction that gives some idea of what is possible with the Sage/biopython combination: http://openwetware.org/wiki/Open_writing_projects/Sage_and_cython_a_brief_introduction ...and the Sage wiki @interact examples might also give some ideas: http://wiki.sagemath.org/interact Cheers, Marshall Hampton University of Minnesota, Duluth From quwubin at gmail.com Tue Sep 9 20:28:55 2008 From: quwubin at gmail.com (Wubin Qu) Date: Wed, 10 Sep 2008 08:28:55 +0800 Subject: [Biopython-dev] BioPythonGUI: Graphical User Interface for BioPython In-Reply-To: References: Message-ID: Hi, Thank you. I am learning Sage now. I think that is another way of GUI and it's great. I'm sure I will learn a lot from Sage. ______________________________ Best regards, Wubin Qu 2008/9/9 Marshall Hampton > > Hi, > > I think I'd mentioned this before on this list, but the BioPythonGUI post > made me think I should again: people interested in GUIs and visualization > with biopython should check out the Sage project: www.sagemath.org. I > help maintain the inclusion of biopython in Sage as an optional package. > Sage is a python-based computational platform that unites a great deal of > mathematical software, and uses a web browser as its GUI. This makes > sharing code very easy. > > I teach a bioinformatics course using Sage and biopython, which has been > working very well. > > I wrote a brief introduction that gives some idea of what is possible with > the Sage/biopython combination: > > http://openwetware.org/wiki/Open_writing_projects/Sage_and_cython_a_brief_introduction > > ...and the Sage wiki @interact examples might also give some ideas: > http://wiki.sagemath.org/interact > > Cheers, > Marshall Hampton > University of Minnesota, Duluth > From bugzilla-daemon at portal.open-bio.org Wed Sep 10 05:03:43 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 10 Sep 2008 05:03:43 -0400 Subject: [Biopython-dev] [Bug 2583] New: small bug in NCBIXML.py Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2583 Summary: small bug in NCBIXML.py Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: minor Priority: P2 Component: Main Distribution AssignedTo: biopython-dev at biopython.org ReportedBy: christen at unice.fr Hi When parsing an xml blast output b_record.sc_match and b_record.sc_mismatch are returned as none this is because the lines self._blast.sc_match=self._parameters.sc_match self._blast.sc_mismatch=self._parameters.sc_mismatch are missing in def _end_Iteration(self): This is a minor bug because it is very rare that a user wants these informations, as usually they know the parameters they used to run blast. Best regards Richard Christen, U of Nice, France -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mjldehoon at yahoo.com Wed Sep 10 10:28:03 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 10 Sep 2008 07:28:03 -0700 (PDT) Subject: [Biopython-dev] NumPy conversion roadmap Message-ID: <909028.58880.qm@web62404.mail.re1.yahoo.com> Hi everybody, Now that Biopython 1.48 is out (thanks Peter!), we can now start to consider the conversion from Numerical Python to NumPy. I'd like to propose the following steps: 1) Let's wait for a week or so before making any NumPy-related commits to see if any serious problems show up with the 1.48 release. 2) Three modules use Numerical Python at the C-level: Bio.Cluster, Bio.KDTree, and Bio.Affy. I have a NumPy-based module ready for Bio.Cluster. For Bio.KDTree and Bio.Affy, see my next mails. 3) Once these three modules are converted, Biopython can be compiled again. We can then consider the modules that use Numerical Python at the Python-level. There are about ten of those. Some of them are heavily used (such as Bio.PDB), whereas others are more obscure. Conversion is usually trivial, but I'd like to suggest that we take this opportunity also to review each of these modules to see if any should be deprecated. Comments, anybody? --Michiel. From mjldehoon at yahoo.com Wed Sep 10 10:28:53 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 10 Sep 2008 07:28:53 -0700 (PDT) Subject: [Biopython-dev] Bio.Affy Message-ID: <790264.35889.qm@web62401.mail.re1.yahoo.com> Hi everybody, The C++ code in Bio.Affy seems to be out of date; it is distributed with the Biopython releases but it is not actually used. There's a comment in setup.py saying that this C++ code was replaced by Python code. Does anybody know more about this? Can the C++ code in Bio.Affy be removed? --Michiel. From mjldehoon at yahoo.com Wed Sep 10 10:35:22 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 10 Sep 2008 07:35:22 -0700 (PDT) Subject: [Biopython-dev] Bio.KDTree Message-ID: <941377.41064.qm@web62401.mail.re1.yahoo.com> Hi everybody, I have a prototype version of Bio.KDTree for NumPy. This code differs from the current Bio.KDTree in that is uses C instead of C++. Thomas (or anybody else), any objections if I upload this version to CVS to replace the current Bio.KDTree? --Michiel. From chapmanb at 50mail.com Wed Sep 10 16:26:13 2008 From: chapmanb at 50mail.com (Brad Chapman) Date: Wed, 10 Sep 2008 16:26:13 -0400 Subject: [Biopython-dev] NumPy conversion roadmap Message-ID: <20080910202613.GR21009@localdomain> Hi all; Congrats on the 1.48 release. Great stuff. Michiel, I wanted to follow up on your NumPy conversion plans. I have those NumPy changes discussed on the main list earlier this month ready to check in, along with tests passing and documentation changes and all those good things. This does very basic conversions to NumPy using the compatibility modules. It sounds like a good path would be for me to check these changes in as a starting point and then you can go with your in depth changes from there. Hopefully, this will save you some time finding all the imports and that kind of fun. Any objections? If not, I can get these in right away and you can go from there. Brad -- Brad Chapman Codon Devices http://www.codondevices.com From bugzilla-daemon at portal.open-bio.org Wed Sep 10 20:29:42 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 10 Sep 2008 20:29:42 -0400 Subject: [Biopython-dev] [Bug 2585] New: Error in Bio.SeqUtils.apply_on_multi_fasta Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2585 Summary: Error in Bio.SeqUtils.apply_on_multi_fasta Product: Biopython Version: 1.48 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev at biopython.org ReportedBy: sbassi at gmail.com Function "apply_on_multi_fasta" (in SeqUtils) has properties that are no longer valid. See this line: arguments = [record.sequence] And this line: results.append('>%s\n%s' % (record.title, result)) This provokes an error when trying to run this function (sorry I don't have the error message in this computer). A possible replacement for both lines: arguments = [record.seq] and: results.append('>%s\n%s' % (record.name, result)) -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 11 04:01:52 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 11 Sep 2008 04:01:52 -0400 Subject: [Biopython-dev] [Bug 2586] New: New version of MeltingTemp.py Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2586 Summary: New version of MeltingTemp.py Product: Biopython Version: 1.48 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev at biopython.org ReportedBy: sbassi at gmail.com This version of MeltingTemp.py has a quick test and some reformatting to make it easier to read (code style changed) -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 11 04:03:54 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 11 Sep 2008 04:03:54 -0400 Subject: [Biopython-dev] [Bug 2586] New version of MeltingTemp.py In-Reply-To: Message-ID: <200809110803.m8B83sr2017438@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2586 ------- Comment #1 from sbassi at gmail.com 2008-09-11 04:03 EST ------- Created an attachment (id=994) --> (http://bugzilla.open-bio.org/attachment.cgi?id=994&action=view) New version of MeltingTemp.py -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mjldehoon at yahoo.com Thu Sep 11 07:06:45 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Thu, 11 Sep 2008 04:06:45 -0700 (PDT) Subject: [Biopython-dev] NumPy conversion roadmap In-Reply-To: <20080910202613.GR21009@localdomain> Message-ID: <828420.78524.qm@web62408.mail.re1.yahoo.com> --- On Wed, 9/10/08, Brad Chapman wrote: > I have those NumPy changes discussed on the main list earlier > this month ready to check in, along with tests passing and > documentation changes and all those good things. > Thanks! Those changes are for Bio.PDB, right? Bio.PDB being a heavily used module, your changes are very welcome. In a sense, Thomas has the last word on changes to Bio.PDB, since he wrote the module, but if there are no objections from Thomas then feel free to submit your changes to CVS. --Michiel. From chapmanb at 50mail.com Thu Sep 11 07:56:33 2008 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 11 Sep 2008 07:56:33 -0400 Subject: [Biopython-dev] NumPy conversion roadmap In-Reply-To: <828420.78524.qm@web62408.mail.re1.yahoo.com> References: <20080910202613.GR21009@localdomain> <828420.78524.qm@web62408.mail.re1.yahoo.com> Message-ID: <20080911115633.GD6200@localdomain> Hi Michiel; > Thanks! > Those changes are for Bio.PDB, right? Bio.PDB being a heavily used > module, your changes are very welcome. In a sense, Thomas has the last > word on changes to Bio.PDB, since he wrote the module, but if there > are no objections from Thomas then feel free to submit your changes to > CVS. Yes, these handle PDB and all other Numeric modules. The changes are not to the code but rather to the imports so rather slight. We can move forward from here to a full port to NumPy if desired, but this should give the same functionality but allow people to have the up to date NumPy libraries. I checked everything in now so it should appear in CVS now. Let me know if there are any problems, and feel free to improve on these changes as y'all find best. Thanks, Brad -- Brad Chapman Codon Devices http://www.codondevices.com From mjldehoon at yahoo.com Sun Sep 14 09:23:53 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Sun, 14 Sep 2008 06:23:53 -0700 (PDT) Subject: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster. Message-ID: <259643.39583.qm@web62401.mail.re1.yahoo.com> Hi everybody, I just committed a bunch of changes to Bio.Cluster, Bio.KDTree, and setup.py that deal with the old Numerical Python to new NumPy conversion. With these changes, Biopython should compile with NumPy; any remaining references to the old Numerical Python are at the Python-level only. Since these are rather big changes, please try with the current version of CVS to see if everything compiles cleanly and all tests pass. Comments, questions, suggestions are welcome. I also uploaded a plain C (instead of C++) version of Bio.KDTree, and adjusted setup.py accordingly. --Michiel. From chapmanb at 50mail.com Sun Sep 14 13:07:07 2008 From: chapmanb at 50mail.com (Brad Chapman) Date: Sun, 14 Sep 2008 13:07:07 -0400 Subject: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster. In-Reply-To: <259643.39583.qm@web62401.mail.re1.yahoo.com> References: <259643.39583.qm@web62401.mail.re1.yahoo.com> Message-ID: <1221412027.6552.1273897487@webmail.messagingengine.com> Hi Michiel; Great stuff. One quick note, it doesn't look like KDTreemodule.c got checked into CVS: gcc: Bio/KDTree/KDTreemodule.c: No such file or directory > ls -l Bio/KDTree/ total 64 -rw-rw-r-- 1 chapmanb chapmanb 2641 2007-04-23 05:45 CKDTree.py drwxrwxr-x 2 chapmanb chapmanb 4096 2008-09-14 12:39 CVS -rw-rw-r-- 1 chapmanb chapmanb 166 2007-04-23 05:45 HISTORY -rw-rw-r-- 1 chapmanb chapmanb 432 2007-04-23 05:45 __init__.py -rw-rw-r-- 1 chapmanb synbio 29504 2008-09-14 09:15 KDTree.c -rw-rw-r-- 1 chapmanb synbio 689 2008-09-14 12:39 KDTree.h -rw-rw-r-- 1 chapmanb synbio 8165 2008-09-14 12:39 KDTree.py -rw-rw-r-- 1 chapmanb synbio 151 2008-09-14 09:15 Neighbor.h Brad On Sun, 14 Sep 2008 06:23:53 -0700 (PDT), "Michiel de Hoon" said: > Hi everybody, > > I just committed a bunch of changes to Bio.Cluster, Bio.KDTree, and > setup.py that deal with the old Numerical Python to new NumPy conversion. > With these changes, Biopython should compile with NumPy; any remaining > references to the old Numerical Python are at the Python-level only. > Since these are rather big changes, please try with the current version > of CVS to see if everything compiles cleanly and all tests pass. > Comments, questions, suggestions are welcome. > > I also uploaded a plain C (instead of C++) version of Bio.KDTree, and > adjusted setup.py accordingly. > > --Michiel. > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev -- Brad Chapman chapmanb at 50mail.com From mjldehoon at yahoo.com Sun Sep 14 13:10:16 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Sun, 14 Sep 2008 10:10:16 -0700 (PDT) Subject: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster. In-Reply-To: <259643.39583.qm@web62401.mail.re1.yahoo.com> Message-ID: <673504.47838.qm@web62403.mail.re1.yahoo.com> Hi everybody, I just noticed that one file is missing in Biopython's CVS. I'll upload it as soon as possible but it may take a day or so. Sorry for the trouble. --Michiel --- On Sun, 9/14/08, Michiel de Hoon wrote: > From: Michiel de Hoon > Subject: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster. > To: biopython-dev at biopython.org > Date: Sunday, September 14, 2008, 9:23 AM > Hi everybody, > > I just committed a bunch of changes to Bio.Cluster, > Bio.KDTree, and setup.py that deal with the old Numerical > Python to new NumPy conversion. With these changes, > Biopython should compile with NumPy; any remaining > references to the old Numerical Python are at the > Python-level only. Since these are rather big changes, > please try with the current version of CVS to see if > everything compiles cleanly and all tests pass. Comments, > questions, suggestions are welcome. > > I also uploaded a plain C (instead of C++) version of > Bio.KDTree, and adjusted setup.py accordingly. > > --Michiel. > > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From mjldehoon at yahoo.com Tue Sep 16 07:12:03 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Tue, 16 Sep 2008 04:12:03 -0700 (PDT) Subject: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster. In-Reply-To: <1221412027.6552.1273897487@webmail.messagingengine.com> Message-ID: <901846.37002.qm@web62403.mail.re1.yahoo.com> Hi everybody, I now uploaded Bio/KDTree/KDTreemodule.c to CVS. Biopython should now compile with the new NumPy (and not any more with the old Numerical Python). --Michiel. --- On Sun, 9/14/08, Brad Chapman wrote: > From: Brad Chapman > Subject: Re: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster. > To: biopython-dev at biopython.org > Date: Sunday, September 14, 2008, 1:07 PM > Hi Michiel; > Great stuff. One quick note, it doesn't look like > KDTreemodule.c got > checked into CVS: > > gcc: Bio/KDTree/KDTreemodule.c: No such file or directory > > > ls -l Bio/KDTree/ > total 64 > -rw-rw-r-- 1 chapmanb chapmanb 2641 2007-04-23 05:45 > CKDTree.py > drwxrwxr-x 2 chapmanb chapmanb 4096 2008-09-14 12:39 CVS > -rw-rw-r-- 1 chapmanb chapmanb 166 2007-04-23 05:45 > HISTORY > -rw-rw-r-- 1 chapmanb chapmanb 432 2007-04-23 05:45 > __init__.py > -rw-rw-r-- 1 chapmanb synbio 29504 2008-09-14 09:15 > KDTree.c > -rw-rw-r-- 1 chapmanb synbio 689 2008-09-14 12:39 > KDTree.h > -rw-rw-r-- 1 chapmanb synbio 8165 2008-09-14 12:39 > KDTree.py > -rw-rw-r-- 1 chapmanb synbio 151 2008-09-14 09:15 > Neighbor.h > > Brad > > On Sun, 14 Sep 2008 06:23:53 -0700 (PDT), "Michiel de > Hoon" > said: > > Hi everybody, > > > > I just committed a bunch of changes to Bio.Cluster, > Bio.KDTree, and > > setup.py that deal with the old Numerical Python to > new NumPy conversion. > > With these changes, Biopython should compile with > NumPy; any remaining > > references to the old Numerical Python are at the > Python-level only. > > Since these are rather big changes, please try with > the current version > > of CVS to see if everything compiles cleanly and all > tests pass. > > Comments, questions, suggestions are welcome. > > > > I also uploaded a plain C (instead of C++) version of > Bio.KDTree, and > > adjusted setup.py accordingly. > > > > --Michiel. > > > > > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biopython-dev > -- > Brad Chapman > chapmanb at 50mail.com > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From bugzilla-daemon at portal.open-bio.org Tue Sep 16 16:04:20 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 16 Sep 2008 16:04:20 -0400 Subject: [Biopython-dev] [Bug 2583] small bug in NCBIXML.py In-Reply-To: Message-ID: <200809162004.m8GK4KKj016559@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2583 ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-16 16:04 EST ------- I'd have looked at this earlier but was on holiday. I recall fixing a few similar issues in the past, but hadn't spotted these. I'll try and deal with this by the end of the week. Thanks Christen! Peter. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue Sep 16 16:07:07 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 16 Sep 2008 16:07:07 -0400 Subject: [Biopython-dev] [Bug 2585] Error in Bio.SeqUtils.apply_on_multi_fasta In-Reply-To: Message-ID: <200809162007.m8GK77S2016681@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2585 ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-16 16:07 EST ------- That does look like a bug - I'll have to look over the history to see how this was originally intended to be used as the current docstring isn't very clear. Another option would be something like: results.append(record.format("fasta")) -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 17 05:38:23 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 17 Sep 2008 05:38:23 -0400 Subject: [Biopython-dev] [Bug 2583] small bug in NCBIXML.py In-Reply-To: Message-ID: <200809170938.m8H9cN2Y024263@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2583 ------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-17 05:38 EST ------- Christen - what version of Biopython are you using? The reason the match/mis-match issue sounded so familiar to me is I fixed it in Biopython 1.46 after Sebastian Bassi reported it on the mailing list in March. If you can confirm you are using Biopython 1.45 or older, then could you try updating you machine? We should then be able to mark this bug as fixed. Thanks Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 17 07:17:23 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 17 Sep 2008 07:17:23 -0400 Subject: [Biopython-dev] [Bug 2586] New version of MeltingTemp.py In-Reply-To: Message-ID: <200809171117.m8HBHNC9028796@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2586 biopython-bugzilla at maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-17 07:17 EST ------- Updated checked in. Thanks Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 17 07:34:34 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 17 Sep 2008 07:34:34 -0400 Subject: [Biopython-dev] [Bug 2585] Error in Bio.SeqUtils.apply_on_multi_fasta In-Reply-To: Message-ID: <200809171134.m8HBYYte029584@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2585 ------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-17 07:34 EST ------- This bug was introduced in CVS revision 1.13 of Bio/SeqUtils/__init__.py when moving from Bio.Fasta.RecordParser (which used Fasta record objects with a title property) to Bio.SeqIO (which uses SeqRecord objects instead). With hindsight this is a clear oversight (which also changed the usage of the function). Your fix looks fine for recovering some of the original behaviour. We should also clarify the docstrings of these (and other functions in this module) to make it explicit where the "file" argument should be a filename. However, I am tempted however to deprecate apply_on_multi_fasta and quicker_apply_on_multi_fasta (and some of the other code here) as to me using a Bio.SeqIO with a for loop is much clearer. e.g. def my_function ... for record in SeqIO.parse(open(filename), "fasta") : my_function(record) versus: def my_function ... apply_on_multi_fasta(filename, my_function) What do you think Sebastian? Did you have a real example for using apply_on_multi_fasta or did you happen to spot the bug? Thanks, Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 17 08:19:40 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 17 Sep 2008 08:19:40 -0400 Subject: [Biopython-dev] [Bug 2585] Error in Bio.SeqUtils.apply_on_multi_fasta In-Reply-To: Message-ID: <200809171219.m8HCJebF031531@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2585 ------- Comment #3 from sbassi at gmail.com 2008-09-17 08:19 EST ------- (In reply to comment #2) > What do you think Sebastian? Did you have a real example for using > apply_on_multi_fasta or did you happen to spot the bug? I don't use this function myself and I also think it is redundant. I spotted it just because I am checking most biopython function for a book on python for bioinformatics I am writing. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Sep 17 10:12:44 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 17 Sep 2008 10:12:44 -0400 Subject: [Biopython-dev] [Bug 2585] Error in Bio.SeqUtils.apply_on_multi_fasta In-Reply-To: Message-ID: <200809171412.m8HECiP2005746@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2585 biopython-bugzilla at maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-17 10:12 EST ------- I've made your suggested fix in CVS, and added a docstring to this and the related functions. I've described them as obsolete but will also suggest their deprecation on the mailing list... Thanks for your report. Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mjldehoon at yahoo.com Wed Sep 17 10:13:50 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 17 Sep 2008 07:13:50 -0700 (PDT) Subject: [Biopython-dev] Numpy conversion Message-ID: <998217.51422.qm@web62404.mail.re1.yahoo.com> Hi everybody, I am now looking at the pure-python modules that make use of Numerical Python / NumPy. Bio.kNN is one of them; this also happens to be the only module that imports Bio.distance, which also depends on NumPy. What I am not sure about is the usage of Bio.kNN. A quick google search didn't reveal much, suggesting that it is not widely used. Bio.kNN currently is not documented in the tutorial, but the code itself is reasonably well documented. How do you guys feel about this module? Should we keep it? --Michiel. From biopython at maubp.freeserve.co.uk Wed Sep 17 10:23:23 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 17 Sep 2008 15:23:23 +0100 Subject: [Biopython-dev] Cleaning up Bio.SeqUtils Message-ID: <320fb6e00809170723w95c87b0r94c4b12574ce174f@mail.gmail.com> Dear all, I've previously mentioned the idea of cleaning up Bio/SeqUtils/__init__.py in passing. I've been reminded about this by Bug 2585 where Sebastian spotted a problem in one of the FASTA related functions. http://bugzilla.open-bio.org/show_bug.cgi?id=2585 I've updated the docstrings in CVS to describe the three functions quick_FASTA_reader, apply_on_multi_fasta and quicker_apply_on_multi_fasta as obsolete but I would like to suggest going further and deprecating them. There are other dubious or redundant functions in Bio/SeqUtils/__init__.py such as a translate function. Again, would there be any objection to deprecating this too? Peter From biopython at maubp.freeserve.co.uk Wed Sep 17 10:29:35 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 17 Sep 2008 15:29:35 +0100 Subject: [Biopython-dev] Numpy conversion In-Reply-To: <998217.51422.qm@web62404.mail.re1.yahoo.com> References: <998217.51422.qm@web62404.mail.re1.yahoo.com> Message-ID: <320fb6e00809170729g49b97488l629c4132c99b44f0@mail.gmail.com> On Wed, Sep 17, 2008 at 3:13 PM, Michiel de Hoon wrote: > Hi everybody, > > I am now looking at the pure-python modules that make use of Numerical Python / NumPy. > Bio.kNN is one of them; this also happens to be the only module that imports Bio.distance, > which also depends on NumPy. > > What I am not sure about is the usage of Bio.kNN. A quick google search didn't reveal much, > suggesting that it is not widely used. Bio.kNN currently is not documented in the tutorial, but > the code itself is reasonably well documented. > > How do you guys feel about this module? Should we keep it? > I've not used it myself, but it sounds handy. Michiel, does this overlap at all with your clustering module? Peter From sbassi at gmail.com Wed Sep 17 18:46:23 2008 From: sbassi at gmail.com (Sebastian Bassi) Date: Wed, 17 Sep 2008 19:46:23 -0300 Subject: [Biopython-dev] Author of "restriction tutorial"? Message-ID: I want to cite in a book the Restriction tutorial (http://biopython.org/DIST/docs/cookbook/Restriction.html) so I need author(s) name(s). I can't find the author name so I ask here to cite it properly. Best, SB. -- Vendo isla: http://www.genesdigitales.com/isla/ Curso Biologia Molecular para programadores: http://tinyurl.com/2vv8w6 Bioinformatics news: http://www.bioinformatica.info Tutorial libre de Python: http://tinyurl.com/2az5d5 From bugzilla-daemon at portal.open-bio.org Wed Sep 17 23:15:51 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 17 Sep 2008 23:15:51 -0400 Subject: [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values In-Reply-To: Message-ID: <200809180315.m8I3Fpk9008139@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2480 ------- Comment #19 from robert.cadena at gmail.com 2008-09-17 23:15 EST ------- A quick fix to this might be to call a .bat file that calls the blastall executable. For example: blastall_wrapper.bat: "c:/Documents and Settings/maldoror/My Documents/blast/bin/blastall.exe" %1 %2 %3 %4 %5 %6 %7 %8 %9 All arguments containing spaces should be escaped with "\"[arg]". For example: my_blast_db should be r"\"\\\"c:/documents and settings/maldoror/my documents/blast/bin/mine\"" When the above value is printed out it should look like: "\"c:/documents ...." finally, set my_blastall_exe to the batch file: "\"c:/documents and settings .../blastall_wrapper.bat\"" You still have to deal with the problem that os.path.exists and os.system expect the command with and without quotes. but, at least the batch file wrapper method should pass the arguments properly. hope it works on your system. best of luck. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From biopython at maubp.freeserve.co.uk Thu Sep 18 05:58:04 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 18 Sep 2008 10:58:04 +0100 Subject: [Biopython-dev] Author of "restriction tutorial"? In-Reply-To: References: Message-ID: <320fb6e00809180258v49f43d4ej7c03551172c9c638@mail.gmail.com> On Wed, Sep 17, 2008 at 11:46 PM, Sebastian Bassi wrote: > I want to cite in a book the Restriction tutorial > (http://biopython.org/DIST/docs/cookbook/Restriction.html) so I need > author(s) name(s). > I can't find the author name so I ask here to cite it properly. > Best, > SB. It is a little surprising the author didn't include his name in the HTML document, but looking at CVS and the mailing list archives, I think this is by Frederic Sohm. http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Doc/cookbook/Restriction/?cvsroot=biopython http://portal.open-bio.org/pipermail/biopython/2005-February/002548.html (I recall reading an earlier thread where Frederic offered the package with documentation, but I haven't found it again). Peter From bugzilla-daemon at portal.open-bio.org Thu Sep 18 06:58:26 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 06:58:26 -0400 Subject: [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values In-Reply-To: Message-ID: <200809181058.m8IAwQLw001437@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2480 ------- Comment #20 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-18 06:58 EST ------- I think I've fixed some of this in CVS. Biopython should now cope with a blast exe or input file with spaces in the name - but thus far I have only tested this on Mac OS X. See Bio/Blast/NCBIStandalone.py revision 1.77 in CVS. You will be able to look at the changes and download them via the following URL shortly: http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py?cvsroot=biopython Dealing with database(s) where the path(s) contain spaces is trickier. I think the best solution here is to setup BLAST so that it knows where to find your databases, and then you can refer to them by name only (no paths, therefore no spaces). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From biopython at maubp.freeserve.co.uk Thu Sep 18 08:15:50 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 18 Sep 2008 13:15:50 +0100 Subject: [Biopython-dev] Modules to be removed from Biopython In-Reply-To: <320fb6e00808080417y483f74c8xd94dd7ca9eea0476@mail.gmail.com> References: <492634.64872.qm@web62414.mail.re1.yahoo.com> <320fb6e00806270950k479eda23ia96d3c2d36557510@mail.gmail.com> <320fb6e00807160540w325fe995mea400b0014fd7c2e@mail.gmail.com> <320fb6e00807220913g64613854j7a1deb5b4357f726@mail.gmail.com> <320fb6e00808080417y483f74c8xd94dd7ca9eea0476@mail.gmail.com> Message-ID: <320fb6e00809180515g59e53bddoa1d83242df198a1@mail.gmail.com> I wrote: >> Bio.expressions was already deprecated, and seems to be a dependency >> of the following modules, which I have now explicitly deprecated in CVS: I plan to remove these four deprecated modules shortly, unless anyone objects: Bio.expressions (deprecated in Biopython 1.44) Bio.config (explicitly deprecated in Biopython 1.48) Bio.dbdefs (explicitly deprecated in Biopython 1.48) Bio.formatdefs (explicitly deprecated in Biopython 1.48) At the same time I would remove the associated bit of unused code in Bio/__init__.py Peter From mjldehoon at yahoo.com Thu Sep 18 10:10:49 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Thu, 18 Sep 2008 07:10:49 -0700 (PDT) Subject: [Biopython-dev] Numpy conversion In-Reply-To: <320fb6e00809170729g49b97488l629c4132c99b44f0@mail.gmail.com> Message-ID: <37659.57326.qm@web62402.mail.re1.yahoo.com> > I've not used it myself, but it sounds handy. Michiel, > does this overlap at all with your clustering module? No, it doesn't. Bio.Cluster contains unsupervised clustering methods only. The k-nearest neighbors in Bio.kNN is a supervised learning method. --Michiel. --- On Wed, 9/17/08, Peter wrote: > From: Peter > Subject: Re: [Biopython-dev] Numpy conversion > To: mjldehoon at yahoo.com > Cc: biopython-dev at biopython.org > Date: Wednesday, September 17, 2008, 10:29 AM > On Wed, Sep 17, 2008 at 3:13 PM, Michiel de Hoon > wrote: > > Hi everybody, > > > > I am now looking at the pure-python modules that make > use of Numerical Python / NumPy. > > Bio.kNN is one of them; this also happens to be the > only module that imports Bio.distance, > > which also depends on NumPy. > > > > What I am not sure about is the usage of Bio.kNN. A > quick google search didn't reveal much, > > suggesting that it is not widely used. Bio.kNN > currently is not documented in the tutorial, but > > the code itself is reasonably well documented. > > > > How do you guys feel about this module? Should we keep > it? > > > > I've not used it myself, but it sounds handy. Michiel, > does this > overlap at all with your clustering module? > > Peter From biopython at maubp.freeserve.co.uk Thu Sep 18 11:00:16 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 18 Sep 2008 16:00:16 +0100 Subject: [Biopython-dev] test_MarkovModel.py and Numeric/numpy work? Message-ID: <320fb6e00809180800ic2752dfoe00801f67b57c65c@mail.gmail.com> Hi all, I'm back from my one week holiday, and after I updated my machine I'm seeing a new failure in test_MarkovModel.py is probably related to the Numeric/numpy work, $ python run_tests.py test_MarkovModel.py test_MarkovModel ... ERROR (output cut) $python test_MarkovModel.py TESTING train_visible Training HMM Classifying [(['0', '0', '1', '2', '3', '3'], 0.0082128906250000053)] STATES: 0 1 2 3 ALPHABET: A C G T INITIAL: 0: 1.00 1: 0.00 2: 0.00 3: 0.00 TRANSITION: 0: 0.20 0.80 0.00 0.00 1: 0.00 0.50 0.50 0.00 2: 0.00 0.00 0.50 0.50 3: 0.00 0.00 0.00 1.00 EMISSION: 0: 0.67 0.11 0.11 0.11 1: 0.08 0.75 0.08 0.08 2: 0.08 0.08 0.75 0.08 3: 0.03 0.03 0.03 0.91 TESTING baum welch Training HMM Traceback (most recent call last): File "test_MarkovModel.py", line 64, in p_emission=p_emission File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/MarkovModel.py", line 181, in _baum_welch if not p_initial.any(): AttributeError: any $ python Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> Numeric.__version__ '24.2' >>> import numpy Traceback (most recent call last): File "", line 1, in ImportError: No module named numpy >>> The above is on Mac OS X 10.5 (Tiger) with Numeric installed, but not numpy. I see something similar but slightly different on a Linux machine with both Numeric and an old version of numpy. Looking at the CVS log, I wonder if this is due to the switch from an array based or, to an if based manipulation of p_initial, p_transition and p_emission? http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/MarkovModel.py.diff?r1=1.3&r2=1.4&cvsroot=biopython Peter From bugzilla-daemon at portal.open-bio.org Thu Sep 18 11:21:59 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 11:21:59 -0400 Subject: [Biopython-dev] [Bug 2588] New: tutorial blast section uses undefined variables Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2588 Summary: tutorial blast section uses undefined variables Product: Biopython Version: 1.48 Platform: Other OS/Version: All Status: NEW Severity: trivial Priority: P2 Component: Documentation AssignedTo: biopython-dev at biopython.org ReportedBy: bsouthey at gmail.com Tutorial Section 6.6.2 'Parsing a file full of BLAST runs' has line: >>> blast_iterator = NCBIStandalone.Iterator(blast_handle, blast_parser) but 'blast_handle' is undefined. This line should probably be: >>> blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser) where result_handle is define in Section 6.6.1 'Parsing plain-text BLAST output': >>> result_handle = open("my_file_of_blast_output.txt") Also: >>> for b_record in b_iterator : probably should be: >>> for b_record in blast_iterator : -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From p.j.a.cock at googlemail.com Thu Sep 18 11:25:16 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 18 Sep 2008 16:25:16 +0100 Subject: [Biopython-dev] Numeric/numpy - Bio/Affy/CelFile.py Message-ID: <320fb6e00809180825q796a7a1ay7fda222a77de678@mail.gmail.com> Michiel & Brad, It was my impression that for the next release of Biopython (or next few releases?) we would support either numpy or Numeric (decided at compile time for the C code, but at run time for pure-python modules). I notice that with CVS revision 1.5 of Bio/Affy/CelFile.py, this file only uses numpy (dropping support for Numeric). http://code.open-bio.org/cgi/viewcvs.cgi/biopython/Bio/Affy/CelFile.py.diff?r1=1.4&r2=1.5&cvsroot=biopython Was this just an oversight, or to resolve some incompatibility between Numeric and numpy? It would be nice to support both... Peter From bugzilla-daemon at portal.open-bio.org Thu Sep 18 11:33:39 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 11:33:39 -0400 Subject: [Biopython-dev] [Bug 2588] tutorial blast section uses undefined variables In-Reply-To: Message-ID: <200809181533.m8IFXde1017191@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2588 biopython-bugzilla at maubp.freeserve.co.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-18 11:33 EST ------- Well spotted! I've fixed those in CVS, plus made b_record into blast_record for consistency with the rest of the chapter. See biopython/Doc/Tutorial.tex CVS revision 1.159 http://code.open-bio.org/cgi/viewcvs.cgi/biopython/Doc/Tutorial.tex?cvsroot=biopython Thanks Bruce, Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 18 17:49:02 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 17:49:02 -0400 Subject: [Biopython-dev] [Bug 2589] New: Errors in running tests in 1.48 Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2589 Summary: Errors in running tests in 1.48 Product: Biopython Version: 1.48 Platform: PC OS/Version: Linux Status: NEW Severity: minor Priority: P2 Component: Unit Tests AssignedTo: biopython-dev at biopython.org ReportedBy: bsouthey at gmail.com I downloaded BioPython 1.48 on x64 Linux fedora rawhide (kernel 2.6.27-0.329.rc6.git2.fc10.x86_64) $python setup.py build $python setup.py test The test that fails is: ERROR: test_MarkovModel ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 152, in runTest self.runSafeTest() File "run_tests.py", line 165, in runSafeTest cur_test = __import__(self.test_name) File "test_MarkovModel.py", line 61, in p_emission=p_emission File "/home/bsouthey/bioinfo/biopython-1.48/build/lib.linux-x86_64-2.5/Bio/MarkovModel.py", line 199, in _baum_welch lpseudo_initial, lpseudo_transition, lpseudo_emission,) File "/home/bsouthey/bioinfo/biopython-1.48/build/lib.linux-x86_64-2.5/Bio/MarkovModel.py", line 255, in _baum_welch_one lp_initial[:] = lp_arcout_t[:,0] ValueError: matrices are not aligned for copy Also these two errors with no explanation because Fdist and SimCoal are not included as required or optional software. Should be added to the list. test_PopGen_FDist ... skipping. Fdist not found (not a problem if you do not intend to use it). test_PopGen_SimCoal ... skipping. SimCoal not found (not a problem if you do not intend to use it). No explanation of what this is: test_GFF ... skipping. Environment is not configured for this test (not important if you do not plan to use Bio.GFF). I know these ones because MySQL is not installed but this test should be cleaner especially since this is involves optional software: test_BioSQL ... skipping. test_BioSQL_SeqIO ... skipping. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 18 18:33:36 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 18:33:36 -0400 Subject: [Biopython-dev] [Bug 2589] Errors in running tests in 1.48 In-Reply-To: Message-ID: <200809182233.m8IMXaai020481@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2589 ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-18 18:33 EST ------- Hi Bruce, The test_MarkovModel problem looks serious, but improvements to the messages from skipped tests are also worthwhile. test_MarkovModel ================ This is interesting, I've not seen this before. What version of Numeric do you have? You can find out at the python prompt with: import Numeric print Numeric.__version__ test_PopGen_FDist and test_PopGen_SimCoal ========================================= These are 3rd party population genetics tools. Do you think they should be listed under http://biopython.org/wiki/Download#Optional_Software test_GFF ======== This unit test requires a GFF wormbase MySQL database to be setup, plus an environment variable for the password. This is fairly complicated to explain, hence "Environment is not configured for this test (not important if you do not plan to use Bio.GFF)." test_BioSQL and test_BioSQL_SeqIO ================================= These require a BioSQL database with python driver to be installed plus the username and password etc to be given in setup_BioSQL.py. What message did you get exactly, and how would you suggest improving the message given? Thanks, Peter -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 18 18:45:00 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 18:45:00 -0400 Subject: [Biopython-dev] [Bug 2589] Errors in running tests in 1.48 In-Reply-To: Message-ID: <200809182245.m8IMj0NI022825@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2589 ------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-18 18:45 EST ------- (In reply to comment #1) > test_PopGen_FDist and test_PopGen_SimCoal > ========================================= > These are 3rd party population genetics tools. Do you think they should > be listed under http://biopython.org/wiki/Download#Optional_Software I've added these on the wiki (and split the list into sections). Is that better now? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 18 18:52:27 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 18:52:27 -0400 Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython In-Reply-To: Message-ID: <200809182252.m8IMqRTk024233@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2251 ------- Comment #15 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-18 18:52 EST ------- For those not following the dev-mailing list, Numeric to numpy changes have begun to be checked into CVS. Brad said he had used Ed's patch for a lot of this - so thanks Ed! -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Sep 18 23:01:37 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 18 Sep 2008 23:01:37 -0400 Subject: [Biopython-dev] [Bug 2589] Errors in running tests in 1.48 In-Reply-To: Message-ID: <200809190301.m8J31bmd012377@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2589 ------- Comment #3 from bsouthey at gmail.com 2008-09-18 23:01 EST ------- (In reply to comment #1) > Hi Bruce, > > The test_MarkovModel problem looks serious, but improvements to the messages > from skipped tests are also worthwhile. > > test_MarkovModel > ================ > This is interesting, I've not seen this before. What version of Numeric do you > have? You can find out at the python prompt with: > > import Numeric > print Numeric.__version__ 24.2 Based on a Google search, this is a 64bit problem with Python 2.5 and Numeric. So either do: 1) Drop the [:] from the left-hand side: lp_initial = lp_arcout_t[:,0] 2) Do a loop: for bi in range(lp_initial.shape[0]): lp_initial[bi] = lp_arcout_t[bi,0] 3) Support NumPy - oh, wait already done... :-) > > test_PopGen_FDist and test_PopGen_SimCoal > ========================================= > These are 3rd party population genetics tools. Do you think they should be > listed under http://biopython.org/wiki/Download#Optional_Software Excellent! It is also good promo on what BioPython can do. > > test_GFF > ======== > This unit test requires a GFF wormbase MySQL database to be setup, plus an > environment variable for the password. This is fairly complicated to explain, > hence "Environment is not configured for this test (not important if you do not > plan to use Bio.GFF)." I did not see where GFF is mentioned so a link would be worthwhile. Also, this is probably the wrong place for the test or it should not be referenced unless asked. > > test_BioSQL and test_BioSQL_SeqIO > ================================= > These require a BioSQL database with python driver to be installed plus the > username and password etc to be given in setup_BioSQL.py. What message did you > get exactly, and how would you suggest improving the message given? test_BioSQL ... skipping. Connection failed, check settings in Tests/setup_BioSQL.py if you plan to use BioSQL: (2002, "Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)") ok test_BioSQL_SeqIO ... skipping. Connection failed, check settings in Tests/setup_BioSQL.py if you plan to use BioSQL: (2002, "Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)") ok I initially thought to note these in the installation but after looking at the BioSQL page, these MySQL tests should not be run to test BioPython. These are BioSQL tests such they should be run after MySQL and BioSQL have been setup. So these should not be tested unless asked for. > > Thanks, > > Peter > No, thanks to all the developers as this is too minor. Bruce -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mjldehoon at yahoo.com Fri Sep 19 09:05:31 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Fri, 19 Sep 2008 06:05:31 -0700 (PDT) Subject: [Biopython-dev] Numeric/numpy - Bio/Affy/CelFile.py In-Reply-To: <320fb6e00809180825q796a7a1ay7fda222a77de678@mail.gmail.com> Message-ID: <78171.17163.qm@web62406.mail.re1.yahoo.com> Actually, I was under the impression that the latest consensus was to go to NumPy directly. It's quite complicated to support both NumPy and Numerical Python, at least at the C level. --Michiel. --- On Thu, 9/18/08, Peter Cock wrote: > From: Peter Cock > Subject: [Biopython-dev] Numeric/numpy - Bio/Affy/CelFile.py > To: "BioPython-Dev Mailing List" > Date: Thursday, September 18, 2008, 11:25 AM > Michiel & Brad, > > It was my impression that for the next release of Biopython > (or next > few releases?) we would support either numpy or Numeric > (decided at > compile time for the C code, but at run time for > pure-python modules). > > I notice that with CVS revision 1.5 of Bio/Affy/CelFile.py, > this file > only uses numpy (dropping support for Numeric). > http://code.open-bio.org/cgi/viewcvs.cgi/biopython/Bio/Affy/CelFile.py.diff?r1=1.4&r2=1.5&cvsroot=biopython > > Was this just an oversight, or to resolve some > incompatibility between > Numeric and numpy? It would be nice to support both... > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From p.j.a.cock at googlemail.com Fri Sep 19 09:57:19 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 19 Sep 2008 14:57:19 +0100 Subject: [Biopython-dev] Numeric/numpy - Bio/Affy/CelFile.py In-Reply-To: <78171.17163.qm@web62406.mail.re1.yahoo.com> References: <320fb6e00809180825q796a7a1ay7fda222a77de678@mail.gmail.com> <78171.17163.qm@web62406.mail.re1.yahoo.com> Message-ID: <320fb6e00809190657j662b8824n6be5ac593c13aaef@mail.gmail.com> On Fri, Sep 19, 2008 at 2:05 PM, Michiel de Hoon wrote: > Actually, I was under the impression that the latest consensus was to go to NumPy directly. It's quite complicated to support both NumPy and Numerical Python, at least at the C level. I was assuming dual support for both numpy or Numeric for the next release based on code like this: try: from Numeric import x, y, z except ImportError: from numpy.oldnumeric import x, y, z where I assumed the C code would have been decided at compile time. If a simple switch from Numeric to numpy is what you and Brad had in mind, that's OK with me but in the python code we should just use simple imports from numpy only. Peter From mjldehoon at yahoo.com Fri Sep 19 11:03:47 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Fri, 19 Sep 2008 08:03:47 -0700 (PDT) Subject: [Biopython-dev] Numeric/numpy - Bio/Affy/CelFile.py In-Reply-To: <320fb6e00809190657j662b8824n6be5ac593c13aaef@mail.gmail.com> Message-ID: <828325.7957.qm@web62406.mail.re1.yahoo.com> > try: > from Numeric import x, y, z > except ImportError: > from numpy.oldnumeric import x, y, z This is the easy part. Keep in mind though that the "from numpy.oldnumeric import x, y, z" approach is only a temporary solution; at some point, the oldnumeric wrapper will disappear from numpy. > where I assumed the C code would have been decided at > compile time. This is the complicated part; it's not just replacing one #include with another. We'd have to use a bunch of #ifdefs to separate the old code from the new code. Anyway I was planning to go through the Numerical Python - dependent code to see if any other changes are needed. If anybody wants to be able to use the old Numerical Python, please let yourself be heard; otherwise I suggest we go directly to NumPy. --Michiel --- On Fri, 9/19/08, Peter Cock wrote: > From: Peter Cock > Subject: Re: [Biopython-dev] Numeric/numpy - Bio/Affy/CelFile.py > To: mjldehoon at yahoo.com > Cc: "BioPython-Dev Mailing List" > Date: Friday, September 19, 2008, 9:57 AM > On Fri, Sep 19, 2008 at 2:05 PM, Michiel de Hoon > wrote: > > Actually, I was under the impression that the latest > consensus was to go to NumPy directly. It's quite > complicated to support both NumPy and Numerical Python, at > least at the C level. > > I was assuming dual support for both numpy or Numeric for > the next > release based on code like this: > > try: > from Numeric import x, y, z > except ImportError: > from numpy.oldnumeric import x, y, z > > where I assumed the C code would have been decided at > compile time. > > If a simple switch from Numeric to numpy is what you and > Brad had in > mind, that's OK with me but in the python code we > should just use > simple imports from numpy only. > > Peter From p.j.a.cock at googlemail.com Fri Sep 19 11:42:26 2008 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 19 Sep 2008 16:42:26 +0100 Subject: [Biopython-dev] Numeric/numpy Message-ID: <320fb6e00809190842i6583f7bard82b03d5ea36f51e@mail.gmail.com> Michiel wrote: >Peter wrote: >> I was assuming dual support for both numpy or Numeric for the next >> release based on code like this: >> >> try: >> from Numeric import x, y, z >> except ImportError: >> from numpy.oldnumeric import x, y, z > > This is the easy part. Keep in mind though that the "from numpy.oldnumeric import x, y, z" approach is only a temporary solution; at some point, the oldnumeric wrapper will disappear from numpy. Yes, if/when the oldnumeric wrapper goes away we'll have more work to do. Something to worry about later. >> where I assumed the C code would have been decided at >> compile time. > > This is the complicated part; it's not just replacing one #include with another. We'd have to use a bunch of #ifdefs to separate the old code from the new code. > > Anyway I was planning to go through the Numerical Python - dependent code to see if any other > changes are needed. If anybody wants to be able to use the old Numerical Python, please let > yourself be heard; otherwise I suggest we go directly to NumPy. > > --Michiel That suits me - how about we post something like this on the main discussion list then?: Dear all, As you probably are well aware, Biopython releases to date have used the now obsolete Numeric python library. This is no longer being maintained and has been superseded by the numpy library. See http://www.scipy.org/History_of_SciPy for more about details on the history of numerical python. Biopython 1.48 should be the last Numeric only release of Biopython - we have already started moving to numpy in CVS. Supporting both Numeric and numpy ought to be fairly straight forward for the pure python modules in Biopython. However, we also have C code which must interact with Numeric/numpy, and trying to support both would be harder. Would anyone be inconvenienced if the next release of Biopython supported numpy ONLY (dropping support for Numeric)? If so please speak up now - either here or on the development mailing list. Otherwise, a simple switch from Numeric to numpy will probably be the most straightforward migration plan. Thank you, ... From bugzilla-daemon at portal.open-bio.org Fri Sep 19 14:26:17 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 19 Sep 2008 14:26:17 -0400 Subject: [Biopython-dev] [Bug 2591] New: GenBank files misparsed for long organism names Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2591 Summary: GenBank files misparsed for long organism names Product: Biopython Version: 1.47 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev at biopython.org ReportedBy: joelb at lanl.gov I've noticed a problem with BioPython 1.47 mis-parsing the organism and lineage in GenBank files from certain bacteria. All of the problem organisms have names longer than 61 characters, and a line wrap is introduced into the SOURCE and ORGANISM records, which causes the mis-parsing. My reading of the GenBank file docs says that lines should be of variable length rather than being split, so it appears this bug is GenBank's problem rather than BioPython's. I have sent e-mail to info at ncbi.nlm.nih.gov about the issue just now. GenBank doesn't seem to have a bug tracker, though, so I'm writing the issue here to document it for other people. The issue exists for a number of organisms (more than 6, though I haven't done the exact count). One example may be found at ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Salmonella_enterica_serovar_Paratyphi_A_AKU_12601/NC_011147.gbk or http://tinyurl.com/47yg5g When parsing this file, the taxonomy list returned begins with ["AKU_12601 Bacteria","Proteobacteria"... Some of the other examples have made it onto web sites which have included the mis-parsed data, e.g. Superfam http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=x6 which shows the error for Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67. I'll append the response from GenBank to this bug if and when I get one. If I don't get one, then I'll try to come up with a workaround. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Sep 19 15:05:45 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 19 Sep 2008 15:05:45 -0400 Subject: [Biopython-dev] [Bug 2591] GenBank files misparsed for long organism names In-Reply-To: Message-ID: <200809191905.m8JJ5jUY028741@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2591 ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2008-09-19 15:05 EST ------- That file starts as follows: LOCUS NC_011147 4581797 bp DNA circular BCT 29-AUG-2008 DEFINITION Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601, complete genome. ACCESSION NC_011147 VERSION NC_011147.1 GI:197361212 KEYWORDS complete genome. SOURCE Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601 ORGANISM Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella. REFERENCE 1 ... The multiline DEFINITION and SOURCE should be fine. However, we expect ORGANISM to be a single line followed by a multiline taxonomy lineage - hense the problem you observed. This may well be an NCBI bug but it seems likely this kind of problem will occur more often in future as more and more (sub)strains of bacteria are sequenced, requiring longer names. Let's wait and hear what the NCBI says - I expect they will have to change the file format definition slightly. If they say this is a valid file, I hope they will also explain officially how we should split up the species and its lineage. One option would be some thing like looking for semi-colons in the following text as indicative of the lineage (rather than as more of the ORGANISM). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From chapmanb at 50mail.com Fri Sep 19 18:34:20 2008 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 19 Sep 2008 18:34:20 -0400 Subject: [Biopython-dev] Numeric/numpy In-Reply-To: <320fb6e00809190842i6583f7bard82b03d5ea36f51e@mail.gmail.com> References: <320fb6e00809190842i6583f7bard82b03d5ea36f51e@mail.gmail.com> Message-ID: <20080919223420.GA13009@localdomain> Peter; Michiel covered most everything here. My initial check-ins are basically the try/except you describe and it looks like Michiel has gone further and worked on real NumPy transitions. My opinion is to post that message to the main list and move forward with converting to MumPy exclusively as people are able to tackle the task for different module. Once something has been converted in a real way, and not just using oldnumeric imports, then the try/except can go away. I suspect not too many people will still be stuck on Numerical, and should be excited to get up to date with that library. Brad > Michiel wrote: > >Peter wrote: > >> I was assuming dual support for both numpy or Numeric for the next > >> release based on code like this: > >> > >> try: > >> from Numeric import x, y, z > >> except ImportError: > >> from numpy.oldnumeric import x, y, z > > > > This is the easy part. Keep in mind though that the "from numpy.oldnumeric import x, y, z" approach is only a temporary solution; at some point, the oldnumeric wrapper will disappear from numpy. > > Yes, if/when the oldnumeric wrapper goes away we'll have more work to > do. Something to worry about later. > > >> where I assumed the C code would have been decided at > >> compile time. > > > > This is the complicated part; it's not just replacing one #include with another. We'd have to use a bunch of #ifdefs to separate the old code from the new code. > > > > Anyway I was planning to go through the Numerical Python - dependent code to see if any other > > changes are needed. If anybody wants to be able to use the old Numerical Python, please let > > yourself be heard; otherwise I suggest we go directly to NumPy. > > > > --Michiel > > That suits me - how about we post something like this on the main > discussion list then?: > > Dear all, > > As you probably are well aware, Biopython releases to date have used > the now obsolete Numeric python library. This is no longer being > maintained and has been superseded by the numpy library. See > http://www.scipy.org/History_of_SciPy for more about details on the > history of numerical python. Biopython 1.48 should be the last > Numeric only release of Biopython - we have already started moving to > numpy in CVS. > > Supporting both Numeric and numpy ought to be fairly straight forward > for the pure python modules in Biopython. However, we also have C code > which must interact with Numeric/numpy, and trying to support both > would be harder. > > Would anyone be inconvenienced if the next release of Biopython > supported numpy ONLY (dropping support for Numeric)? If so please > speak up now - either here or on the development mailing list. > Otherwise, a simple switch from Numeric to numpy will probably be the > most straightforward migration plan. > > Thank you, > > ... > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev -- Brad Chapman Codon Devices http://www.codondevices.com From mjldehoon at yahoo.com Fri Sep 19 23:00:09 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Fri, 19 Sep 2008 20:00:09 -0700 (PDT) Subject: [Biopython-dev] test_MarkovModel.py and Numeric/numpy work? In-Reply-To: <320fb6e00809180800ic2752dfoe00801f67b57c65c@mail.gmail.com> Message-ID: <200283.98234.qm@web62404.mail.re1.yahoo.com> This is an example where the old Numerical Python and the new NumPy need different code at the Python-level. The Numerical Python -dependent code was: p_initial = _safe_copy_and_check(p_initial, (N,)) or _random_norm(N) Here, _safe_copy_and_check returns an array. NumPy does not allow interpreting an array as a boolean, so instead we have to use: p_initial = _safe_copy_and_check(p_initial, (N,)) if not p_initial.any(): p_initial = _random_norm(N) which is the code Brad uploaded to CVS. However, Numerical Python arrays don't have the .any() method, so this fails with the old Numerical Python. Let's first see if anybody wants to continue using the old Numerical Python. If so, we can add some try:except: around the call to p_initial.any(). If not, then Brad's code is fine. --Michiel. --- On Thu, 9/18/08, Peter wrote: > From: Peter > Subject: [Biopython-dev] test_MarkovModel.py and Numeric/numpy work? > To: "BioPython-Dev Mailing List" > Date: Thursday, September 18, 2008, 11:00 AM > Hi all, > > I'm back from my one week holiday, and after I updated > my machine I'm > seeing a new failure in test_MarkovModel.py is probably > related to the > Numeric/numpy work, > > $ python run_tests.py test_MarkovModel.py > test_MarkovModel ... ERROR > (output cut) > > $python test_MarkovModel.py > TESTING train_visible > Training HMM > Classifying > [(['0', '0', '1', '2', > '3', '3'], 0.0082128906250000053)] > STATES: 0 1 2 3 > ALPHABET: A C G T > INITIAL: > 0: 1.00 > 1: 0.00 > 2: 0.00 > 3: 0.00 > TRANSITION: > 0: 0.20 0.80 0.00 0.00 > 1: 0.00 0.50 0.50 0.00 > 2: 0.00 0.00 0.50 0.50 > 3: 0.00 0.00 0.00 1.00 > EMISSION: > 0: 0.67 0.11 0.11 0.11 > 1: 0.08 0.75 0.08 0.08 > 2: 0.08 0.08 0.75 0.08 > 3: 0.03 0.03 0.03 0.91 > TESTING baum welch > Training HMM > Traceback (most recent call last): > File "test_MarkovModel.py", line 64, in > > p_emission=p_emission > File > "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/MarkovModel.py", > line 181, in _baum_welch > if not p_initial.any(): > AttributeError: any > > $ python > Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) > [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin > Type "help", "copyright", > "credits" or "license" for more > information. > >>> import Numeric > >>> Numeric.__version__ > '24.2' > >>> import numpy > Traceback (most recent call last): > File "", line 1, in > ImportError: No module named numpy > >>> > > The above is on Mac OS X 10.5 (Tiger) with Numeric > installed, but not > numpy. I see something similar but slightly different on a > Linux > machine with both Numeric and an old version of numpy. > > Looking at the CVS log, I wonder if this is due to the > switch from an > array based or, to an if based manipulation of p_initial, > p_transition > and p_emission? > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/MarkovModel.py.diff?r1=1.3&r2=1.4&cvsroot=biopython > > Peter > _______________________________________________ > Biopython-dev mailing list > Biopython-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython-dev From mjldehoon at yahoo.com Fri Sep 19 23:01:18 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Fri, 19 Sep 2008 20:01:18 -0700 (PDT) Subject: [Biopython-dev] Numeric/numpy In-Reply-To: <320fb6e00809190842i6583f7bard82b03d5ea36f51e@mail.gmail.com> Message-ID: <415448.81411.qm@web62403.mail.re1.yahoo.com> OK, I'll send your message to the biopython mailing list. --Michiel. --- On Fri, 9/19/08, Peter Cock wrote: > From: Peter Cock > Subject: Re: [Biopython-dev] Numeric/numpy > To: mjldehoon at yahoo.com > Cc: "BioPython-Dev Mailing List" > Date: Friday, September 19, 2008, 11:42 AM > Michiel wrote: > >Peter wrote: > >> I was assuming dual support for both numpy or > Numeric for the next > >> release based on code like this: > >> > >> try: > >> from Numeric import x, y, z > >> except ImportError: > >> from numpy.oldnumeric import x, y, z > > > > This is the easy part. Keep in mind though that the > "from numpy.oldnumeric import x, y, z" approach is > only a temporary solution; at some point, the oldnumeric > wrapper will disappear from numpy. > > Yes, if/when the oldnumeric wrapper goes away we'll > have more work to > do. Something to worry about later. > > >> where I assumed the C code would have been decided > at > >> compile time. > > > > This is the complicated part; it's not just > replacing one #include with another. We'd have to use a > bunch of #ifdefs to separate the old code from the new code. > > > > Anyway I was planning to go through the Numerical > Python - dependent code to see if any other > > changes are needed. If anybody wants to be able to use > the old Numerical Python, please let > > yourself be heard; otherwise I suggest we go directly > to NumPy. > > > > --Michiel > > That suits me - how about we post something like this on > the main > discussion list then?: > > Dear all, > > As you probably are well aware, Biopython releases to date > have used > the now obsolete Numeric python library. This is no longer > being > maintained and has been superseded by the numpy library. > See > http://www.scipy.org/History_of_SciPy for more about > details on the > history of numerical python. Biopython 1.48 should be the > last > Numeric only release of Biopython - we have already started > moving to > numpy in CVS. > > Supporting both Numeric and numpy ought to be fairly > straight forward > for the pure python modules in Biopython. However, we also > have C code > which must interact with Numeric/numpy, and trying to > support both > would be harder. > > Would anyone be inconvenienced if the next release of > Biopython > supported numpy ONLY (dropping support for Numeric)? If so > please > speak up now - either here or on the development mailing > list. > Otherwise, a simple switch from Numeric to numpy will > probably be the > most straightforward migration plan. > > Thank you, > > ... From biopython at maubp.freeserve.co.uk Sat Sep 20 07:31:20 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 20 Sep 2008 12:31:20 +0100 Subject: [Biopython-dev] Modules to be removed from Biopython In-Reply-To: <320fb6e00809180515g59e53bddoa1d83242df198a1@mail.gmail.com> References: <492634.64872.qm@web62414.mail.re1.yahoo.com> <320fb6e00806270950k479eda23ia96d3c2d36557510@mail.gmail.com> <320fb6e00807160540w325fe995mea400b0014fd7c2e@mail.gmail.com> <320fb6e00807220913g64613854j7a1deb5b4357f726@mail.gmail.com> <320fb6e00808080417y483f74c8xd94dd7ca9eea0476@mail.gmail.com> <320fb6e00809180515g59e53bddoa1d83242df198a1@mail.gmail.com> Message-ID: <320fb6e00809200431h2ace4e4dge0cc9835e8d8d53f@mail.gmail.com> On Thu, Sep 18, 2008 at 1:15 PM, Peter wrote: > I wrote: >>> Bio.expressions was already deprecated, and seems to be a dependency >>> of the following modules, which I have now explicitly deprecated in CVS: > > I plan to remove these four deprecated modules shortly, unles