http://permalink.gmane.org/gmane.comp.lang.perl.bio.general hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17736 Firstly, thanks Mauricio for getting this set up....it should be really useful for everyone and make adding tests so much easier by focusing attention on problem areas! In fact, it could help users make the transition from using Bioperl to contributing code by giving them an entry point into understanding the modules. Increasing test coverage in a group of modules would make a good student project! Heikki, You should find this page useful: http://search.cpan.org/~pjcj/Devel-Cover-0.64/lib/Devel/Cover/Tutorial.pod I use the following as a list of priorities for code coverage: 1) Get the "subroutine" metric to 100% - every subroutine should have at least 1 test to check it's returning the correct value/object given at least one set of arguments. 2) Get the "statement" metric as close to 100% as possible by providing various inputs so that each statement is tested for BOTH the true and false possibilities. 3) Work on the "branch" and "path" metrics if after performing the above 2, these are still in low cove Nathan S. Watson-Haigh 2008-10-06T02:39:54 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17735 It might not be at all appropriate, and hopefully there's better solutions, but for relative positioning stuff you can try playing with Bio::Map stuff. Sendu Bala 2008-10-06T21:57:53 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17734 I have a community that likes to refer to positions as offsets, e.g. 100 bases upstream of the beginning of the exon, or 5 bases after the splice site.... They think of it as 34532+2 or 23451-23 (funny, if you hold down the shift key when you type that, you get < at >#$%!-< at >#, which is how I feel about it...). Are there any exising Bio::Location classes that would make keeping track of this info easier? g. George Hartzell 2008-10-06T21:27:11 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17733 hello, I see there is Bio::Tools::Run::Phylo::Phylip::ProtDist but I can't find a module supporting the dnadist program in doc.bp.o. I even tried substituting ::ProtDist for ::DnaDist and ::DNADist there, but those are 404. Is there any reason why phylip support only includes proteins, and not nucleotide, or am I missing something? regards FF Felipe Figueiredo 2008-10-06T20:42:36 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17732 Disregard that, Adam gave me the tip on the '-report html_basic' option for `cover`, which generates the tables as we want. Reports are now updated to sortable views. Mauricio. Mauricio Herrera Cuadra wrote: Mauricio Herrera Cuadra 2008-10-02T15:56:49 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17731 Actually I have a family of kvm images with a host of gbrowse databases (of various types, including Bio::DB::GFF and Bio::SeqFeature::Store) running in it. I would be very happy to contribute this to the cause. Lincoln On Wed, Oct 1, 2008 at 9:36 AM, Chris Fields <cjfields< at >illinois.edu> wrote: Lincoln Stein 2008-10-02T15:41:00 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17730 We are using 0.64 to generate the reports. Maybe the feature is not enabled by default? Any hints on that? Mauricio. Nathan S. Watson-Haigh wrote: Mauricio Herrera Cuadra 2008-10-02T14:30:31 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17729 Hi Sendu, The JS modifications made it into Devel::Cover 0.62, so no need for my modified Devel::Cover code now: http://search.cpan.org/src/PJCJ/Devel-Cover-0.62/CHANGES The latest version is now 0.64. Nath -----Original Message----- From: Sendu Bala [mailto:bix< at >sendu.me.uk] Sent: Wednesday, 1 October 2008 6:43 PM To: Mauricio Herrera Cuadra Cc: bioperl-l; Nathan Haigh Subject: Re: Test coverage for BioPerl now available Mauricio Herrera Cuadra wrote: Brilliant, thanks for doing this Mauricio. Could you, in any case, put Nathan's version in the private module area of the user running Build.PL, just so we have it in the meantime? Nathan S. Watson-Haigh 2008-10-02T05:07:29 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17728 I need to produce an alignment between a hunk of genomic sequence (in the sense that it hasn't had introns edited out or anything) that's on the order of a 1000 bases to a genome/chromosome/fragment of similar genomic sequence. In an ideal situation they'll be the same, differences will come from variations in the sources (e.g. the hunk might have been clipped out of genome revision X and the current genome might be X+i, or the hunk might have come from a paper (who knows where it came from...). Nothing across species or across evolutionary time or anything fun. I'm happy to narrow the region of the genome hunk down using some/an/... heuristic first to avoid running dp against an entire chromosome. I need the alignment to account for all of the bases in the hunk. In dynamic programming terms, if the hunk is along the vertical axis, the path through the matrix would have to run from the top to the bottom (or vice versa). The projection of the path onto the horizontal/genomic axis can start/end wherever George Hartzell 2008-10-02T00:32:48 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17727 Awesome! Thanks for pushing this forward. g. George Hartzell 2008-10-01T16:33:23 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17726 _______________________________________________ Bioperl-l mailing list Bioperl-l< at >lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l Chris Fields 2008-10-01T13:36:33 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17725 Beyond bioperl-db (which Jason mentioned a solution for) and bioperl- pedigree which other distributions would we be talking about? I think bioperl-ext would be too problematic under the current build scheme. I think Jason answered that one. Fantastic work Mauricio, thanks for taking the time to do this! chris Chris Fields 2008-10-01T12:54:20 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17724 Awesome work Mauricio, thanks for taking the time to do this. im sure it will greatly benefit us. Spiros On Tue, Sep 30, 2008 at 10:56 PM, Mauricio Herrera Cuadra <mauricio< at >open-bio.org> wrote: Spiros Denaxas 2008-10-01T09:13:30 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17723 Great, Mauricio! This should be a big help in encouraging everyone to contribute tests. Thanks for taking the time to do this. Dave Dave Messina 2008-10-01T09:09:52 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17722 Brilliant, thanks for doing this Mauricio. Could you, in any case, put Nathan's version in the private module area of the user running Build.PL, just so we have it in the meantime? Sendu Bala 2008-10-01T08:43:10 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17721 Thanks for doing this Mauricio! Great to have this resource and to follow up on the excellent efforts by Nathan and Sendu to get this ball rolling.. We have a couple of Virtual Hosts through Chris Dagdigian and BioTeam's donated resources that we can setup postgres and mysql instances for biosql and even Bio::DB::GFF & Bio::DB::SeqFeature testing. Let's see what Chris's plans are for the current VM instance - we have talked about also starting to port some of the websites to separate instances of the VM to spread the load a little bit more. One idea that can follow out of doing this work is some sort of testable reference servers for some of the bio{*} tools to access some basic datasets and hosting. Maybe with a simple Swissprot instance and a slice of a genbank division so that working gbrowse backend & biosql instances can be used for code testing and development purposes. -jason On Sep 30, 2008, at 2:56 PM, Mauricio Herrera Cuadra wrote: Jason Stajich jason< at >bioperl.org Jason Stajich 2008-10-01T08:07:49 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17720 Cool! I have trouble understanding the values in different columns. Could you whip together a wiki page that explains in plain English how to read them? -Heikki On Tuesday 30 September 2008 23:56:04 Mauricio Herrera Cuadra wrote: Heikki Lehvaslaiho 2008-10-01T07:31:13 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17719 Hi all, Daily-updated test coverage reports are now available for those BioPerl packages which make use of the Build.PL mechanism (except bioperl-db): http://bioperl.org/test-coverage/bioperl-live/ http://bioperl.org/test-coverage/bioperl-network/ http://bioperl.org/test-coverage/bioperl-run/ These reports will help us to know the current 'quality' of the code in SVN for most of the BioPerl modules. This idea was started by Nathan Haigh and Sendu a long time ago and it was my fault to not implement on time the necessary script to run the process on a daily basis, so apologies for that. There are still a few things to be done in order to have this working as it should: - Nathan, current Devel::Cover module from CPAN doesn't include the JS modifications to make table columns sortable. Do you know what happened to the code you contributed to the author for that? - Reports could be generated for the rest of the BioPerl packages as soon as they're migrated to the Build.PL infrastructure. Anyone up Mauricio Herrera Cuadra 2008-09-30T21:56:04 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17718 Eric, If the Bio::DB::GFF database to Genbank submission route doesn't get you where you want, you can also look at storing your data in a GMOD Chado database, then using Bulkfiles to produce the Genbank Submission file set. - Don Gilbert Find a GenBank Submit output from Chado dbs in this tool release http://eugenes.org/gmod/GMODTools/ GMODTools-1.2b.zip 20-Jun-2008 - adding (in progress) Genbank Submission table writer, 'bulkfiles -format=genbanktbl', with output suited to submit to NCBI as per these specifications http://www.ncbi.nlm.nih.gov/Genbank/eukaryotic_genome_submission.html see also http://gmod.org/wiki/GMODTools and this test case with genbank-submit output http://gmod.org/wiki/GMODTools_TestCase Don Gilbert 2008-09-30T17:23:56 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17717 Eric. CC-ing Gbrowse since this is regarding Gbrowse data-store. I've definitely done exactly this although I remember I had to tweak the features a bit to make sure i had some some of the necessary stuff to sequin. If you want to get a specific segment you just do what you already have in your code: my $segment = $db->segment($contig_name); Or you can iterate through all the features - depends on how you named your segments/contigs/chromsomes, I named mine "contig:scaffold" for type:source my $iterator = $dbh->get_seq_stream(-type=>'scaffold'); while (my $s = $iterator->next_seq) { } Now You *should* be able to pass this segment object to $seqio- >write_seq($segment); However Bio::DB::GFF::Feature doesn't implement the whole SeqI APi so you probably have to create your own sequence and move the features over: y $iterator = $dbh->get_seq_stream(-type=>'scaffold'); while (my $s = $iterator->next_seq) { my $seq = Bio::Seq->new(); $seq->primary_seq($s->seq); for my $feature ( Jason Stajich 2008-09-30T16:48:17 http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17716 Hi all, I have newly sequenced contigs, with CDS predictions, loaded into a Bio::DB::GFF-readable format (i.e., loaded into a MySQL database via Bio::DB::GFF). I'd like to export each contig, with its annotated CDSes, into a single GenBank-formatted record for each contig (in order to be able submit this stuff to GenBank, without having to waste time with Sequin). Is there some straightforward way of getting Bio::DB::GFF to do that? Some time ago, when I last had to decipher BioPerl, I came up with code that would let me export protein translations of the contigs' CDSes in GenBank format: ------------------------------------------------------------------- #!/usr/bin/env perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::GFF; my $query_database = $ARGV[0]; my $dna = q{}; my $db = Bio::DB::GFF->new( -dsn => $query_database); my $gb_file = 'example.gb'; my $seq_out = Bio::SeqIO->new( -file => ">$gb_file", -format => 'genbank', ); my < at >contigs = sort Erich Schwarz 2008-09-29T05:57:43 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.perl.bio.general