Where and where will be the next BioJava bootcamp in th UK? [EMAIL PROTECTED] wrote: > > Send Biojava-l mailing list submissions to > [EMAIL PROTECTED] > > To subscribe or unsubscribe via the World Wide Web, visit > http://biojava.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > Today's Topics: > > 1. North American BioJava Bootcamp August 18-22 in Montreal > (Sylvain Foisy) > 2. genbank contig stuff (Matthew Pocock) > 3. Re: genbank contig stuff (Matthew Pocock) > 4. Re: Remove features from a sequence (Matthew Pocock) > 5. Re: Remove features from a sequence (Keith James) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 26 Jun 2003 13:20:31 -0400 > From: Sylvain Foisy <[EMAIL PROTECTED]> > Subject: [Biojava-l] North American BioJava Bootcamp August 18-22 in > Montreal > To: <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="ISO-8859-1" > > Hi, > > BioneQ, the Quebec Bioinformatics Network, is organizing the first North > American BioJava Bootcamp from August 18th to 22nd. We have invited Matthew > Pocock to come to Montreal to present the material that has been presented > to the European Bootcamps for quite some time now. On the agenda > (preliminary): > > -Sequence I/O and manipulations; > -BLAST and FASTA parsing; > -Using databases with BioJava; > -Intro to Sequence GUI. > > The bootcamp will be at the Universite de Montreal and the registration fee > is $250US. If you are interested, use the following link to register: > > http://132.204.90.239/bioneq/biojava_workshop.jsp > > Please paste in your CV for evaluation of programming experience/knowledge. > Places are quite limited (20) so register soon. > > Cordially > > Sylvain > > =================================================================== > Sylvain Foisy, Ph. D. > Directeur - operations / Project Manager > BioneQ - Reseau quebecois de bio-informatique > U. de Montreal / Genome-Quebec > > Adresse postale: > > Departement de biochimie > Pavillon principal > 2900, boul. Édouard-Montpetit > Montréal (Québec) H3T 1J4 > > Tel: (514) 343-6111 x.4066 > Courriel: [EMAIL PROTECTED] > =================================================================== > > ------------------------------ > > Message: 2 > Date: Thu, 26 Jun 2003 19:48:05 +0100 > From: Matthew Pocock <[EMAIL PROTECTED]> > Subject: [Biojava-l] genbank contig stuff > To: biojava-l <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Hi, > > Has anybody looked at supporting genbank records with CONTIG blocks > rather than sequences in them? > > Matthew > -- > BioJava Consulting LTD - Support and training for BioJava > http://www.biojava.co.uk > > ------------------------------ > > Message: 3 > Date: Thu, 26 Jun 2003 19:57:50 +0100 > From: Matthew Pocock <[EMAIL PROTECTED]> > Subject: [Biojava-l] Re: genbank contig stuff > To: Matthew Pocock <[EMAIL PROTECTED]> > Cc: biojava-l <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Sory - I fired that off without thinking much. > > I just downloaded the genbank file NT_010783 from the ncbi. Our parsers > spewed lots of errors about features not being within the range 1..0, > and after a little poking arround in the code, I found that a zero > length sequence was being generated. In despiration, I looked at the > physical genbank file. Instead of sequences, it contains a CONTIG > section with a single big join() describing how to build it from other > entries. > > Has anybody modified our genbank parser to process entries like this? To > be honest, I'm not quite sure where to start. > > Matthew > > ------------------------------ > > Message: 4 > Date: Fri, 27 Jun 2003 10:29:30 +0100 > From: Matthew Pocock <[EMAIL PROTECTED]> > Subject: Re: [Biojava-l] Remove features from a sequence > To: "Schreiber, Mark" <[EMAIL PROTECTED]> > Cc: [EMAIL PROTECTED] > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Done. SimpleFeatureHolder wraps it's features() iterator using > ListUtils.nonRemoveIterator(). All in cvs. > > Matthew > > ps Developers may wish to use this wrapper method in other places > > >>So, on balance, I guess we should throw NotImplementedException on > >>remove(). Unless somebody has a bright idea? > > ------------------------------ > > Message: 5 > Date: 27 Jun 2003 11:50:47 +0100 > From: Keith James <[EMAIL PROTECTED]> > Subject: Re: [Biojava-l] Remove features from a sequence > To: Matthew Pocock <[EMAIL PROTECTED]> > Cc: [EMAIL PROTECTED] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=us-ascii > > >>>>> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes: > > Matthew> Done. SimpleFeatureHolder wraps it's features() iterator > Matthew> using ListUtils.nonRemoveIterator(). All in cvs. > > Thanks! I'll go on a hunt for other places where this needs to be > used... > > Keith > > -- > > - Keith James <[EMAIL PROTECTED]> bioinformatics programming support - > - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK - > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > End of Biojava-l Digest, Vol 6, Issue 29 > ****************************************
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