Let's restart Bioperl !

Georg Fuellen fuellen@dali.mathematik.uni-bielefeld.de
Mon, 11 Nov 1996 21:21:20 +0000 (GMT)

Hello everyone,
      [Long time, no hear. I've been buried with applications for
      funding for my research topic (this implicated some progress
      on the theory side of phylogenetic inference), taking part in 
      competitions for the VSNS-BCD Internet course, and other things..]

But.. I'm now strongly determined to get the following released during the
next 2 weeks: 

   Bio::Seq(skeleton, almost done), 
   Bio::Aln(75% done), 
   Bio::Phy(phylogenies) and 
   Bio::Eva(handling of the latter three, including statistics).

And I'd appreciate your help !!

***If you've got any relevant news, own code, etc, please send me email now !

***Please, reply to the short questions below (about the current Bio::Seq,
which passes a rather longish test program already :-)

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The current code is at http://www.techfak.uni-bielefeld.de/bcd/Tec/Bioperl/Code/
testSeq.pl is the test program, and the Bio/ directory has the module Seq.pm .
testAli.pl and Bio/Aln.pm are getting ready.

And finally here are my questions -re- Bio::Seq; pls contemplate them, since I'd
like to avoid changes later because I got the design wrong early on !
quoting from http://www.techfak.uni-bielefeld.de/bcd/Tec/Bioperl/Code/Bio/Seq.pm
#Q. 1: Is it OK to use accessor functions for input data checking, during
#      _initialize & parseFasta,etc ? That is, should the current accessors be
#      enhanced to provide detailed data/type checking, and be
#      called whenever data are assigned to the internal hash, 
#      during initialization & parsing data from files ? (The current 
#      checks in _initialize would then be replaced by accessor calls.)
#Q. 2: Is the current $SeqType/$SeqForm system satisfactory ?
#      Basically, now the tables are just used for mapping names (like "Fasta")
#      into a unique number code (like "7"). It's no longer ok to have
#      either the number code _or_ the longword as a format specification)
#      That is, `` grep {$SeqForm[$SeqForm{$_}] = $_} keys(%SeqForm); ''
#      is no longer done, and `` $self->{ffmt} = $SeqForm[$ffmt] || 
#      $SeqForm[$SeqForm{$ffmt}] || 'Unknown'; ''  is no longer supported.

Please see the code for details !
best wishes,