back in action / preSeq.pm

[Georg Fuellen]

Chris wrote,

> Hi folks,
> 
> Good to see everybody back in action on this list.
> 
> My makefiles for PreSeq and Parse work fine, the only thing I need to do is write some type of 
> robust shell script called 'configure' that will do some quick in-place editing on PreSeq.pm and 
> Parse.pm that will be able turn off/on the use of Parse.pm

I'm not sure -- isn't this supposed to be part of the makefile business ?
Also, make should configure the ``current working directory''.

> Georg has metioned a bug in PreSeq and Steve C. has mentioned that he has made minor local 
> additions to his copy of Preseq. If both of you folks could email me your info, I will 
> incorporate the necessary changes into a new release.

See below.

> Also- inside GI we have finally gotten around to replacing our numerous scripts that have been 
> lying around for Blast/Fasta search result parsing. We now have a really nice object oriented 
> Blast.pm module and the Fasta.pm will be done shortly. Both of these modules are quite 
> standalone, capable of firing up a local or networked search and returning all kinds of 
> different info raw or in various sorted ways. I was thinking that although these modules do not 
> quite fit into our schema, they might be quite useful to the individual researcher.

Will the modules be available at some point ?

> One problem that was totally glossed over at the OIB meeting is that a majority of researchers 
> out there do not have the support of bioinformatics groups containing dozens of computer 
> scientists. While perl might not scale to super-industrial bioinformatics applications, there is 
> a huge need for simple, robust tools that are useable by individuals. I really think that this 
> is one area where BioPerl can be of tremendous help. Any thoughts?

Yes, there is much more than a small niche for BioPerl, we just need to get going...

> regards,
> Chris Dagdigian
> cdagdigian@genetics.com
> 
> 

best wishes,
georg
P.S. for Chris: one small bug revealed by examples/parse_parse.pl;
all the other tests look fine.
examples/parse_parse.pl currently produces,
   Printing contents of newly created sequence object:

ID       : No_Id_Given
Type     :Amino
Monomer  :3
Origin   :UnknownOrigin
Seq      :HASH(0x100921c4)
          ****************
===
also, please patch PreSeq's _file_read() (do an s/Seq/PreSeq
in this subroutine).
Otherwise I get this weird
>>>>>
Can't call method "import" in empty package "PreSeq" at t/univaln.t line 17.
BEGIN failed--compilation aborted at t/univaln.t line 17.
<<<<<
I guess this stupid error really means that somewhere deeply hidden
in PreSeq.pm an undeclared module (i.e. Seq) is being referred to ??!!
(I've got Perl 5.002 installed here).