[Biophp-dev] scripts

[Serge Gregorio]

Frankie, 

Your code seems to be working fine.  I'll
do more tests on it.  Btw, could you be more specific as to what you were looking for last time?  The traceback thing?  I might have some links for you...

Cayte,

We sure could use your help.  Umm... what's on the 
table?  Well, Sean's working on the eFetch/eUtils
that would interface with NCBI's server, Nico is
working on developing a Parser class that allows
users to parse data in different formats using a
uniform syntax, Frankie's working on Scoring Matrices
(Blosum, etc.), while I'm working on parsers for
different data formats (for the last one, see:
http://genephp.sf.net/demo_set.html).

There's no one working on parsers for mmCIF format
(the successor to the very complex PDB file).

Also, while I've written a parser for GenBank files,
it still does not have support for their spankingly
new experimental format (GBCON.SEQ) for complex 
sequences.  To quote from NCBI's Release Guide 
(gbrel.txt), Dec 2001 version:

"Three Supplemental files provide the accession numbers of GenBank entries that are new, updated, or deleted since the previous release:

a. gbchg.txt	- Entries updated since the previous   
   release.
b. gbdel.txt	- Entries deleted since the previous 
   release.
c. gbnew.txt	- Entries new since the previous 
   release.

  An experimental file called gbcon.seq provides an alternative representation for complex sequences, such as "segmented sets" and complete-genomes that have
been split into pieces. The GenBank README describes the experimental CON division of GenBank in more detail:

   ftp://ftp.ncbi.nih.gov/genbank/README.genbank"

Allan S seems more interested in the esoteric
computational bio algorithms.

So, there you have it.  Welcome aboard!

To all:  I'm looking for "blackbox testers" who 
could prepare test cases and run them against the
scripts at the SF demo site:

   http://genephp.sf.net/demo_set.html

   (Look at the Parser Scripts group).

I plan to put a facility there where you can
easily submit/post bugs/errors in any of the
parser scripts if you find any.  

If you're interested just holler!  =(

Regards,

Serge Gregorio


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