[Bioperl-l] COG software?

[Rick Westerman]

      Fernan Aguero wrote a very nice long explanation of his experiences 
with NCBI's 'dignitor' program which can be used to run coginator in a 
batch mode.  Unfortunately he ended on a pessimistic note saying that the 
file formats have changed since he last used the program and that the 
program itself has not been updated.

     He also said "Perhaps you can get someone versed in C to help you and 
port a modified dignitor it in Perl or some other language familiar to you?"

     Alas, I am well versed in 'C' (15-20 years) but still shudder at the 
thought of poring through 1500+ lines of undocumented 'C' code.   It seems 
simpler to create a program from scratch.  My Perl experience is young (~ 1 
year) and bioperl even younger but it could be an interesting project and 
would cause me to use bioperl more.  Side note:  I was looking through the 
blast parsing modules last week and there was a comment about every true 
bioperl hacker having to write a blast parsing module at least once ... so 
true.  (I won't release mine but it works for what I use it for)

Fernan continues:

>But one alternative, clearly, is to someway 'hack' the cognitor page
>at NCBI and make it run your requests remotely from a script. Don't be
>too aggresive on the NCBI servers or they may ban you.

     I had considered this but rejected it because of what you mentioned -- 
aggressive use of the server -- and because a batch input method implies a 
need to parse down the mass output to something manageable so that a 
program needs to be written in any case.

    Thank you Fernan and Jason.  I have appreciated the long replies to my 
question.






-- Rick

Rick Westerman
westerman@purdue.edu

Phone: (765) 494-0505                         FAX: (765) 496-7255
S049 WSLR bldg. Purdue Univ. W. Lafayette, IN 47907-1153

Bioinformatics specialist at the Genomics Initiative.
Part time system manager of Biochemistry department.

href="http://www.biochem.purdue.edu/~westerm"