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EMBLtoGCG

Rodrigo Lopez rodrigol at bioslave.uio.no
Tue Apr 16 07:18:08 EST 1996


Dear GCG managers,

*** This message is not intended for the GCG & EGCG user but to the 
*** manager of these packages!
*** STANDARD DISCLAIMER APPLIES!!!!!!

I have found a small bug on EMBLToGCG which produces a corrupted
header when using the -PROTein parameter. The ShortName becomes
a set of control characters which results in programs such as
FastA failing to build alignments when searching for a database
prepared using:

% embltogcg -prot 

To correct this problem:

% gcg
% gcgsupport
% getsrc source embltogcg.c
% vi embltogcg.c

locate the formatHeader function
the first if (line 571) statement and onwards currently reads:

  if (IsSwiss || IsProtein)
    strcpy(header->type, "P"); 
  else {
    CapTokens(shortName); 
    strcpy(header->shortName, shortName); 
    strcpy(header->type, "N"); 
  }

Should read:

  if (IsSwiss || IsProtein){
    CapTokens(shortName); 
    strcpy(header->shortName, shortName); 
    strcpy(header->type, "P"); 
  } else {
    CapTokens(shortName); 
    strcpy(header->shortName, shortName); 
    strcpy(header->type, "N"); 
  }

% fetch makefile.mm
% vi makefile.mm

locate the section for building C applications and change 
"name" for "embltogcg".

% make makefile
% make embltogcg

!!!! Test the routine (for example):!!!!
NOTE: This is your new local version.

% ./embltogcg -prot trembl.dat -dir=trembldir

If the header "SN:" section contains the appropriate ShortName for the 
library then evrything is ok. If not: Revise the source all over again!
If everything seems ok:

% putsrc source embltogcg.c
% buildapp embltogcg

That's all folks!

Enjoy!

R:)





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