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:)
