src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c 1.5
1.5 2009/08/23 19:51:26 kent
Coping with addition of sp| at start of fasta protein name in varSplice section of SwissProt.
Index: src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c 17 Mar 2007 18:12:41 -0000 1.4
+++ src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c 23 Aug 2009 19:51:26 -0000 1.5
@@ -59,12 +59,14 @@
ZeroVar(&seq);
while (faPepSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
char *row[4];
- int rowSize = chopString(seq.name, "-|", row, ArraySize(row));
+ char *name = seq.name;
+ if (startsWith("sp|", name)) // Skip over sp| introduced Aug 2009
+ name += 3;
+ int rowSize = chopString(name, "-|", row, ArraySize(row));
if (rowSize != 3)
- errAbort("Expecting name to be in format accession-N|DISP_ID, got %s\n", seq.name);
- chopString(seq.name, "-|", row, ArraySize(row));
+ errAbort("Expecting name to be in format accession-N|DISP_ID, got %s\n", name);
char *acc = row[0];
char *version = row[1];
char *displayId = row[2];
int accLen = strlen(acc);