src/hg/mouseStuff/mafToFa/mafToFa.c 1.2

Index: src/hg/mouseStuff/mafToFa/mafToFa.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/mouseStuff/mafToFa/mafToFa.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/mouseStuff/mafToFa/mafToFa.c	28 Mar 2009 20:48:10 -0000	1.1
+++ src/hg/mouseStuff/mafToFa/mafToFa.c	29 Mar 2009 05:16:57 -0000	1.2
@@ -1,78 +1,87 @@
 /* mafToFa - convert maf file to fasta. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "maf.h"
 #include "options.h"
 
 static char const rcsid[] = "$Id$";
 
+boolean stripDotsDashes;
+
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafToFa - convert maf file to fasta\n"
   "usage:\n"
   "   mafToFa in.maf out.fa\n"
   "options:\n"
-  "   -xxx=XXX\n"
+  "   -stripDotsDashes     : remove dot and dash (.-) characters from aligned sequences\n"
   );
 }
 
 static struct optionSpec options[] = {
+   {"stripDotsDashes", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 char *skipDot(char *src)
 /* skip past dot in src name */
 {
 char *dot = strchr(src, '.');
 if (dot == NULL)
     return src;
 else
     return dot+1;
 }
 
 
-void mafAliToFa(struct mafAli *maf, FILE *pslFh)
+void mafAliToFa(struct mafAli *maf, FILE *of)
 /* convert a MAF alignment to a fa */
 {
 struct mafComp *c;
 for (c = maf->components ; c ; c = c->next )
     {
     int start = c->start;
     int end   = c->start+c->size;
+    if (stripDotsDashes)
+	{
+	stripChar(c->text, '.');
+	stripChar(c->text, '-');
+	}
     reverseIntRange(&start, &end, c->srcSize);
-    fprintf(pslFh, ">%s.%d.%d.%c.%d\n%s\n", c->src, start, end, c->strand, c->srcSize, c->text);
+    fprintf(of, ">%s.%d.%d.%c.%d\n%s\n", c->src, start, end, c->strand, c->srcSize, c->text);
     }
-fprintf(pslFh,"\n");
+fprintf(of,"\n");
 }
 
 void mafToFa(char *inName, char *outName)
 /* mafToFa - convert maf file to fasta. */
 {
 struct mafFile *mf = mafOpen(inName);
 FILE *faFh = mustOpen(outName, "w");
 struct mafAli *maf;
 
 while ((maf = mafNext(mf)) != NULL)
     {
     mafAliToFa(maf, faFh);
     mafAliFree(&maf);
     }
 carefulClose(&faFh);
 mafFileFree(&mf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 ++argv;
 --argc;
 if (argc != 2)
     usage();
+stripDotsDashes = optionExists("stripDotsDashes");
 mafToFa(argv[0], argv[1]);
 return 0;
 }