src/hg/gigAssembler/goldToAgp/goldToAgp.c 1.4

Index: src/hg/gigAssembler/goldToAgp/goldToAgp.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/gigAssembler/goldToAgp/goldToAgp.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/gigAssembler/goldToAgp/goldToAgp.c	6 May 2003 07:22:19 -0000	1.3
+++ src/hg/gigAssembler/goldToAgp/goldToAgp.c	7 Jul 2009 18:45:01 -0000	1.4
@@ -1,195 +1,193 @@
 /* goldToAgp - convert from ooGreedy "gold" format to the official
  * ".agp" format for golden paths. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "portable.h"
 
 static char const rcsid[] = "$Id$";
 
 
 void usage()
 /* Print usage instructions and exit */
 {
 errAbort(
   "goldToAgp - convert from ooGreedy 'gold' format to the official\n"
   "'.agp' format for golden paths through a contig. \n"
   "usage:\n"
   "  goldToAgp gsDir version chromDir(s)\n"
   "This will look for gsDir/fin/trans gsDir/draft/trans and gsdir/predraft/trans\n"
   "to define name translations.  It will then translate in chromDir/ctg*/gold.version\n"
   "into chromDir/ctg*/ctg*.agp\n");
 }
 
 struct fragData 
 /* Info on fragment */
     {
     char *ucscName;	/* Name on UCSC side. */
     char *ffaName;      /* Greg Schuler name. */
     char *accVer;       /* Genbank accession.version. */
     int subStart;	/* Start in Genbank submission coordinates. (1 based) */
     int subEnd;         /* End in Genbank submission coordinates. (inclusive) */
     char *type;     /* Phase in agp sense "F" "D" or "P" */
     };
 
 struct fragData *parseFragData(char *words[], char *phase, int whereIx)
 /* Parse frag data from a line. */
 {
 struct fragData *fd;
-int wordCount;
 char *s, *e;
 
 AllocVar(fd);
 fd->ucscName = cloneString(words[0]);
 fd->ffaName = cloneString(words[1]);
 s = words[whereIx];
 if (s[0] != '(')
     errAbort("Format error 1 in trans file: %s\n", s);
 s += 1;
 if ((e = strchr(s, ':')) == NULL)
     errAbort("Format error 2 in trans file: %s\n", s);
 *e++ = 0;
 fd->accVer = cloneString(s);
 s = e;
 if ((e = strchr(s, '.')) == NULL || e[1] != '.' || !isdigit(s[0]))
     errAbort("Format error 3 in trans file: %s\n", s);
 *e++ = 0;
 fd->subStart = atoi(s);
 s = e+1;
 if (!isdigit(s[0]))
     errAbort("Format error 4 in trans file: %s\n", s);
 fd->subEnd = atoi(s);
 fd->type = phase;
 return fd;
 }
 
 void hashTrans(char *dir, char *subDir, char *type, struct hash *hash)
 /* Read trans file in dir/subdir/trans into hash. */
 {
 char fileName[512];
 struct lineFile *lf;
 int lineSize;
 char *line;
 int wordCount;
 char *words[16];
 struct fragData *fd;
 
 sprintf(fileName, "%s/%s/trans", dir, subDir);
 printf("Reading in %s\n", fileName);
 lf = lineFileOpen(fileName, TRUE);
 while (lineFileNext(lf, &line, &lineSize))
     {
     wordCount = chopLine(line, words);
     if (wordCount != 7 && wordCount != 3)
 	errAbort("Bad line %d of %s\n", lf->lineIx, lf->fileName);
     fd = parseFragData(words, type, wordCount-1);
     hashAdd(hash, fd->ucscName, fd);
     }
 lineFileClose(&lf);
 }
 
 void translateOne(char *goldName, char *agpName, char *contig, struct hash *hash)
 /* Translate one gold to agp. */
 {
 struct lineFile *lf = lineFileOpen(goldName, TRUE);
 FILE *f = mustOpen(agpName, "w");
 int lineSize, wordCount;
 char *line, *words[16];
-int i;
 
 printf("Translating %s to %s\n", goldName, agpName);
 while (lineFileNext(lf, &line, &lineSize))
     {
     wordCount = chopLine(line, words);
     if (wordCount != 8 && wordCount != 9)
 	errAbort("Bad line %d of %s\n", lf->lineIx, lf->fileName);
     fprintf(f, "%s\t%s\t%s\t%s\t", contig, words[1], words[2], words[3]);
     if (wordCount == 8)
 	{
 	if (!sameWord(words[4], "N"))
 	    errAbort("Bad N line %d of %s\n", lf->lineIx, lf->fileName);
 	fprintf(f, "N\t%s\t%s\t%s\n", words[5], words[6], words[7]);
 	}
     else
 	{
 	struct fragData *fd;
 	char *frag = words[5];
 	int fragStartInClone;
 
 	if (startsWith("NT_", frag))
 	    {
 	    chopSuffix(frag);
 	    fprintf(f, "%s\t%s.0\t%s\t%s\t\%s\n", "F", 
 	        frag, 	words[6], words[7], words[8]);
 	    }
 	else
 	    {
 	    fd = hashFindVal(hash, frag);
 	    if (fd == NULL)
 		errAbort("%s isn't in trans files\n", frag);
 	    fragStartInClone = fd->subStart - 1;
 	    fprintf(f, "%s\t%s\t%d\t%d\t%s\n",
 		    fd->type, fd->accVer,
 		    fragStartInClone + atoi(words[6]),
 		    fragStartInClone + atoi(words[7]),
 		    words[8]);
 	    }
 	}
     }
 lineFileClose(&lf);
 fclose(f);
 }
 
 void goldToAgp(char *gsDir, int version, char *chromDirs[], int chromCount)
 /* goldToAgp - convert from ooGreedy "gold" format to the official
  * ".agp" format for golden paths. */
 {
 struct hash *seqHash = newHash(18);
 int i;
 char *chrom;
 char goldFileName[512];
 char agpFileName[512];
 char contigName[256];
 char  *ctgName;
 struct slName *dirList, *dirEl;
 char chromRoot[128], chromSuperDir[256], chromExt[64];
 
 hashTrans(gsDir, "fin", "F", seqHash);
 hashTrans(gsDir, "draft", "D", seqHash);
 hashTrans(gsDir, "predraft", "P", seqHash);
 hashTrans(gsDir, "extras", "D", seqHash);
 // hashTrans(gsDir, "missing", "O", seqHash);
 for (i=0; i<chromCount; ++i)
     {
     chrom = chromDirs[i];
     dirList = listDir(chrom, "ctg*");
     splitPath(chrom, chromSuperDir, chromRoot, chromExt);
     for (dirEl = dirList; dirEl != NULL; dirEl = dirEl->next)
 	{
 	ctgName = dirEl->name;
 	sprintf(contigName, "%s/%s", chromRoot, ctgName);
 	sprintf(goldFileName, "%s/%s/gold.%d", chrom, ctgName, version);
 	sprintf(agpFileName, "%s/%s/%s.agp", chrom, ctgName, ctgName);
 	if (fileExists(goldFileName))
 	    {
 	    translateOne(goldFileName, agpFileName, contigName, seqHash);
 	    }
 	else
 	    {
 	    warn("%s doesn't exist\n", goldFileName);
 	    }
 	}
     slFreeList(&dirList);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 4 || !isdigit(argv[2][0]))
     usage();
 goldToAgp(argv[1], atoi(argv[2]), argv+3, argc-3);
 return 0;
 }