src/cdnaAli/findCdna/findCdna.c 1.5

Index: src/cdnaAli/findCdna/findCdna.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/cdnaAli/findCdna/findCdna.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/cdnaAli/findCdna/findCdna.c	20 Jun 2006 19:20:07 -0000	1.4
+++ src/cdnaAli/findCdna/findCdna.c	23 Sep 2009 18:42:15 -0000	1.5
@@ -1,164 +1,164 @@
 /* Quick lookup of cDNA based on binary search of index file, etc. */
 #include "common.h"
 #include "snof.h"
 
 void *mustAlloc(int size)
 {
 void *ret;
 ret = malloc(size);
 if (ret == NULL)
     {
     fprintf(stderr, "Out of memory %d bytes\n", size);
     exit(-2);
     }
 return ret;
 }
 
 void printTo(FILE *f, char untilC)
 {
 int c;
 
 for (;;)
     {
     c = getc(f);
     if (c == EOF)
         break;
     if (c == untilC)
         {
         putchar(c);
         break;
         }
     }
 for (;;)
     {
     c = getc(f);
     if (c == untilC || c == EOF)
 	break;
     putchar(c);
     }
 }
 
 struct nameList
     {
     struct nameList *next;
     char *name;
     };
 
 struct nameList *newNameList(char *name)
 {
 int len = strlen(name);
 struct nameList *nl;
 int allocSize = len+1+sizeof(*nl);
 nl = mustAlloc(allocSize);
 nl->next = NULL;
 nl->name = (char *)(nl+1);
 strcpy(nl->name, name);
 return nl;
 }
 
 struct nameList *findCdnaNames(char *geneName, struct snof *snof, FILE *f)
 {
 char lineBuf[1024*2];
 char *words[256];
 int wordCount;
 int i;
 struct nameList *list = NULL;
 long offset;
 
 if (!snofFindOffset(snof, geneName, &offset))
     return NULL;
 fseek(f, offset, SEEK_SET);
-fgets(lineBuf, sizeof(lineBuf), f);
+mustGetLine(f, lineBuf, sizeof(lineBuf));
 wordCount = chopString(lineBuf, whiteSpaceChopper, words, ArraySize(words));
 assert(strcmp(words[0], geneName) == 0);
 for (i=1; i<wordCount; ++i)
     {
     struct nameList *el;
     el = newNameList(words[i]);
     el->next = list;
     list = el;
     }
 slReverse(&list);
 return list;
 }
 
 int main(int argc, char *argv[])
 {
 FILE *faFile, *g2cFile, *inputFile;
 long faOffset;
 char *faName = "\\biodata\\celegans\\cDNA\\allcdna.fa";
 char *faIndexName = "\\biodata\\celegans\\cDNA\\allcdna";
 char *g2cName = "\\biodata\\celegans\\cDNA\\gene2cdna.txt";
 char *g2cIndexName = "\\biodata\\celegans\\cDNA\\gene2cdna";
 char *inputName;
 struct snof *faSnof;
 struct snof *g2cSnof;
 
 if (argc != 2)
     {
     fprintf(stderr, "Usage: %s inputFile\n", argv[0]);
     exit(-1);
     }
 
 /* Grab input file name and open file. */
 inputName = argv[1];
 inputFile = mustOpen(inputName, "r");
 
 /* Open fa file (with actual sequence) */
 faFile = mustOpen(faName, "rb");
 
 /* Open file that has list of cDNA's and genes */
 g2cFile = mustOpen(g2cName, "r");
 
 /* Open and initialize index file. */
 if ((faSnof = snofOpen(faIndexName)) == NULL)
     {
     fprintf(stderr, "%s isn't a good index file, sorry\n", faIndexName);
     exit(-1);
     }
 
 if ((g2cSnof = snofOpen(g2cIndexName)) == NULL)
     {
     fprintf(stderr, "%s isn't a good index file, sorry\n", g2cIndexName);
     exit(-1);
     }
 
 /* Loop through each line of input file.  Grab gene name from it.
  * Then scan through g2c file to find names of cDNAs that go with it. */
 for (;;)
     {
     char lineBuf[256];
     char *words[16];
     int wordCount;
     if (fgets(lineBuf, sizeof(lineBuf), inputFile) == NULL)
 	break;
     printf("%s", lineBuf);
     wordCount = chopString(lineBuf, whiteSpaceChopper, words, ArraySize(words));
     if (wordCount > 0)
 	{
 	char *geneName = words[0];
  	struct nameList *cdnaNames = findCdnaNames(geneName, g2cSnof, g2cFile);
 	struct nameList *el;
 	printf(">>Gene %s\n", geneName);
         if (cdnaNames == NULL)
             printf("No cDNA\n");
 	for (el = cdnaNames; el != NULL; el = el->next)
 	    {
             if (!snofFindOffset(faSnof, el->name, &faOffset))
 		{
 		fprintf(stderr, "Can't find cDNA %s\n", el->name);
 		}
 	    else
 		{
 		fseek(faFile, faOffset, SEEK_SET);
 		printTo(faFile, '>');
 		}
 	    }
 	printf("\n");
 	}
     }
 snofClose(&faSnof);
 snofClose(&g2cSnof);
 return 0;
 }