int main(int argc, char *argv[])
{
char *listName = "finished.new";
char *fofName = "unfinished_acc.fof";
char *outName = "frags.txt";
FILE *out = mustOpen(outName, "w");
struct fof *fof = fofOpen(fofName, NULL);
struct kvt *kvt = newKvt(64);
char line[512];
int lineCount = 0;
FILE *lf;
char *keyText;
char *s, *t;
int size;
lf = mustOpen(listName, "r");
while (fgets(line, sizeof(line), lf))
{
++lineCount;
kvtClear(kvt);
s = trimSpaces(line);
t = strchr(s, '.');
if (t != NULL)
*t = 0;
keyText = fofFetchString(fof, s, &size);
kvtParseAdd(kvt, keyText);
fprintf(out, "%s phase %s frags %s\n", s, kvtLookup(kvt, "pha"), kvtLookup(kvt, "frg"));
freez(&keyText);
}
freeKvt(&kvt);
return 0;
}
int main(int argc, char *argv[])
/* Check parameters, set up, loop through each GenBank file. */
{
char *gbName;
int argi = 1;
struct hash *estAuthorHash = NULL;
char *pepFa;
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
gByAccPrefixSize = optionInt("byAccPrefix", 0);
gbIdxName = optionVal("gbidx", NULL);
pepFa = optionVal("pepFa", NULL);
gbType = gbParseType(optionVal("type", "mrna,est"));
gbOrg = optionVal("org", NULL);
inclXMs = optionExists("inclXMs");
if (gByAccPrefixSize > 4) /* keep small to avoid tons of open files */
errAbort("max value of -byAccPrefix is 4");
gCurAccPrefix[0] = '\0';
faName = argv[argi++];
raName = argv[argi++];
estAuthorHash = newHash(23);
kvt = newKvt(5*1024);
gbfInit();
if (pepFa != NULL)
gPepFa = gbFaOpen(pepFa,"w");
char *blackList = optionVal("blackList", NULL);
if (blackList != NULL)
blackListRanges = genbankBlackListParse(blackList);
while (argi < argc)
{
gbName = argv[argi++];
printf("Processing %s into %s and %s\n", gbName, faName, raName);
procOneGbFile(gbName, estAuthorHash);
}
gbFaClose(&faFile);
gbFaClose(&gPepFa);
carefulClose(&raFile);
carefulClose(&gbIdxFile);
return 0;
}
int main(int argc, char *argv[])
{
char *com;
char **raFiles = NULL;
int raCount = 0;
char *expFile;
char *expression;
size_t size;
struct keyExp *exp;
int i;
if (argc < 4)
usage();
expFile = argv[1];
com = argv[2];
if (sameWord(com, "count"))
{
command = ctCount;
out = stdout;
raCount = argc-3;
raFiles = argv+3;
}
else if (sameWord(com, "print"))
{
if (argc < 5)
usage();
command = ctPrint;
selectKey = argv[3];
out = stdout;
raCount = argc-4;
raFiles = argv+4;
}
else if (sameWord(com, "save"))
{
if (argc < 6)
usage();
command = ctPrint;
selectKey = argv[3];
out = mustOpen(argv[4], "w");
raCount = argc-5;
raFiles = argv+5;
}
else if (sameWord(com, "stats"))
{
if (argc < 6)
usage();
command = ctStats;
selectKey = argv[3];
out = mustOpen(argv[4], "w");
raCount = argc-5;
raFiles = argv+5;
statHash = newHash(20);
}
else if (sameWord(com, "hist"))
{
if (argc < 6)
usage();
command = ctHist;
selectKey = argv[3];
out = mustOpen(argv[4], "w");
raCount = argc-5;
raFiles = argv+5;
statHash = newHash(18);
}
if (sameWord(expFile, "all"))
exp = NULL;
else
{
readInGulp(expFile, &expression, &size);
exp = keyExpParse(expression);
}
kvt = newKvt(128);
for (i=0; i<raCount; ++i)
{
scanFile(exp, raFiles[i]);
}
printf("%d matched %s\n", matchCount, expFile);
if (command == ctStats)
{
struct useCount *u;
slSort(&useCounts, cmpUse);
for (u = useCounts; u != NULL; u = u->next)
{
fprintf(out, "%d %s\n", u->count, u->what);
}
printf("%d unique values for %s\n", slCount(useCounts), selectKey);
}
else if (command == ctHist)
{
struct useCount *u;
fillInVal(useCounts);
slSort(&useCounts, cmpVal);
fprintf(out, "value uses\n");
fprintf(out, "------------\n");
for (u=useCounts; u != NULL; u = u->next)
{
fprintf(out, "%5d %5d\n", u->val, u->count);
}
}
return 0;
}
