コード例 #1
0
ファイル: checkTableCoords.c プロジェクト: maximilianh/kent
void processExcludes(char *exclude)
/* Combine alwaysExclude and command like -exclude arg (if given), and 
 * process into a list.  If it contains "genbank", add genbankExclude. */
{
struct dyString *allExcludes = newDyString(512);
char *patterns[128];
int numPats = 0, i = 0;

dyStringAppend(allExcludes, alwaysExclude);
if (exclude != NULL)
    dyStringPrintf(allExcludes, ",%s", exclude);
numPats = chopCommas(allExcludes->string, patterns);
for (i=0;  i < numPats;  i++)
    {
    if (sameWord(patterns[i], "genbank"))
	{
	char *gbPatterns[128];
	int gbNumPats = 0, j = 0;
	char *gbExclude = cloneString(genbankExclude);
	gbNumPats = chopCommas(gbExclude, gbPatterns);
	for (j=0;  j < gbNumPats;  j++)
	    {
	    struct slName *pat = newSlName(gbPatterns[j]);
	    slAddHead(&excludePatterns, pat);
	    }
	freeMem(gbExclude);
	}
    else
	{
	struct slName *pat = newSlName(patterns[i]);
	slAddHead(&excludePatterns, pat);
	}
    }
dyStringFree(&allExcludes);
}
コード例 #2
0
struct slName *getFileList(char *listFile, char *bulkDir)
/* Get list of files to work on from listFile. */
{
char **faFiles;
char *faBuf;
int faCount;
int i;
char path[512], dir[256], name[128], extension[64];
struct slName *list = NULL, *el;

readAllWords(listFile, &faFiles, &faCount, &faBuf);
for (i = 0; i<faCount; ++i)
    {
    splitPath(faFiles[i], dir, name, extension);
    sprintf(path, "%s/%s.%s",
	bulkDir,
	name, "psl");
    if (fileExists(path))
	{
	el = newSlName(path);
	slAddHead(&list, el);
	}
    }
slReverse(&list);
return list;
}
コード例 #3
0
void jkUniq(char *fileName)
/* Remove dupe lines from file. */
{
struct slName *lineList = NULL, *lineEl;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
int lineSize;
struct hash *hash = newHash(0);
FILE *f;

while (lineFileNext(lf, &line, &lineSize))
    {
    if (!hashLookup(hash, line))
	{
	hashAdd(hash, line, NULL);
	lineEl = newSlName(line);
	slAddHead(&lineList, lineEl);
	}
    }
slReverse(&lineList);
lineFileClose(&lf);
f = mustOpen(fileName, "w");
for (lineEl = lineList; lineEl != NULL; lineEl = lineEl->next)
    {
    fputs(lineEl->name, f);
    fputc('\n', f);
    }
fclose(f);
slFreeList(&lineList);
freeHash(&hash);
}
コード例 #4
0
int main(int argc, char *argv[])
{
char *inName, *name;
int chunkSize = 4048*1024;
FILE *in;
int accSize = 0;
int newAccSize;
int oneSize;
char line[512];
int lineCount;
char *words[16];
int wordCount;
struct slName *bacs = NULL, *bn;
char *dirName;
char *outDir;

if (argc != 4)
    usage();
inName = argv[1];
dirName = argv[2];
outDir = argv[3];


in = mustOpen(inName, "r");

while (fgets(line, sizeof(line), in))
    {
    char *sizeString;
    ++lineCount;
    wordCount = chopLine(line, words);
    if (wordCount == 0)
	continue;
    if (wordCount != 9)
	errAbort("Line %d of %s doesn't look like an ls -l line", lineCount, inName);
    sizeString = words[4];
    if (!isdigit(sizeString[0]))
	errAbort("Line %d of %s doesn't look like an ls - l line", lineCount, inName);
    name = words[8];
    oneSize = atoi(sizeString);
    newAccSize = accSize + oneSize;
    if (newAccSize > chunkSize)
	{
	finishJob(&bacs, accSize);
	accSize = oneSize;
	if (oneSize > chunkSize)
	    warn("Size %d of %s exceed chunk size %d", oneSize, name, chunkSize);
	}
    else
	{
	accSize = newAccSize;
	}
    bn = newSlName(name);
    slAddHead(&bacs, bn);
    }
if (bacs != NULL)
    finishJob(&bacs, accSize);
printf("%d total jobs\n", jobCount);
writeInLists(outDir, dirName);
//writeJobs("job", "in", startMachine, stopMachine, "cc");
}
コード例 #5
0
ファイル: osunix.c プロジェクト: Bioinformaticsnl/SimSeq
struct slName *listDirRegEx(char *dir, char *regEx, int flags)
/* Return an alphabetized list of all files that match 
 * the regular expression pattern in directory.
 * See REGCOMP(3) for flags (e.g. REG_ICASE)  */
{
struct slName *list = NULL, *name;
struct dirent *de;
DIR *d;
regex_t re;
int err = regcomp(&re, regEx, flags | REG_NOSUB);
if(err)
    errAbort("regcomp failed; err: %d", err);

if ((d = opendir(dir)) == NULL)
    return NULL;
while ((de = readdir(d)) != NULL)
    {
    char *fileName = de->d_name;
    if (differentString(fileName, ".") && differentString(fileName, ".."))
	{
	if (!regexec(&re, fileName, 0, NULL, 0))
	    {
	    name = newSlName(fileName);
	    slAddHead(&list, name);
	    }
	}
    }
closedir(d);
regfree(&re);
slNameSort(&list);
return list;
}
コード例 #6
0
ファイル: osunix.c プロジェクト: Bioinformaticsnl/SimSeq
struct slName *listDir(char *dir, char *pattern)
/* Return an alphabetized list of all files that match 
 * the wildcard pattern in directory. */
{
struct slName *list = NULL, *name;
struct dirent *de;
DIR *d;

if ((d = opendir(dir)) == NULL)
    return NULL;
while ((de = readdir(d)) != NULL)
    {
    char *fileName = de->d_name;
    if (differentString(fileName, ".") && differentString(fileName, ".."))
	{
	if (pattern == NULL || wildMatch(pattern, fileName))
	    {
	    name = newSlName(fileName);
	    slAddHead(&list, name);
	    }
	}
    }
closedir(d);
slNameSort(&list);
return list;
}
コード例 #7
0
static int releaseSanity(struct gbRelease* release, char *database)
/* Run sanity checks on a release */
{
unsigned orgCats;
int checkedSetCnt = 0;

/* check if native, and/or xeno should be included */
orgCats = getLoadOrgCats(database, release->srcDb, GB_MRNA);
if (orgCats != 0)
    {
    if (checkRelease(release, database, GB_MRNA, orgCats, NULL))
        checkedSetCnt++;
    }

orgCats = getLoadOrgCats(database, release->srcDb, GB_EST);
if (orgCats != 0)
    {
    struct slName* prefixes, *prefix;
    boolean checkedSome = FALSE;
    if (gOptions.accPrefixRestrict != NULL)
        prefixes = newSlName(gOptions.accPrefixRestrict);
    else
        prefixes = gbReleaseGetAccPrefixes(release, GB_PROCESSED, GB_EST);
    for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
        {
        if (checkRelease(release, database, GB_EST, orgCats, prefix->name))
            checkedSome = TRUE;
        }
    slFreeList(&prefixes);
    if (checkedSome)
        checkedSetCnt++;
    }
return checkedSetCnt;
}
コード例 #8
0
ファイル: mafToProtein.c プロジェクト: elmargb/kentUtils
void pushPosString(struct speciesInfo *si)
{
flushPosString(si);

struct slName *newName = newSlName(si->posString);
slAddTail(&si->posStrings, newName);

freez(&si->posString);
}
コード例 #9
0
static struct slName* parseDbXrefStr(char* xrefStr)
/* Split while-space seperated list of db_xref values into a list */
{
struct slName* head = NULL;
char *xref;

while ((xref = nextWord(&xrefStr)) != NULL)
    slSafeAddHead(&head, newSlName(xref));
return head;
}
コード例 #10
0
ファイル: checkTableCoords.c プロジェクト: maximilianh/kent
struct slName *getTableNames(struct sqlConnection *conn)
/* Return a list of names of tables that have not been excluded by 
 * command line options. */
{
char *query = hoursOld ? "NOSQLINJ show table status" : "NOSQLINJ show tables";
struct sqlResult *sr = sqlGetResult(conn, query);
struct slName *tableList = NULL;
char **row = NULL;
int startTime = clock1();
int ageThresh = hoursOld * 3600;

while((row = sqlNextRow(sr)) != NULL)
    {
    struct slName *tableName = NULL;
    struct slName *pat = NULL;
    boolean gotMatch = FALSE;
    if (hoursOld)
	{
	if (row[11] != NULL)
	    {
	    int tableUpdateTime = sqlDateToUnixTime(row[11]);
	    int ageInSeconds = startTime - tableUpdateTime;
	    if (ageInSeconds > ageThresh)
		continue;
	    }
	else
	    {
	    verbose(2,
		    "Got NULL update time for table %s.%s with hoursOld=%d\n",
		    sqlGetDatabase(conn), row[0], hoursOld);
	    }
	}
    for (pat = excludePatterns;  pat != NULL;  pat=pat->next)
	{
	if (wildMatch(pat->name, row[0]))
	    {
	    gotMatch = TRUE;
	    break;
	    }
	}
    if (gotMatch)
	continue;
    if (verboseLevel() >= 3 || justList)
	fprintf(stderr, "Adding %s\n", row[0]);
    tableName = newSlName(row[0]);
    slAddHead(&tableList, tableName);
    }
sqlFreeResult(&sr);
if (justList)
    exit(0);
slReverse(&tableList);
return tableList;
}
コード例 #11
0
ファイル: options.c プロジェクト: Puneet-Shivanand/zinba
static void parseMultiOption(struct hash *hash, char *name, char* val, struct optionSpec *spec)
/* process multiple instances of an option, requres that the optionSpec of the option */
{
struct slName *valList;
switch (spec->flags & OPTION_TYPE_MASK)
    {
    case OPTION_STRING:
        valList = hashFindVal(hash, name);
        if (valList == NULL)   /* first multi option */
            {
            valList = newSlName(val);
            hashAdd(hash, name, valList);
            }
        else
            {
            struct slName *el = newSlName(val);
            slAddTail(valList, el); /* added next multi option */
            }
        break;
    default:
        errAbort("UNIMPLEMENTED: multiple instances of a non-string option is not currently implemented");
    }
}
コード例 #12
0
struct slName *getWhiteListFromFile()
/* Read in the -justThese file and store the names of the enzymes */
/* in a list of slNames. */
{
struct slName *whiteList = NULL;
struct lineFile *lf = lineFileOpen(justThese, TRUE);
char *line;
while (lineFileNextReal(lf, &line))
    {
    struct slName *newName = newSlName(line);
    slAddHead(&whiteList, newName);
    }
lineFileClose(&lf);
return whiteList;
}
コード例 #13
0
ファイル: obscure.c プロジェクト: andrelmartins/bigWig
struct slName *readAllLines(char *fileName)
/* Read all lines of file into a list.  (Removes trailing carriage return.) */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct slName *list = NULL, *el;
char *line;

while (lineFileNext(lf, &line, NULL))
     {
     el = newSlName(line);
     slAddHead(&list, el);
     }
slReverse(&list);
return list;
}
コード例 #14
0
ファイル: gbGetTestSubset.c プロジェクト: davidhoover/kent
struct slName* loadAccList(char *fname)
{
struct slName* accList = NULL;
struct lineFile* accFh;
char *line;
accFh = lineFileOpen(fname, TRUE);

while (lineFileNextReal(accFh, &line))
    {
    line = trimSpaces(line);
    slSafeAddHead(&accList, newSlName(line));
    }

lineFileClose(&accFh);
return accList;
}
コード例 #15
0
static void readMappingResults(char **argv) {
	FILE *fp;
	char buf[500], chr[50], id[500];
	int beg, i, j, len;
	char *ch;
	struct slName *ali;
	struct hashEl *el;
	struct rbTree *tr;

	aliHash = newHash(8);
	
	for (i = 4; i <= 5; i++) {
		fp = mustOpen(argv[i], "r");
		while (fgets(buf, 500, fp)) {
			
			if (ncbi && i >= 6 && i <= 7) {
				if (sscanf(buf, "%[^\t]\t%*c %s %d %d", id, chr, &beg, &len) != 4)
					errAbort("error: %s", buf);
				if ((ch = strchr(id, ' ')))
					*ch = '\0';
				if (i >= 6 && i <= 7) {
					j = strlen(id);
					sprintf(id+j, "/%d", i-5);
				}
			}
			
			else {	
				if (sscanf(buf, "%[^\t]\t%*c %s %d %d", id, chr, &beg, &len) != 4){
					errAbort("error: %s", buf);
				}
					if ((ch = strchr(id, ' ')))
                                        	*ch = '\0';
				
			}
			ali = newSlName(id);
			el = hashLookup(aliHash, chr);
			if (el == NULL) {
				tr = rangeTreeNew();
				hashAdd(aliHash, chr, tr);
			}
			else 
				tr = (struct rbTree *)(el->val);
			rangeTreeAddValHead(tr, beg, beg + len - 1, &ali);
		}
		fclose(fp);
	}
}
コード例 #16
0
void randomEst(char *database, int count, char *output)
/* randomEst - Select random ESTs from database. */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char **row;
int i, elIx, okCount = 0;
struct slName *list = NULL, *el;
FILE *f = NULL;
char **array = NULL;
struct dnaSeq *seq;
struct hash *uniqHash = newHash(0);

hSetDb(database);
printf("Scanning database\n");
sr = sqlGetResult(conn, "select acc,type,direction from mrna");
while ((row = sqlNextRow(sr)) != NULL)
    {
    if (sameString(row[1], "EST") && sameString(row[2], "3"))
        {
	el = newSlName(row[0]);
	slAddHead(&list, el);
	++okCount;
	}
    }
sqlFreeResult(&sr);
printf("Got %d 3' ESTs\n", okCount);
AllocArray(array, okCount);
for (i=0, el = list; el != NULL; el = el->next, ++i)
    array[i] = el->name;

printf("Selecting %d to put into %s\n", count, output);
f = mustOpen(output, "w");
for (i=0; i<count; ++i)
    {
    char *name;
    elIx = rand()%okCount;
    name = array[elIx];
    if (!hashLookup(uniqHash, name))
	{
	hashAdd(uniqHash, name, NULL);
	seq = hRnaSeq(name);
	faWriteNext(f, seq->name, seq->dna, seq->size);
	freeDnaSeq(&seq);
	}
    }
}
コード例 #17
0
void fillInExpHash(char *expFileName, struct hash **expHash, struct slName **expNames, int *expCount)
/** Read all of the names from the expFileName and store them in a hash. */
{
struct lineFile *lf = lineFileOpen(expFileName, TRUE);
char *line = NULL;
int lineSize = 0;
struct slName *name = NULL;
*expCount = 0;
*expHash = newHash(5);
while(lineFileNextReal(lf, &line))
    {
    hashAddInt(*expHash, line, (*expCount)++);
    name = newSlName(line);
    slAddHead(expNames, name);
    }
slReverse(expNames);
}
コード例 #18
0
ファイル: dbTrash.c プロジェクト: apmagalhaes/kentUtils
void checkExtFile(struct sqlConnection *conn)
/* check extFile table for files that have been removed */
{
char query[256];
struct sqlResult *sr;
char **row;
char buffer[4 * 1024];
char *name = buffer;
struct slName *list = NULL;

if (! sqlTableExists(conn, CT_EXTFILE))
    {
    verbose(2,"WARNING: -extFile option specified, extFile table does not exist\n");
    verbose(2,"at this time (Jan 2009), the extFile table is unused.\n");
    return;
    }

sqlSafef(query,sizeof(query),"select id,path from %s",CT_EXTFILE);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
    {
    if (topDir != NULL)
	safef(buffer, sizeof buffer, "%s/%s",topDir, row[1]);
    else
	name = row[1];

    if (!fileExists(name))
	{
	struct slName *new = newSlName(row[0]);
	slAddHead(&list, new);
	}
    }
sqlFreeResult(&sr);

struct slName *one;
for(one = list; one; one = one->next)
    {
    sqlSafef(query,sizeof(query),"delete from %s where id='%s'",
	CT_EXTFILE, one->name);
    if (extDel)
	sqlUpdate(conn, query);
    verbose(2,"%s\n",query);
    }
slFreeList(&list);
}
コード例 #19
0
struct slName *findIsoligamers(struct cutter *enz, struct cutter *enzList)
/* Find isoligamers to an enzyme in a list of enzymes.  */
{
struct slName *list = NULL;
struct cutter *cur;
if (!enz || !enzList)
    return NULL;
for (cur = enzList; cur != NULL; cur = cur->next)
    {
    if (!sameString(cur->name, enz->name) && (sameStickyEnd(enz, cur)))
	{
	struct slName *newname = newSlName(cur->name);
	slAddHead(&list, newname);
	}
    }
slReverse(&list);
return list;
}
コード例 #20
0
ファイル: chkAlignTbls.c プロジェクト: davidhoover/kent
static void buildChromSizes(char *db)
/* build table of chromosome sizes and list of chromosomes */
{
struct sqlConnection *conn =  hAllocConn(db);
struct sqlResult *sr;
char **row;
gChromSizes = hashNew(8);

sr = sqlGetResult(conn, NOSQLINJ "SELECT chrom,size FROM chromInfo");
while ((row = sqlNextRow(sr)) != NULL)
    {
    unsigned sz = gbParseUnsigned(NULL, row[1]);
    hashAddInt(gChromSizes, row[0], sz);
    slSafeAddHead(&gChroms, newSlName(row[0]));
    }
sqlFreeResult(&sr);
hFreeConn(&conn);
}
コード例 #21
0
ファイル: pa.c プロジェクト: davidhoover/kent
struct slName *getOrderList(char *file)
/* Read in the species list. */
{
struct lineFile *lf = lineFileOpen(file, TRUE);
char *row[1];
struct slName *nameList = NULL;

while (lineFileRow(lf, row))
    {
    struct slName *name = newSlName(row[0]);

    slAddHead(&nameList, name);
    }

slReverse(&nameList);
lineFileClose(&lf);

return nameList;
}
コード例 #22
0
ファイル: snpException.c プロジェクト: davidhoover/kent
struct slName *getChromList(char *db)
/* Get list of all chromosomes. */
{
struct sqlConnection *conn  = hAllocConn(db);
struct sqlResult     *sr    = NULL;
char                **row   = NULL;
struct slName        *list  = NULL;
struct slName        *el    = NULL;
char                 *query = NOSQLINJ "select chrom from chromInfo";

sr = sqlGetResult(conn, query);
while ((row=sqlNextRow(sr))!=NULL)
    {
    el = newSlName(row[0]);
    slAddHead(&list, el);
    }
slReverse(&list);
sqlFreeResult(&sr);
hFreeConn(&conn);
return list;
}
コード例 #23
0
void bedCons(char *database, char *refAliTrack, char *bedTrack)
/* bedCons - Look at conservation of a BED track vs. a refence
 * (nonredundant) alignment track. */
{
    struct slName *chromList, *chrom;
    struct stats *stats = NULL;
    struct hash *otherHash = makeOtherHash(database, "mouseChrom");

    if (optionExists("chrom"))
        chromList = newSlName(optionVal("chrom", NULL));
    else
        chromList = hAllChromNames(database);
    AllocVar(stats);
    for (chrom = chromList; chrom != NULL; chrom = chrom->next)
    {
        uglyf("%s\n", chrom->name);
        oneChrom(database, chrom->name, refAliTrack, bedTrack, otherHash, stats);
    }

    printStats(stats);
}
コード例 #24
0
ファイル: oswin9x.c プロジェクト: JinfengChen/pblat
struct slName *listDir(char *dir, char *pattern)
/* Return an alphabetized list of all files that match 
 * the wildcard pattern in directory. */
{
long hFile;
struct _finddata_t fileInfo;
struct slName *list = NULL, *name;
boolean otherDir = FALSE;
char *currentDir;

if (dir == NULL || sameString(".", dir) || sameString("", dir))
    dir = "";
else
    {
    currentDir = getCurrentDir();
    setCurrentDir(dir);
    otherDir = TRUE;
    }

if (pattern == NULL)
    pattern = *;
if( (hFile = _findfirst( pattern, &fileInfo)) == -1L )
    return NULL;

do
    {
    if (!sameString(".", fileInfo.name) && !sameString("..", fileInfo.name))
        {
        name = newSlName(fileInfo.name);
        slAddHead(&list, name);
        }
    }
while( _findnext( hFile, &fileInfo) == 0 );
_findclose( hFile );
if (otherDir)
    setCurrentDir(currentDir);
slNameSort(&list);
return list;
}
コード例 #25
0
ファイル: snpException.c プロジェクト: davidhoover/kent
struct slName *getGroupList(char *db, char *group)
/* Get list of all rsIds from where clause. */
{
struct sqlConnection *conn  = hAllocConn(db);
struct sqlResult     *sr    = NULL;
char                **row   = NULL;
struct slName        *list  = NULL;
struct slName        *el    = NULL;
char                  query[256];

sqlSafef(query,sizeof(query),"select name from snp %s", group);
sr = sqlGetResult(conn, query);
while ((row=sqlNextRow(sr))!=NULL)
    {
    el = newSlName(row[0]);
    slAddHead(&list, el);
    }
slReverse(&list);
sqlFreeResult(&sr);
hFreeConn(&conn);
return list;
}
コード例 #26
0
ファイル: wormdna.c プロジェクト: CRG-Barcelona/libbeato
struct slName *wormGeneToOrfNames(char *name)
/* Returns list of cosmid.N type ORF names that are known by abc-12 type name. */
{
struct slName *synList = NULL;
char synFileName[512];
FILE *synFile;
char lineBuf[128];
int nameLen = strlen(name);

/* genes are supposed to be lower case. */
tolowers(name);

/* Open synonym file and loop through each line of it */
sprintf(synFileName, "%ssyn", wormFeaturesDir());
if ((synFile = fopen(synFileName, "r")) == NULL)
    errAbort("Can't find synonym file '%s'. (errno: %d)\n", synFileName, errno);
while (fgets(lineBuf, ArraySize(lineBuf), synFile))
    {
    /* If first part of line matches chop up line. */
    if (strncmp(name, lineBuf, nameLen) == 0)
	{
	char *syns[32];
	int count;
	count = chopString(lineBuf, whiteSpaceChopper, syns, ArraySize(syns));

	/* Looks like we got a synonym.  Add all the aliases. */
	if (strcmp(name, syns[0]) == 0)
	    {
	    int i;
	    for (i=1; i<count; ++i)
                slAddTail(&synList, newSlName(syns[i]));
	    break;
	    }
	}
    }
fclose(synFile);
return synList;
}
コード例 #27
0
void findCutters(char *gcgFile, char *genome, char *outputFile)
/* findCutters - Find REBASE restriction enzymes using their GCG file. */
{
struct cutter *cutters = readGcg(gcgFile);
struct dnaSeq *seqs = dnaLoadAll(genome);
struct slName *whiteList = NULL;
if (justThis)
    whiteList = newSlName(justThis);
if (justThese)
    {
    struct slName *listFromJustThese = getWhiteListFromFile();
    whiteList = slCat(whiteList, listFromJustThese);
    }
if (justThese || justThis)
    cullCutters(&cutters, TRUE, whiteList, 0);
if (countsOnly)
    findCounts(cutters, seqs, outputFile);
else
    findBeds(cutters, seqs, outputFile);
cutterFreeList(&cutters);
freeDnaSeqList(&seqs);
slNameFreeList(&whiteList);
}
コード例 #28
0
ファイル: gbIndex.c プロジェクト: davidhoover/kent
static void getReleasePartitions(struct gbSelect** selectList,
                                 struct gbRelease* release,
                                 unsigned state,
                                 unsigned types,
                                 unsigned orgCats,
                                 char *limitAccPrefix)
/* Get partitions for a release and add to list */
{
if (types & GB_MRNA)
    getTypePartitions(selectList, release, GB_MRNA, orgCats, NULL);
if ((types & GB_EST) && (release->srcDb != GB_REFSEQ))
    {
    struct slName* prefixes, *prefix;
    if (limitAccPrefix != NULL)
        prefixes = newSlName(limitAccPrefix);
    else
        prefixes = gbReleaseGetAccPrefixes(release, state, GB_EST);

    for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
        getTypePartitions(selectList, release, GB_EST, orgCats, prefix->name);
    slFreeList(&prefixes);
    }
}
コード例 #29
0
void expToRna(char *database, char *rnaTable, char *expTable, char *outName)
/* expToRna - Make a little two column table that associates 
 * rnaClusters with expression info. */
{
struct slName *chromList = NULL, *chromEl;
char *chrom = optionVal("chrom", NULL);
FILE *f = mustOpen(outName, "w");

if (chrom != NULL)
    chromList = newSlName(chrom);
else
    chromList = hAllChromNames(database);
for (chromEl = chromList; chromEl != NULL; chromEl = chromEl->next)
    {
    chrom = chromEl->name;
    uglyf("%s\n", chrom);
    doOneChrom(database, chrom, rnaTable, expTable, f);
    }
printf("%d dupe, %d uniq, %d miss, %d total, %d hits\n", 
	dupeCount, uniqCount, missCount,
	dupeCount + uniqCount + missCount,
	hitCount);
}
コード例 #30
0
ファイル: pal.c プロジェクト: blumroy/kentUtils
static char * getConservationTrackName( struct sqlConnection *conn)
{
struct slName *dbList = hTrackDbList();
struct slName *dbl = dbList;
char *ret = NULL;

for(; dbl; dbl = dbl->next)
    {
    char query[512];
    sqlSafef(query, sizeof query,
	"select tableName from %s where shortLabel='Conservation'", dbl->name);

    struct sqlResult *sr = sqlGetResult(conn, query);
    char **row;
    struct slName *tableList = NULL;
    while ((row = sqlNextRow(sr)) != NULL)
	{
	struct slName *name = newSlName(row[0]);
	slAddHead(&tableList, name);
	}
    sqlFreeResult(&sr);

    struct slName *l = tableList;

    for(; l; l = l->next)
	if (sqlTableExists(conn, l->name))
	    ret = cloneString(l->name);

    slFreeList(&tableList);

    if (ret != NULL)
	break;
    }
slFreeList(&dbList);

return ret;
}