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);
}
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;
}
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);
}
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");
}
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;
}
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;
}
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;
}
void pushPosString(struct speciesInfo *si)
{
flushPosString(si);
struct slName *newName = newSlName(si->posString);
slAddTail(&si->posStrings, newName);
freez(&si->posString);
}
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;
}
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;
}
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");
}
}
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;
}
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;
}
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;
}
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);
}
}
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);
}
}
}
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);
}
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);
}
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;
}
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);
}
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;
}
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;
}
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);
}
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;
}
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;
}
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;
}
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);
}
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);
}
}
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);
}
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;
}