int main(int argc, char *argv[])
{
char *sourceName, *destRootName;
int maxSize;
char destName[512];
char faName[512];
int destIx;
int size, start;
struct dnaSeq *seq;
if (argc != 4)
usage();
sourceName = argv[1];
maxSize = atoi(argv[2]);
if (maxSize < 1)
usage();
destRootName = argv[3];
printf("reading %s\n", sourceName);
seq = faReadDna(sourceName);
for (start = 0, destIx = 1; start < seq->size; start += size, ++destIx)
{
size = seq->size - start;
if (size > maxSize)
size = maxSize;
sprintf(destName, "%s%02d.fa", destRootName, destIx);
sprintf(faName, "%s.%d", seq->name, destIx);
printf("writing %s\n", destName);
faWrite(destName, faName, seq->dna+start, size);
}
return 0;
}
void showDetailedMatch(char *bacAcc, int contig, int qStart, int qSize, int tStart, int tSize, char *repeatMask)
/* Process a click on active area. */
{
struct dnaSeq *queryList, *query, *target;
struct ffAli *ali;
boolean rc;
char needleName[128], hayName[128];
makeFileNames(bacAcc, repeatMask);
queryList = faReadAllDna(unfinBac);
target = faReadDna(finBac);
query = slElementFromIx(queryList, contig);
if (!ffFindEitherStrandN(query->dna + qStart, qSize, target->dna + tStart, tSize,
ffCdna, &ali, &rc))
{
errAbort("Couldn't align %s and %s", unfinBac, finBac);
}
sprintf(needleName, "%s contig %d %d-%d", bacAcc, contig, qStart, qStart+qSize);
sprintf(hayName, "%s finished %d-%d", bacAcc, tStart, tStart+tSize);
query->dna[qStart+qSize] = 0;
target->dna[tStart+tSize] = 0;
ffShowAli(ali, needleName, query->dna + qStart, 0,
hayName, target->dna + tStart, 0, rc);
}
void hgNibSeq(char *database, char *destDir, int faCount, char *faNames[])
/* hgNibSeq - convert DNA to nibble-a-base and store location in database. */
{
char dir[256], name[128], chromName[128], ext[64];
char nibName[512];
struct sqlConnection *conn = sqlConnect(database);
char query[512];
int i;
char *faName;
struct dnaSeq *seq = NULL;
unsigned long total = 0;
int size;
if (!strchr(destDir, '/'))
errAbort("Use full path name for nib file dir\n");
makeDir(destDir);
if ((!appendTbl) || !sqlTableExists(conn, tableName))
createTable(conn);
for (i=0; i<faCount; ++i)
{
faName = faNames[i];
splitPath(faName, dir, name, ext);
sprintf(nibName, "%s/%s.nib", destDir, name);
printf("Processing %s to %s\n", faName, nibName);
if (preMadeNib)
{
FILE *nibFile;
nibOpenVerify(nibName, &nibFile, &size);
carefulClose(&nibFile);
}
else
{
seq = faReadDna(faName);
if (seq != NULL)
{
size = seq->size;
uglyf("Read DNA\n");
nibWrite(seq, nibName);
uglyf("Wrote nib\n");
freeDnaSeq(&seq);
}
}
strcpy(chromName, chromPrefix);
strcat(chromName, name);
sqlSafef(query, sizeof query, "INSERT into %s VALUES('%s', %d, '%s')",
tableName, chromName, size, nibName);
sqlUpdate(conn,query);
total += size;
}
sqlDisconnect(&conn);
printf("%lu total bases\n", total);
}
void agpCloneCheck(char *agpFile, char *gsDir)
/* agpCloneCheck - Check that have all clones in an agp file (and the right version too). */
{
struct lineFile *lf = lineFileOpen(agpFile, TRUE);
char *line, *words[16];
int lineSize, wordCount, i;
char clonePath[512];
char clone[128], *cloneVer;
static char *phases[3] = {"fin", "draft", "predraft",};
boolean found;
while (lineFileNext(lf, &line, &lineSize))
{
if (line[0] == '#')
continue;
wordCount = chopLine(line, words);
if (wordCount == 0)
continue;
if (wordCount < 5)
errAbort("Bad line %d of %s", lf->lineIx, lf->fileName);
if (words[4][0] == 'N' || words[4][0] == 'U')
continue;
cloneVer = words[5];
strcpy(clone, cloneVer);
chopSuffix(clone);
found = FALSE;
for (i = 0; i < 3; ++i)
{
char *phase = phases[i];
sprintf(clonePath, "%s/%s/fa/%s.fa", gsDir, phase, clone);
if (fileExists(clonePath))
{
struct dnaSeq *seq = faReadDna(clonePath);
char *e = strchr(seq->name, '_');
if (e != NULL) *e = 0;
if (!sameString(seq->name, cloneVer))
printf("%s\t(wrong version %s)\n", cloneVer, seq->name);
else if (i != 0)
printf("%s\t(not finished)\n", cloneVer);
found = TRUE;
}
}
if (!found)
printf("%s\t(not found)\n", cloneVer);
}
}
void flagMhcClones(char *mhcFile, char *gsDir)
/* flagMhcClones - Look for clones Stephan wants in MHC.. */
{
struct lineFile *lf = lineFileOpen(mhcFile, TRUE);
char *line, *words[16];
int lineSize, wordCount, i;
char clonePath[512];
char *clone, *cloneVer;
static char *phases[3] = {"fin", "draft", "predraft",};
boolean found;
while (lineFileNext(lf, &line, &lineSize))
{
if (line[0] == '#')
continue;
wordCount = chopLine(line, words);
if (wordCount == 0)
continue;
lineFileExpectWords(lf, 7, wordCount);
clone = words[0];
cloneVer = words[1];
found = FALSE;
for (i = 0; i < 3; ++i)
{
char *phase = phases[i];
sprintf(clonePath, "%s/%s/fa/%s.fa", gsDir, phase, clone);
if (fileExists(clonePath))
{
struct dnaSeq *seq = faReadDna(clonePath);
char *e = strchr(seq->name, '_');
if (e != NULL) *e = 0;
if (!sameString(seq->name, cloneVer))
printf("%s\t(wrong version %s)\n", cloneVer, seq->name);
else if (i != 0)
printf("%s\t(not finished)\n", cloneVer);
found = TRUE;
}
}
if (!found)
printf("%s\t(not found)\n", cloneVer);
}
}
struct hash *loadGeno(char *genoFile)
/* load genome sequences into a hash. This supports the multi-sequence
* specs of twoBitLoadAll */
{
struct dnaSeq *genos = NULL, *geno;
struct hash *genoHash = hashNew(0);
if (nibIsFile(genoFile))
genos = nibLoadAllMasked(NIB_MASK_MIXED|NIB_BASE_NAME, genoFile);
else if (twoBitIsSpec(genoFile))
genos = twoBitLoadAll(genoFile);
else
genos = faReadDna(genoFile);
while ((geno = slPopHead(&genos)) != NULL)
{
tolowers(geno->dna);
hashAdd(genoHash, geno->name, geno);
}
return genoHash;
}
void countCosmids(char *listFileName, FILE *out)
/* Read each cosmid in list file and find out how big it is. */
{
FILE *listFile = mustOpen(listFileName, "r");
char line[512], *s;
int lineCount;
struct dnaSeq *seq;
char path[512];
while (fgets(line, sizeof(line), listFile))
{
++lineCount;
s = trimSpaces(line);
sprintf(path, "%s/%s", "C:/biodata/cbriggsae/finish", s);
seq = faReadDna(path);
++cosmidCount;
cosmidTotalSize += seq->size;
freeDnaSeq(&seq);
}
fclose(listFile);
cosmidAverageSize = round((double)cosmidTotalSize/cosmidCount);
fprintf(out, "%d cosmids, average length %d\n", cosmidCount, cosmidAverageSize);
}
