void convertPslFile(struct sqlConnection *conn, char *pslFile, FILE *genePredFh)
/* convert mrnas in a psl file to genePred objects */
{
struct lineFile *lf = pslFileOpen(pslFile);
char *row[PSL_NUM_COLS];
while (lineFileNextRowTab(lf, row, PSL_NUM_COLS))
convertPslFileRow(conn, row, genePredFh);
lineFileClose(&lf);
}
static void parseIndex(struct gbRelease* release, struct gbIgnore* ignore,
char *path)
/* read and parse ignore file */
{
char* row[IGIDX_NUM_COLS];
struct lineFile* lf = lineFileOpen(path, TRUE);
while (lineFileNextRowTab(lf, row, ArraySize(row)))
parseRow(release, ignore, lf, row);
lineFileClose(&lf);
}
static struct hash *loadSizes(char *szFile)
/* load sizes into a hash */
{
struct hash *sizes = hashNew(0);
struct lineFile *lf = lineFileOpen(szFile, TRUE);
char *row[2];
while (lineFileNextRowTab(lf, row, 2))
hashAddInt(sizes, row[0], sqlSigned(row[1]));
return sizes;
}
void hgCeOrfToGene(char *database, char *geneNames,
char *geneTable, char *table)
/* hgCeOrfToGene - Make orfToGene table for C.elegans from
* GENE_DUMPS/gene_names.txt. */
{
struct lineFile *lf = lineFileOpen(geneNames, TRUE);
struct sqlConnection *conn;
struct sqlResult *sr;
char query[256];
char **row;
char *tempDir = ".";
FILE *f = hgCreateTabFile(tempDir, table);
char *words[4];
struct hash *orfHash = newHash(17);
/* Make hash to look up gene names. */
while (lineFileNextRowTab(lf, words, ArraySize(words)))
{
char *gene = words[0];
char *orfs = words[3];
char *type = words[2];
char *orf[128];
int i, orfCount;
if (sameString(type, "Gene"))
{
orfCount = chopString(orfs, ",", orf, ArraySize(orf));
if (orfCount >= ArraySize(orf))
errAbort("Too many ORFs line %d of %s", lf->lineIx, lf->fileName);
for (i=0; i<orfCount; ++i)
hashAdd(orfHash, orf[i], cloneString(gene));
}
}
lineFileClose(&lf);
/* For each orf in gene table write out gene name if possible,
* otherwise orf name. */
conn = sqlConnect(database);
safef(query, sizeof(query), "select name from %s", geneTable);
sr = sqlGetResult(conn,query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *orf = row[0];
char *gene = hashFindVal(orfHash, orf);
if (gene == NULL)
gene = orf;
fprintf(f, "%s\t%s\n", orf, gene);
}
sqlFreeResult(&sr);
createTable(conn, table, unique);
hgLoadTabFile(conn, tempDir, table, &f);
}
/* read qNames and sizes into a hash of querySizeCnt objet */
static struct hash* querySizeCntLoad(char *querySizeFile)
{
struct hash* querySizesTbl = hashNew(queryHashPowTwo);
struct lineFile *lf = lineFileOpen(querySizeFile, TRUE);
char *row[2];
while (lineFileNextRowTab(lf, row, ArraySize(row)))
querySizeCntGet(querySizesTbl, row[0], sqlUnsigned(row[1]));
lineFileClose(&lf);
return querySizesTbl;
}
void loadCdsFile(char *cdsFile)
/* read a CDS file into the global hash */
{
struct lineFile *lf = lineFileOpen(cdsFile, TRUE);
char *row[2];
gCdsTable = hashNew(20);
while (lineFileNextRowTab(lf, row, 2))
hashAdd(gCdsTable, row[0],
lmCloneString(gCdsTable->lm, row[1]));
lineFileClose(&lf);
}
struct itemAttr* loadAttrFile(char* itemAttrFile)
/* load itemAttr records into memory and sort */
{
struct itemAttr *itemAttrs = NULL;
struct lineFile *lf = lineFileOpen(itemAttrFile, TRUE);
char *row[ITEMATTR_NUM_COLS];
while (lineFileNextRowTab(lf, row, ITEMATTR_NUM_COLS))
slSafeAddHead(&itemAttrs, itemAttrLoad(row));
lineFileClose(&lf);
slSort(&itemAttrs, itemAttrCmp);
return itemAttrs;
}
void processFrameFile(FILE *sortFh, char *framesFile)
/* read records from one frame file, adding bin and write to pipe to sort */
{
struct lineFile *inLf = lineFileOpen(framesFile, TRUE);
struct mafFrames mf;
char *row[MAFFRAMES_NUM_COLS];
while (lineFileNextRowTab(inLf, row, MAFFRAMES_NUM_COLS))
{
mafFramesStaticLoad(row, &mf);
fprintf(sortFh, "%d\t", binFromRange(mf.chromStart, mf.chromEnd));
mafFramesTabOut(&mf, sortFh);
}
lineFileClose(&inLf);
}
void loadCoverQSizes(char* coverQSizeFile)
/* load coverage query sizes */
{
struct lineFile *lf = lineFileOpen(coverQSizeFile, TRUE);
char *row[2];
coverQSizes = hashNew(0);
while (lineFileNextRowTab(lf, row, ArraySize(row)))
{
int qSize = sqlSigned(row[1]);
hashAdd(coverQSizes, row[0], intToPt(qSize));
}
lineFileClose(&lf);
}
struct hash *polyASizeLoadHash(char *fileName)
/* load a tab-separated file of polyASize objects into a hash table. Objects
* are stored in the local mem of the hash, and thus freed when the hash is
* freed. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[POLYASIZE_NUM_COLS];
struct hash *pasHash = hashNew(22);
while (lineFileNextRowTab(lf, row, ArraySize(row)))
loadPolyASizeRec(pasHash, row);
lineFileClose(&lf);
return pasHash;
}
struct mahoney *vgLoadMahoneyList(char *fileName)
/* Load data from tab-separated file (not whitespace separated) */
{
struct mahoney *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[MAHONEY_NUM_COLS];
while (lineFileNextRowTab(lf, row, ArraySize(row)))
{
el = mahoneyLoad(row);
fixPrimers(el);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
void convertCelFile(struct lqRecord ***lqMatrix, struct hash *nmerHash, char *celFile, char *outputFormat)
{
struct lineFile *lf = lineFileOpen(celFile, TRUE);
char *line=NULL;
int lineSize, x, y, i,j;
char *words[5];
struct lqRecord *pm = NULL, *mm=NULL;
char *outFile = needMem(sizeof(char)*(strlen(celFile)+5));
FILE *out = NULL;
int numCols=0, numRows=0;
struct cel ***celMatrix = NULL;
safef(outFile, strlen(celFile)+5, "%s.tab", celFile);
out = mustOpen(outFile, "w");
parseCelRowsCols(lf, &numRows, &numCols);
if(numCols == 0 || numRows == 0)
errAbort("Couldn't find a 'Cols=' or a 'Rows=' in %s, is this a cel file?\n", celFile);
/* Allocate the matrix. */
celMatrix = needMem(sizeof(struct lqRecord *)*numRows);
for(i=0; i<numRows; i++)
celMatrix[i] = needMem(sizeof(struct lqRecord *)*numCols);
while(lineFileNextRowTab(lf, words, 5))
{
struct cel *cel = parseCelRow(words);
celMatrix[cel->x][cel->y] = cel;
if(cel->x + 1 == numRows && cel->y +1 == numCols)
break;
}
outputPairsFile(out, numRows, numCols, lqMatrix, celMatrix);
/* Cleanup. */
for(i=0;i<numRows;i++)
for(j=0; j<numCols; j++)
if(celMatrix[i][j] != NULL)
freez(&celMatrix[i][j]);
for(i=0; i<numRows; i++)
freez(&celMatrix[i]);
freez(&celMatrix);
lineFileClose(&lf);
freez(&outFile);
carefulClose(&out);
}
struct stanMad *stanMadLoadAll(char *fileName)
/* Load all stanMad from a tab-separated file.
* Dispose of this with stanMadFreeList(). */
{
struct stanMad *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[40];
while (lineFileNextRowTab(lf, row, ArraySize(row)))
{
if(strstr(row[0], "EXP"))
continue;
el = stanMadLoad(row);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct hash *hashNmerFile(char *file)
{
struct lineFile *lf = lineFileOpen(file, TRUE);
struct hash *nmerHash = newHash(15);
struct nmerAlign *nmerList = NULL, *nmer;
char key[256];
char *words[6];
while(lineFileNextRowTab(lf, words, 6))
{
nmer = parseNmerAlignRow(words);
snprintf(key, sizeof(key), "%s-%s", nmer->seq, nmer->name);
nmerList = hashFindVal(nmerHash, key);
if(nmerList == NULL)
hashAddUnique(nmerHash, key, nmer);
else
slAddTail(&nmerList, nmer);
}
lineFileClose(&lf);
return nmerHash;
}
struct mgcLibraryTbl *mgcLibraryTblLoad(char *fileName)
/* load a file of mgcLibrary objects, building a hash by library id */
{
struct mgcLibraryTbl *mlt;
char *row[MGCLIBRARY_NUM_COLS];
char key[64];
struct lineFile *lf;
AllocVar(mlt);
mlt->idHash = hashNew(12); /* 4096 */
lf = gzLineFileOpen(fileName);
while (lineFileNextRowTab(lf, row, MGCLIBRARY_NUM_COLS))
{
struct mgcLibrary *mgcLibrary = mgcLibraryLoad(row);
safef(key, sizeof(key), "%d", mgcLibrary->id_lib);
hashAdd(mlt->idHash, key, mgcLibrary);
}
gzLineFileClose(&lf);
return mlt;
}
static void processOrgCatOi(struct gbSelect* select, unsigned orgCat)
/* process files in an update an organism category. OIs are only available
* for native, however this follow the structure of the PSL code */
{
char inOi[PATH_LEN], *row[EST_ORIENT_INFO_NUM_COLS];
struct lineFile* inOiLf;
unsigned orgCatsHold = select->orgCats;
select->orgCats = orgCat;
gbAlignedGetPath(select, "oi.gz", NULL, inOi);
inOiLf = gzLineFileOpen(inOi);
while (lineFileNextRowTab(inOiLf, row, EST_ORIENT_INFO_NUM_COLS))
{
struct estOrientInfo* oi = estOrientInfoLoad(row);
processOi(select, oi);
estOrientInfoFree(&oi);
}
gzLineFileClose(&inOiLf);
select->orgCats = orgCatsHold;
}
void migrateOrientInfos(struct migrateAligns* migrate, FILE* outOiFh)
/* Migrate estOrientInfo records */
{
char inOi[PATH_LEN];
struct lineFile* inOiLf;
char *row[EST_ORIENT_INFO_NUM_COLS];
gbAlignedGetPath(migrate->prevSelect, "oi.gz", NULL, inOi);
if (fileExists(inOi))
{
gbVerbEnter(2, "migrating from %s", inOi);
inOiLf = gzLineFileOpen(inOi);
while (lineFileNextRowTab(inOiLf, row, ArraySize(row)))
{
struct estOrientInfo *oi = estOrientInfoLoad(row);
migrateOrientInfo(migrate, oi, inOi, outOiFh);
estOrientInfoFree(&oi);
}
gzLineFileClose(&inOiLf);
gbVerbLeave(2, "migrating from %s", inOi);
}
}
void copyOrientInfos(struct gbSelect* select, FILE* outOiFh,
struct recCounts* recCounts)
/* Copy an OI file from the work directory, if it exists, count alignments
* for index. */
{
char inOi[PATH_LEN];
struct lineFile* inOiLf;
char *row[EST_ORIENT_INFO_NUM_COLS];
gbAlignedGetPath(select, "oi", gWorkDir, inOi);
if (fileExists(inOi))
{
gbVerbEnter(2, "installing from %s", inOi);
inOiLf = gzLineFileOpen(inOi);
while (lineFileNextRowTab(inOiLf, row, ArraySize(row)))
{
struct estOrientInfo *oi = estOrientInfoLoad(row);
copyOrientInfo(select, oi, inOi, outOiFh, recCounts);
estOrientInfoFree(&oi);
}
gzLineFileClose(&inOiLf);
gbVerbLeave(2, "installing from %s", inOi);
}
}
void hgLoadNetDist(char *inTab, char *db, char *outTable)
{
char *tempDir = ".";
FILE *f = hgCreateTabFile(tempDir, outTable);
struct sqlConnection *hConn = sqlConnect(db);
FILE *missingFile=NULL;
int missingCount=0;
struct lineFile *lf=NULL;
char *row[3];
int rowCount=3;
if (sqlRemap)
{
fetchRemapInfo(db);
missingHash = newHash(16);
missingFile = mustOpen("missing.tab","w");
}
/* read edges from file */
lf=lineFileOpen(inTab, TRUE);
/* print final values, remapping if needed */
while (lineFileNextRowTab(lf, row, rowCount))
{
char *geneI = row[0];
char *geneJ = row[1];
char *dij = row[2];
char *gi=NULL, *gj=NULL;
if (sqlRemap)
{ /* it is possible for each id to have multiple remap values in hash */
struct hashEl *hi=NULL, *hj=NULL, *hjSave=NULL;
hi = hashLookup(aliasHash,geneI);
hj = hashLookup(aliasHash,geneJ);
missingCount += handleMissing(hi, geneI, missingHash, missingFile);
missingCount += handleMissing(hj, geneJ, missingHash, missingFile);
hjSave = hj;
/* do all combinations of i and j */
for(;hi;hi=hashLookupNext(hi))
{
gi = (char *)hi->val;
for(;hj;hj=hashLookupNext(hj))
{
gj = (char *)hj->val;
fprintf(f,"%s\t%s\t%s\n",gi,gj,dij);
}
hj = hjSave; /* reset it */
}
}
else
{
gi=geneI;
gj=geneJ;
fprintf(f,"%s\t%s\t%s\n",gi,gj,dij);
}
}
lineFileClose(&lf);
carefulClose(&f);
if (sqlRemap)
{
carefulClose(&missingFile);
if (missingCount == 0)
unlink("missing.tab");
else
printf("hgLoadNetDist %d id-remapping misses, see missing.tab\n", missingCount);
}
createTable(hConn, outTable);
hgLoadTabFile(hConn, tempDir, outTable, &f);
hgRemoveTabFile(tempDir, outTable);
}
struct hash *makeProbeBed(char *inGff, char *outBed)
/* Convert probe location GFF file to BED. */
{
struct lineFile *lf = lineFileOpen(inGff, TRUE);
char *row[9];
struct hash *hash = newHash(16);
FILE *f = mustOpen(outBed, "w");
while (lineFileNextRowTab(lf, row, ArraySize(row)))
{
int chromIx = romanToArabicChrom(row[0], lf);
int start = lineFileNeedNum(lf, row, 3) - 1;
int end = lineFileNeedNum(lf, row, 4);
char *s = row[8];
char *probe, *orf, *note;
char *boundAt = "Bound at ";
struct tfBinding *tfbList = NULL, *tfb;
if (!startsWith("Probe ", s))
errAbort("Expecting 9th column to start with 'Probe ' line %d of %s",
lf->lineIx, lf->fileName);
probe = nextWord(&s);
orf = nextWord(&s);
chopOff(orf, ';');
note = nextWord(&s);
if (!sameWord("Note", note))
errAbort("Expecting 'note' in 9th column line %d of %s",
lf->lineIx, lf->fileName);
s = skipLeadingSpaces(s);
if (!parseQuotedString(s, s, NULL))
errAbort("Expecting quoted string in 9th column line %d of %s",
lf->lineIx, lf->fileName);
if (startsWith("Bad Probe", s))
continue;
else if (startsWith("Not bound", s))
{
/* Ok, we do nothing. */
}
else if (startsWith(boundAt, s))
{
while (s != NULL && startsWith(boundAt, s))
{
char *word, *by;
double binding;
s += strlen(boundAt);
word = nextWord(&s);
binding = atof(word);
by = nextWord(&s);
if (!sameString("by:", by))
errAbort("Expecting by: line %d of %s", lf->lineIx, lf->fileName);
while ((word = nextWord(&s)) != NULL)
{
char lastChar = 0, *e;
e = word + strlen(word) - 1;
lastChar = *e;
if (lastChar == ';' || lastChar == ',')
*e = 0;
AllocVar(tfb);
tfb->binding = binding;
tfb->tf = cloneString(word);
slAddHead(&tfbList, tfb);
if (lastChar == ';')
break;
}
s = skipLeadingSpaces(s);
}
slReverse(&tfbList);
}
else
{
errAbort("Expecting %s in note line %d of %s", boundAt,
lf->lineIx, lf->fileName);
}
fprintf(f, "chr%d\t%d\t%d\t", chromIx+1, start, end);
fprintf(f, "%s\t%d\t", orf, slCount(tfbList));
for (tfb = tfbList; tfb != NULL; tfb = tfb->next)
fprintf(f, "%s,", tfb->tf);
fprintf(f, "\t");
for (tfb = tfbList; tfb != NULL; tfb = tfb->next)
fprintf(f, "%4.3f,", tfb->binding);
fprintf(f, "\n");
hashAdd(hash, orf, NULL);
}
lineFileClose(&lf);
carefulClose(&f);
return hash;
}
void checkGff(char *gff, struct hash *chromHash)
/* Check that CDS portions of GFF file have start
* codons where they are supposed to. */
{
struct lineFile *lf = lineFileOpen(gff, TRUE);
char *row[10];
int cdsCount = 0, goodCount = 0, badCount = 0;
verbose(2,"# scanning %d fields of gff file:\n#\t'%s'\n", gffRowCount, gff);
while (lineFileNextRowTab(lf, row, gffRowCount))
{
if (startsWith("CDS", row[2]))
{
int start = lineFileNeedNum(lf, row, 3) - 1;
int end = lineFileNeedNum(lf, row, 4);
int size = end-start;
char strand = row[6][0];
char chrom[64];
struct dnaSeq *seq;
char *startCodon;
if (size < 1)
{
errAbort("start not before end line %d of %s",
lf->lineIx, lf->fileName);
}
if (strand != '+' && strand != '-')
{
errAbort("Expecting strand got %s line %d of %s",
row[6], lf->lineIx, lf->fileName);
}
if (startsWith("2-micron", row[0])) // need to stop processing here
break;
if (!startsWith("chr", row[0]))
continue;
if (startsWith("chrMito", row[0])) // change name to UCSC chrM
safef(chrom, sizeof(chrom), "%s", "chrM");
else
safef(chrom, sizeof(chrom), "%s", row[0]);
if ((seq = hashFindVal(chromHash, chrom)) == NULL)
errAbort("Unknown chromosome %s line %d of %s",
row[0], lf->lineIx, lf->fileName);
if (end > seq->size)
{
printf("end (%d) greater than %s size (%d) line %d of %s",
end, chrom, seq->size, lf->lineIx, lf->fileName);
++badCount;
continue;
}
startCodon = seq->dna + start;
if (strand == '-')
reverseComplement(startCodon, size);
if (!startsWith("ATG", startCodon))
{
char *s = startCodon;
verbose(3,"# not ATG: %s:%d-%d\t%c%c%c\t%c\n",
chrom, start, end, s[0], s[1], s[2], strand);
++badCount;
}
else
++goodCount;
if (verboseLevel()>=4)
{
char *s = startCodon;
if (gffRowCount > 9)
printf("%s\t%d\t%c%c%c\t%c\t%s\n", chrom, start, s[0], s[1], s[2], strand, row[9]);
else
printf("%s\t%d\t%c%c%c\t%c\t%s\n", chrom, start, s[0], s[1], s[2], strand, row[8]);
}
if (strand == '-')
reverseComplement(startCodon, size);
++cdsCount;
}
}
lineFileClose(&lf);
printf("# good %d, bad %d, total %d\n", goodCount, badCount, cdsCount);
}
void initGapAid(char *gapFileName)
/* Initialize gap aid structure for faster gap
* computations. */
{
int i, tableSize, startLong = -1;
char *sizeDesc[2];
char *words[128];
if (gapFileName != NULL)
{
struct lineFile *lf = lineFileOpen(gapFileName, TRUE);
int count;
lineFileNextRowTab(lf, sizeDesc, 2);
tableSize = atoi(sizeDesc[1]);
AllocArray(gapInitPos,tableSize);
AllocArray(gapInitQGap,tableSize);
AllocArray(gapInitTGap,tableSize);
AllocArray(gapInitBothGap,tableSize);
while (count = lineFileChopNext(lf, words, tableSize+1))
{
if (sameString(words[0],"smallSize"))
{
aid.smallSize = atoi(words[1]);
}
if (sameString(words[0],"position"))
{
for (i=0 ; i<count-1 ; i++)
gapInitPos[i] = atoi(words[i+1]);
}
if (sameString(words[0],"qGap"))
{
for (i=0 ; i<count-1 ; i++)
gapInitQGap[i] = atoi(words[i+1]);
}
if (sameString(words[0],"tGap"))
{
for (i=0 ; i<count-1 ; i++)
gapInitTGap[i] = atoi(words[i+1]);
}
if (sameString(words[0],"bothGap"))
{
for (i=0 ; i<count-1 ; i++)
gapInitBothGap[i] = atoi(words[i+1]);
}
}
if (aid.smallSize == 0)
errAbort("missing smallSize parameter in %s\n",gapFileName);
lineFileClose(&lf);
}
else
{
/* if no gap file, then setup default values */
/* Set up to handle small values */
aid.smallSize = 111;
tableSize = 11;
AllocArray(gapInitPos,tableSize);
AllocArray(gapInitQGap,tableSize);
AllocArray(gapInitTGap,tableSize);
AllocArray(gapInitBothGap,tableSize);
for (i = 0 ; i < tableSize ; i++)
{
gapInitPos[i] = gapInitPosDefault[i];
gapInitTGap[i] = gapInitTGapDefault[i];
gapInitQGap[i] = gapInitQGapDefault[i];
gapInitBothGap[i] = gapInitBothGapDefault[i];
}
}
AllocArray(aid.qSmall, aid.smallSize);
AllocArray(aid.tSmall, aid.smallSize);
AllocArray(aid.bSmall, aid.smallSize);
for (i=1; i<aid.smallSize; ++i)
{
aid.qSmall[i] =
interpolate(i, gapInitPos, gapInitQGap, tableSize);
aid.tSmall[i] =
interpolate(i, gapInitPos, gapInitTGap, tableSize);
aid.bSmall[i] = interpolate(i, gapInitPos,
gapInitBothGap, tableSize);
}
/* Set up to handle intermediate values. */
for (i=0; i<tableSize; ++i)
{
if (aid.smallSize == gapInitPos[i])
{
startLong = i;
break;
}
}
if (startLong < 0)
errAbort("No position %d in initGapAid()\n", aid.smallSize);
aid.longCount = tableSize - startLong;
aid.qPosCount = tableSize - startLong;
aid.tPosCount = tableSize - startLong;
aid.bPosCount = tableSize - startLong;
aid.longPos = cloneMem(gapInitPos + startLong, aid.longCount * sizeof(int));
aid.qLong = cloneMem(gapInitQGap + startLong, aid.qPosCount * sizeof(double));
aid.tLong = cloneMem(gapInitTGap + startLong, aid.tPosCount * sizeof(double));
aid.bLong = cloneMem(gapInitBothGap + startLong, aid.bPosCount * sizeof(double));
/* Set up to handle huge values. */
aid.qLastPos = aid.longPos[aid.qPosCount-1];
aid.tLastPos = aid.longPos[aid.tPosCount-1];
aid.bLastPos = aid.longPos[aid.bPosCount-1];
aid.qLastPosVal = aid.qLong[aid.qPosCount-1];
aid.tLastPosVal = aid.tLong[aid.tPosCount-1];
aid.bLastPosVal = aid.bLong[aid.bPosCount-1];
aid.qLastSlope = calcSlope(aid.qLastPosVal, aid.qLong[aid.qPosCount-2],
aid.qLastPos, aid.longPos[aid.qPosCount-2]);
aid.tLastSlope = calcSlope(aid.tLastPosVal, aid.tLong[aid.tPosCount-2],
aid.tLastPos, aid.longPos[aid.tPosCount-2]);
aid.bLastSlope = calcSlope(aid.bLastPosVal, aid.bLong[aid.bPosCount-2],
aid.bLastPos, aid.longPos[aid.bPosCount-2]);
// uglyf("qLastPos %d, qlastPosVal %f, qLastSlope %f\n", aid.qLastPos, aid.qLastPosVal, aid.qLastSlope);
// uglyf("tLastPos %d, tlastPosVal %f, tLastSlope %f\n", aid.tLastPos, aid.tLastPosVal, aid.tLastSlope);
// uglyf("bLastPos %d, blastPosVal %f, bLastSlope %f\n", aid.bLastPos, aid.bLastPosVal, aid.bLastSlope);
}
void bioImageLoad(char *setRaFile, char *itemTabFile)
/* bioImageLoad - Load data into bioImage database. */
{
struct hash *raHash = raReadSingle(setRaFile);
struct hash *rowHash;
struct lineFile *lf = lineFileOpen(itemTabFile, TRUE);
char *line, *words[256];
struct sqlConnection *conn = sqlConnect(database);
int rowSize;
int submissionSetId;
struct hash *fullDirHash = newHash(0);
struct hash *screenDirHash = newHash(0);
struct hash *thumbDirHash = newHash(0);
struct hash *treatmentHash = newHash(0);
struct hash *bodyPartHash = newHash(0);
struct hash *sliceTypeHash = newHash(0);
struct hash *imageTypeHash = newHash(0);
struct hash *sectionSetHash = newHash(0);
struct dyString *dy = dyStringNew(0);
/* Read first line of tab file, and from it get all the field names. */
if (!lineFileNext(lf, &line, NULL))
errAbort("%s appears to be empty", lf->fileName);
if (line[0] != '#')
errAbort("First line of %s needs to start with #, and then contain field names",
lf->fileName);
rowHash = hashRowOffsets(line+1);
rowSize = rowHash->elCount;
if (rowSize >= ArraySize(words))
errAbort("Too many fields in %s", lf->fileName);
/* Check that have all required fields */
{
char *fieldName;
int i;
for (i=0; i<ArraySize(requiredSetFields); ++i)
{
fieldName = requiredSetFields[i];
if (!hashLookup(raHash, fieldName))
errAbort("Field %s is not in %s", fieldName, setRaFile);
}
for (i=0; i<ArraySize(requiredItemFields); ++i)
{
fieldName = requiredItemFields[i];
if (!hashLookup(rowHash, fieldName))
errAbort("Field %s is not in %s", fieldName, itemTabFile);
}
for (i=0; i<ArraySize(requiredFields); ++i)
{
fieldName = requiredFields[i];
if (!hashLookup(rowHash, fieldName) && !hashLookup(raHash, fieldName))
errAbort("Field %s is not in %s or %s", fieldName, setRaFile, itemTabFile);
}
}
/* Create/find submission record. */
submissionSetId = saveSubmissionSet(conn, raHash);
/* Process rest of tab file. */
while (lineFileNextRowTab(lf, words, rowSize))
{
int fullDir = cachedId(conn, "location", "name",
fullDirHash, "fullDir", raHash, rowHash, words);
int screenDir = cachedId(conn, "location", "name",
screenDirHash, "screenDir", raHash, rowHash, words);
int thumbDir = cachedId(conn, "location",
"name", thumbDirHash, "thumbDir", raHash, rowHash, words);
int bodyPart = cachedId(conn, "bodyPart",
"name", bodyPartHash, "bodyPart", raHash, rowHash, words);
int sliceType = cachedId(conn, "sliceType",
"name", sliceTypeHash, "sliceType", raHash, rowHash, words);
int imageType = cachedId(conn, "imageType",
"name", imageTypeHash, "imageType", raHash, rowHash, words);
int treatment = cachedId(conn, "treatment",
"conditions", treatmentHash, "treatment", raHash, rowHash, words);
char *fileName = getVal("fileName", raHash, rowHash, words, NULL);
char *submitId = getVal("submitId", raHash, rowHash, words, NULL);
char *taxon = getVal("taxon", raHash, rowHash, words, NULL);
char *isEmbryo = getVal("isEmbryo", raHash, rowHash, words, NULL);
char *age = getVal("age", raHash, rowHash, words, NULL);
char *sectionSet = getVal("sectionSet", raHash, rowHash, words, "");
char *sectionIx = getVal("sectionIx", raHash, rowHash, words, "0");
char *gene = getVal("gene", raHash, rowHash, words, "");
char *locusLink = getVal("locusLink", raHash, rowHash, words, "");
char *refSeq = getVal("refSeq", raHash, rowHash, words, "");
char *genbank = getVal("genbank", raHash, rowHash, words, "");
char *priority = getVal("priority", raHash, rowHash, words, "200");
int sectionId = 0;
int oldId;
// char *xzy = getVal("xzy", raHash, rowHash, words, xzy);
if (sectionSet[0] != 0 && !sameString(sectionSet, "0"))
{
struct hashEl *hel = hashLookup(sectionSetHash, sectionSet);
if (hel != NULL)
sectionId = ptToInt(hel->val);
else
{
sqlUpdate(conn, "insert into sectionSet values(default)");
sectionId = sqlLastAutoId(conn);
hashAdd(sectionSetHash, sectionSet, intToPt(sectionId));
}
}
dyStringClear(dy);
dyStringAppend(dy, "select id from image ");
dyStringPrintf(dy, "where fileName = '%s' ", fileName);
dyStringPrintf(dy, "and fullLocation = %d", fullDir);
oldId = sqlQuickNum(conn, dy->string);
if (oldId != 0)
{
if (replace)
{
dyStringClear(dy);
dyStringPrintf(dy, "delete from image where id = %d", oldId);
sqlUpdate(conn, dy->string);
}
else
errAbort("%s is already in database line %d of %s",
fileName, lf->lineIx, lf->fileName);
}
dyStringClear(dy);
dyStringAppend(dy, "insert into image set\n");
dyStringPrintf(dy, " id = default,\n");
dyStringPrintf(dy, " fileName = '%s',\n", fileName);
dyStringPrintf(dy, " fullLocation = %d,\n", fullDir);
dyStringPrintf(dy, " screenLocation = %d,\n", screenDir);
dyStringPrintf(dy, " thumbLocation = %d,\n", thumbDir);
dyStringPrintf(dy, " submissionSet = %d,\n", submissionSetId);
dyStringPrintf(dy, " sectionSet = %d,\n", sectionId);
dyStringPrintf(dy, " sectionIx = %s,\n", sectionIx);
dyStringPrintf(dy, " submitId = '%s',\n", submitId);
dyStringPrintf(dy, " gene = '%s',\n", gene);
dyStringPrintf(dy, " locusLink = '%s',\n", locusLink);
dyStringPrintf(dy, " refSeq = '%s',\n", refSeq);
dyStringPrintf(dy, " genbank = '%s',\n", genbank);
dyStringPrintf(dy, " priority = %s,\n", priority);
dyStringPrintf(dy, " taxon = %s,\n", taxon);
dyStringPrintf(dy, " isEmbryo = %s,\n", isEmbryo);
dyStringPrintf(dy, " age = %s,\n", age);
dyStringPrintf(dy, " bodyPart = %d,\n", bodyPart);
dyStringPrintf(dy, " sliceType = %d,\n", sliceType);
dyStringPrintf(dy, " imageType = %d,\n", imageType);
dyStringPrintf(dy, " treatment = %d\n", treatment);
sqlUpdate(conn, dy->string);
}
}
