void readStsInfo(struct lineFile *sif)
/* Read in current stsInfo file */
{
struct stsInfo2 *si;
struct sts *s;
struct primer *p;
struct gb *gb;
char name[16], *words[52];
int i;
stsHash = newHash(20);
dbStsIdHash = newHash(20);
primerHash = newHash(20);
nameHash = newHash(24);
gbAccHash = newHash(20);
ucscIdHash = newHash(20);
/* Read in all rows */
while (lineFileChopTab(sif, words))
{
si = stsInfo2Load(words);
/* Determine next ucsc id to be used */
if (si->identNo >= nextUcscId)
nextUcscId = si->identNo + 1;
/* Create sts struct */
if (sameString(si->organism, "H**o sapiens\0"))
{
AllocVar(s);
s->next = NULL;
s->si = si;
s->fa = NULL;
s->mapped = isMapped(si);
s->dbstsIdExists = FALSE;
slAddHead(&sList, s);
safef(name, ArraySize(name), "%d", si->identNo);
hashAdd(stsHash, name, s);
/* Add ids to dbStsIdHash */
if (si->dbSTSid)
hashAddInt(dbStsIdHash, name, si->dbSTSid);
/* Add sts records to ucscId hash */
if (si->dbSTSid)
{
safef(name, ArraySize(name), "%d", si->dbSTSid);
hashAdd(ucscIdHash, name, s);
}
for (i = 0; i < si->otherDbstsCount; i++)
{
safef(name, ArraySize(name), "%d", si->otherDbSTS[i]);
if (!hashLookup(ucscIdHash, name))
hashAdd(ucscIdHash, name, s);
}
/* Add names to name hash and genbank hash */
hashAdd(nameHash, si->name, s);
for (i = 0; i < si->gbCount; i++)
{
hashAdd(nameHash, si->genbank[i], s);
AllocVar(gb);
gb->next = NULL;
gb->acc = cloneString(si->genbank[i]);
gb->s = s;
gb->gbSeq = FALSE;
hashAdd(gbAccHash, gb->acc, gb);
}
for (i = 0; i < si->gdbCount; i++)
hashAdd(nameHash, si->gdb[i], s);
for (i = 0; i < si->nameCount; i++)
hashAdd(nameHash, si->otherNames[i], s);
/* Create primer info if available and add to hash */
if (differentString(si->leftPrimer, "\0"))
{
AllocVar(p);
p->next = NULL;
p->dbStsId = si->dbSTSid;
p->left = cloneString(si->leftPrimer);
p->right = cloneString(si->rightPrimer);
p->dist = cloneString(si->distance);
p->ucscId = si->identNo;
safef(name, ArraySize(name), "%d", p->dbStsId);
hashAdd(primerHash, name, p);
}
}
else
{
stsInfo2Free(&si);
}
}
}
void loadGeneToMotif(struct sqlConnection *conn, char *fileName, char *table,
struct hash *geneToModuleHash, struct hash *moduleAndMotifHash,
struct hash *motifHash, struct hash *positionsHash,
char *regionTable)
/* Load file which is a big matrix with genes for rows and motifs for
* columns. There is a semicolon-separated list of numbers in the matrix
* where a gene has the motif, and an empty (tab separated) field
* where there is no motif. The numbers are relative to the
* region associated with the gene in the positionsHash.
* Only load bits of this where motif actually occurs in module associated
* with gene. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
FILE *f = hgCreateTabFile(tmpDir, table);
char *motifNames[32*1024], *row[32*1024];
int motifCount, rowSize, i;
char *gene, *module;
int geneCount = 0, total = 0;
struct dyString *dy = dyStringNew(512);
struct genomePos *motifPosList = NULL, *motifPosForGene;
struct genomePos *regionPosList = NULL, *regionPos;
/* Read first line, which is labels. */
if (!lineFileNextReal(lf, &line))
errAbort("Empty file %s", fileName);
subChar(line, ' ', '_');
motifCount = chopLine(line, motifNames);
if (motifCount >= ArraySize(motifNames))
errAbort("Too many motifs line 1 of %s", fileName);
lineFileExpectAtLeast(lf, 2, motifCount);
motifNames[0] = NULL;
for (i=1; i<motifCount; ++i)
{
char name[64];
motifNames[i] = cloneString(fixMotifName(motifNames[i],name,sizeof(name)));
if (!hashLookup(motifHash, motifNames[i]))
errAbort("Motif %s is in %s but not modules_motifs.gxm",
motifNames[i], fileName);
}
/* Read subsequent lines. */
while ((rowSize = lineFileChopTab(lf, row)) != 0)
{
lineFileExpectWords(lf, motifCount, rowSize);
gene = row[0];
module = hashFindVal(geneToModuleHash, gene);
if (module == NULL)
{
warn("WARNING: Gene %s in line %d of %s but not module_assignments.tab",
gene, lf->lineIx, lf->fileName);
continue;
}
regionPos = NULL;
for (i=1; i<rowSize; ++i)
{
if (row[i][0] != 0)
{
if (hashLookup2(moduleAndMotifHash, module, motifNames[i]))
{
regionPos = hashFindVal(positionsHash, gene);
if (regionPos == NULL)
{
warn("WARNING: %s in %s but not gene_positions.tab",
gene, fileName);
i = rowSize; continue;
}
motifPosForGene = convertMotifPos(row[i], regionPos,
hashMustFindVal(motifHash, motifNames[i]), lf);
motifPosList = slCat(motifPosForGene, motifPosList);
++total;
}
}
}
if (regionPos != NULL)
{
slAddHead(®ionPosList, regionPos);
}
++geneCount;
}
lineFileClose(&lf);
/* Output sorted table of all motif hits. */
{
struct genomePos *pos;
slSort(&motifPosList, genomePosCmp);
for (pos = motifPosList; pos != NULL; pos = pos->next)
{
int start = pos->start;
int end = pos->end;
if (start < 0) start = 0;
fprintf(f, "%d\t", binFromRange(start, end));
fprintf(f, "%s\t", pos->chrom);
fprintf(f, "%d\t%d\t", start, end);
fprintf(f, "%s\t", pos->motif);
fprintf(f, "%d\t", pos->score);
fprintf(f, "%c\t", pos->strand);
fprintf(f, "%s\n", pos->name);
}
sqlDyStringPrintf(dy,
"CREATE TABLE %s (\n"
" bin smallInt unsigned not null,\n"
" chrom varChar(255) not null,\n"
" chromStart int not null,\n"
" chromEnd int not null,\n"
" name varchar(255) not null,\n"
" score int not null,\n"
" strand char(1) not null,\n"
" gene varchar(255) not null,\n"
" #Indices\n"
" INDEX(gene(12)),\n"
" INDEX(name(16)),\n"
" INDEX(chrom(8),bin)\n"
")\n", table);
sqlRemakeTable(conn, table, dy->string);
verbose(1, "%d genes, %d motifs, %d motifs in genes\n",
geneCount, motifCount-1, total);
hgLoadTabFile(conn, tmpDir, table, &f);
// hgRemoveTabFile(tmpDir, table);
verbose(1, "Loaded %s table\n", table);
slFreeList(&motifPosList);
}
/* Now output sorted table of upstream regions. */
{
FILE *f = hgCreateTabFile(tmpDir, regionTable);
struct genomePos *pos;
dyStringClear(dy);
sqlDyStringPrintf(dy,
"CREATE TABLE %s (\n"
" bin smallInt unsigned not null,\n"
" chrom varChar(255) not null,\n"
" chromStart int not null,\n"
" chromEnd int not null,\n"
" name varchar(255) not null,\n"
" score int not null,\n"
" strand char(1) not null,\n"
" #Indices\n"
" INDEX(name(16)),\n"
" INDEX(chrom(8),bin)\n"
")\n", regionTable);
sqlRemakeTable(conn, regionTable, dy->string);
slSort(®ionPosList, genomePosCmp);
for (pos = regionPosList; pos != NULL; pos = pos->next)
{
int start = pos->start;
int end = pos->end;
if (start < 0) start = 0;
fprintf(f, "%d\t", binFromRange(start, end));
fprintf(f, "%s\t", pos->chrom);
fprintf(f, "%d\t%d\t", start, end);
fprintf(f, "%s\t", pos->name);
fprintf(f, "%d\t", pos->score);
fprintf(f, "%c\n", pos->strand);
}
hgLoadTabFile(conn, tmpDir, regionTable, &f);
// hgRemoveTabFile(tmpDir, regionTable);
}
}
void readZfinMapping(struct lineFile *zmf)
/* Read in ZFIN IDs and mapping panel data */
{
char *words[6], *name = NULL, *nameLower = NULL, *id = NULL, *panel = NULL;
char *chrom = NULL, *units = NULL;
double pos;
int i = 0, j, index = -1, k;
struct zfin *zf = NULL;
struct panel *p = NULL;
boolean foundPos = FALSE;
zfinMarkerHash = newHash(16);
zfinIdHash = newHash(16);
while (lineFileChopTab(zmf, words) )
{
/* get ZFIN Id, name and panel */
id = cloneString(words[0]);
name = cloneString(words[1]);
nameLower = cloneString(words[1]);
panel = cloneString(words[2]);
chrom = cloneString(words[3]);
pos = sqlDouble(words[4]);
units = cloneString(words[5]);
/* check if this name exists already in hash */
touppers(name);
zf = hashFindVal(zfinMarkerHash, name);
if (zf == NULL)
{
/* allocate memory for zfin struct if not in hash */
AllocVar(zf);
/* find panel and add marker information */
/* first initialize */
zf->panelArray = needMem(sizeof(struct panel*) * NUMPANELS);
for (i = 0; i < NUMPANELS; i++)
{
zf->panelArray[i] = NULL;
}
zf->zfinId = cloneString(id);
zf->name = cloneString(nameLower);
zf->acc = NULL;
zf->zfAlias = NULL;
}
/* find index number for this panel */
for (j = 0; j < NUMPANELS; j++)
{
if (sameString(panel, markerPanels[j]))
index = j;
}
if (zf->panelArray[index] == NULL)
{
/* allocate memory for panel struct for panel data */
AllocVar(p);
/* initialize chrom and pos arrays */
for (k = 0; k < NUMPOS; k++)
{
p->chrom[k] = NULL;
p->pos[k] = -1;
}
p->name = cloneString(nameLower);
p->panel = cloneString(panel);
p->units = cloneString(units);
}
else
p = zf->panelArray[index];
foundPos = FALSE;
for (k = 0; k < NUMPOS && (!foundPos); k++)
{
if (p->chrom[k] == NULL)
{
if (!sameString(p->name, nameLower))
fprintf(stderr, "The entry in position %d does not match %s\n", index, nameLower);
else
{
p->chrom[k] = cloneString(chrom);
p->pos[k] = pos;
foundPos = TRUE;
}
}
}
zf->panelArray[index] = p;
/* name is already in upper case, add zfin to zfinMarkerHash */
addHashElUnique(zfinMarkerHash, name, zf);
/* if new ZFIN struct add the name to the zfinIdHash keyed by ZFIN ID */
if (hashFindVal(zfinIdHash, id) == NULL)
addHashElUnique(zfinIdHash, id, nameLower);
}
}
