struct slName *subtractFiles(struct slName *fileList)
/* Subtract two files using subtractLists */
{
struct slName *initialList = slNameLoadReal(fileList->name);
struct slName *subtractMe = slNameLoadReal(fileList->next->name);
struct slName *diffList = subtractLists(initialList, subtractMe);
slNameFreeList(&initialList);
slNameFreeList(&subtractMe);
return diffList;
}
static void showTableFieldsCt(char *db, char *table, boolean withGetButton)
/* Put up html table with a check box for each field of custom
* track. */
{
struct customTrack *ct = ctLookupName(table);
char *type = ct->dbTrackType;
if (type == NULL)
type = ct->tdb->type;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct asObject *asObj = asForTdb(conn, ct->tdb);
if (asObj)
{
struct slName *fieldList = NULL;
if (ct->dbTableName != NULL)
{
if (isVcfTable(table, NULL))
fieldList = vcfGetFields();
else
fieldList = sqlListFields(conn, ct->dbTableName);
}
if (fieldList == NULL)
fieldList = asColNames(asObj);
showTableFieldsOnList(db, table, asObj, fieldList, FALSE, withGetButton);
asObjectFree(&asObj);
slNameFreeList(&fieldList);
}
else
showBedTableFields(db, table, ct->fieldCount, withGetButton);
hFreeConn(&conn);
}
static struct slName *setup_labels(char *long_form, struct slName *bw_list, struct slName **labels_from_bw_list)
{
struct slName *lf_labels = NULL;
if (long_form && !sameString(long_form, "on"))
/* first check labels from CL */
{
lf_labels = slNameListFromComma(long_form);
int num_labels = slCount(lf_labels);
if (num_labels != slCount(bw_list))
errAbort("number of labels provided should equal the number of bigWigs given");
}
/* from file */
else
{
if (*labels_from_bw_list)
{
if (slCount(*labels_from_bw_list) == slCount(bw_list))
lf_labels = *labels_from_bw_list;
else
slNameFreeList(labels_from_bw_list);
}
if (!lf_labels)
lf_labels = slNameCloneList(bw_list);
}
return lf_labels;
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *database = cgiOptionalString("db");
char *rtdbServer = cfgOption("rtdb.server");
char *rtdbPort = cfgOption("rtdb.port");
char *rtdbChoices = cfgOption("rtdb.databases");
struct slName *dbs = slNameListFromComma(rtdbChoices);
cart = theCart;
cartWebStart(cart, database, "MGC RTDB Update");
if (!rtdbServer)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
if (!rtdbPort)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
/* create HMTL form if button wasn't pressed. Otherwise, run the update */
if (!cgiVarExists("RTDBSubmit"))
makeForm(dbs);
else if ((database == NULL) || (!slNameInList(dbs, database)))
{
makeForm(dbs);
printf("<br>Error: Select one of databases listed.");
}
else
updateServer(rtdbServer, rtdbPort, database);
cartWebEnd();
slNameFreeList(&dbs);
}
void testDb(struct htmlPage *orgPage, char *org, char *db)
/* Test on one database. */
{
struct hash *genomeRa = hgReadRa(org, db, dataDir, "genome.ra", NULL);
char *canonicalTable = hashMustFindVal(genomeRa, "canonicalTable");
char *accColumn = hashMustFindVal(genomeRa, "idColumn");
struct slName *geneList = sqlRandomSampleWithSeed(db, canonicalTable, "transcript", clRepeat, seed);
struct htmlPage *dbPage;
struct slName *ptr;
verbose(1, "genelist:\n");
for (ptr = geneList; ptr != NULL; ptr = ptr->next)
verbose(1, "%s\n", ptr->name);
htmlPageSetVar(orgPage, NULL, "db", db);
htmlPageSetVar(orgPage, NULL, searchVarName, "");
dbPage = quickSubmit(orgPage, NULL, org, db, NULL, NULL, "dbEmptyPage", "submit", "go");
quickErrReport();
if (dbPage != NULL)
{
testDbColumns(dbPage, org, db, geneList);
testDbSorts(dbPage, org, db, accColumn, geneList);
testDbFilters(dbPage, org, db, accColumn, geneList);
}
htmlPageFree(&dbPage);
hashFree(&genomeRa);
slNameFreeList(&geneList);
}
static void returnPreview(struct customPp *cpp, struct slName **pList)
/* Return list of lines back to cpp for reuse. */
{
struct slName *el;
slReverse(pList);
for (el = *pList; el != NULL; el = el->next)
customPpReuse(cpp, el->name);
slNameFreeList(pList);
}
struct slName *intersectFiles(struct slName *fileList)
/* Successively intersect files. */
{
struct slName *isectList = slNameLoadReal(fileList->name);
struct slName *curFile = fileList->next;
struct slName *cur;
while (curFile != NULL)
{
struct hash *isectHash = hashList(isectList);
struct slName *someWords = slNameLoadReal(curFile->name);
struct slName *bothWords = thoseInHash(isectHash, someWords, FALSE);
slNameFreeList(&someWords);
slNameFreeList(&isectList);
isectList = bothWords;
freeHashAndVals(&isectHash);
curFile = curFile->next;
}
return isectList;
}
void cgapSageUi(struct trackDb *tdb)
/* CGAP SAGE UI options. Highlight certain libs/tissues and filter by score. */
{
struct sqlConnection *conn = hAllocConn(database);
struct slName *tissueList = getListFromCgapSageLibs(conn, "tissue", FALSE, TRUE);
char *tissueHl = cartUsualString(cart, "cgapSage.tissueHl", "All");
puts("<BR><B>Tissue:</B>");
cgapSageDropList(tissueList, NULL, "cgapSage.tissueHl", tissueHl);
hFreeConn(&conn);
slNameFreeList(&tissueList);
}
struct slName *unionFiles(struct slName *fileList)
/* Successively union files. */
{
struct slName *initialList = slNameLoadReal(fileList->name);
struct hash *theHash = hashList(initialList);
struct slName *nextFile = fileList->next;
struct slName *unionList = NULL;
struct slName *cur;
while (nextFile != NULL)
{
struct slName *someWords = slNameLoadReal(nextFile->name);
addMoreToHash(theHash, someWords);
slNameFreeList(&someWords);
nextFile = nextFile->next;
}
unionList = hashToList(theHash);
hashFree(&theHash);
slNameFreeList(&initialList);
return unionList;
}
void parseAli(char *orderFileName, char *fastaFile,
alignFunc afunc, columnFunc cfunc, void *closure)
/* Parse a file of alignments. */
{
struct hash *seqHash = newHash(5);
struct slName *list = getOrderList(orderFileName);
int numSpecies = fillSeqHash(list, seqHash);
struct lineFile *lf = lineFileOpen(fastaFile, TRUE);
parseFasta(lf, numSpecies, list, seqHash, afunc, cfunc, closure);
slNameFreeList(&list);
}
void metaBigSetRgList(struct metaBig* mb, char* commaSep, boolean isBlackList)
/* sets the whitelist (or blacklist) */
{
struct slName* commas = slNameListFromComma(commaSep);
struct slName* rgName;
struct hash* rgHash = newHash(10);
for (rgName = commas; rgName != NULL; rgName = rgName->next)
hashAdd(rgHash, rgName->name, rgName->name);
slNameFreeList(&commas);
mb->rgList = rgHash;
mb->rgListIsBlack = isBlackList;
}
void submitToDir(struct sqlConnection *conn, struct sqlConnection *conn2, struct sqlConnection *connSp,
char *outDir, char *inJax)
/* Create directory full of visiGeneLoad .ra/.tab files from
* jackson database connection. Creates a pair of files for
* each submission set. Returns outDir. */
{
struct dyString *query = dyStringNew(0);
struct slName *ref, *refList = sqlQuickList(conn, NOSQLINJ "select distinct(_Refs_key) from GXD_Assay");
int refCount = 0;
makeDir(outDir);
for (ref = refList; ref != NULL; ref = ref->next)
{
char path[PATH_LEN];
char *pub=NULL;
boolean skip;
/* Check that it isn't on our skip list - one that we
* have already in the database from a higher resolution
* source. */
dyStringClear(query);
sqlDyStringPrintf(query, "select title from BIB_Refs where _Refs_key = %s",
ref->name);
pub = sqlQuickString(conn, query->string);
if (!pub)
{
verbose(1,"ref %s: missing title from BIB_Refs, ref skipped\n",ref->name);
continue;
}
skip = oneSubmissionSet ? oneSubmissionSet != sqlSigned(ref->name) : FALSE;
if (!skip)
{
safef(path, sizeof(path), "%s/%s", outDir, ref->name);
submitRefToFiles(conn, conn2, connSp, ref->name, path, inJax);
refCount += 1;
if (testMax != 0 && refCount >= testMax)
errAbort("Reached testMax %d output dirs [%s]\n", testMax, path);
}
freeMem(pub);
}
verbose(1,"refCount=%d\n",refCount);
slNameFreeList(&refList);
dyStringFree(&query);
}
/* free species info list */
void freeSpeciesInfo(struct speciesInfo *list)
{
struct speciesInfo *siNext;
for(; list ; list = siNext)
{
siNext = list->next;
freez(&list->nucSequence);
freez(&list->aaSequence);
slNameFreeList(&list->posStrings);
}
}
void sets(char *operation, struct slName *fileList)
/* sets - Do set operations on one-word-per-line files.. */
{
struct slName *finalList = NULL, *cur;
if (sameWord(operation, "intersect"))
finalList = intersectFiles(fileList);
else if (sameWord(operation, "union"))
finalList = unionFiles(fileList);
else if (sameWord(operation, "subtract") && (slCount(fileList) == 2))
finalList = subtractFiles(fileList);
else if (sameWord(operation, "symetricDiff"))
{
struct slName *theUnion = unionFiles(fileList);
struct slName *theIntersect = intersectFiles(fileList);
finalList = subtractLists(theUnion, theIntersect);
slNameFreeList(&theUnion);
slNameFreeList(&theIntersect);
}
else
usage();
/* Output here */
for (cur = finalList; cur != NULL; cur = cur->next)
printf("%s\n", cur->name);
}
void checkTableForFields(struct sqlConnection *conn, char *tableName)
/* Do basic checks on the table to make sure it's kosher. i.e. */
/* chrom, chromStart, name all exist along with the table itself. */
{
struct slName *fieldList;
if (!sqlTableExists(conn, tableName))
errAbort("table %s not found.", tableName);
fieldList = sqlListFields(conn, tableName);
if (!slNameInList(fieldList, "chrom"))
errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName);
if (!slNameInList(fieldList, "chromStart"))
errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName);
if (!slNameInList(fieldList, "name"))
errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName);
slNameFreeList(&fieldList);
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct slName *fileList = NULL;
int i;
optionInit(&argc, argv, options);
if (argc < 4)
usage();
/* make a list out of the filenames. */
for (i = 2; i < argc; i++)
slNameAddHead(&fileList, argv[i]);
slReverse(&fileList);
sets(argv[1], fileList);
slNameFreeList(&fileList);
return 0;
}
void annoOptionFreeList(struct annoOption **pList)
/* Free the same things that we clone above. */
{
if (pList == NULL)
return;
struct annoOption *afo, *nextAfo;
for (afo = *pList; afo != NULL; afo = nextAfo)
{
nextAfo = afo->next;
freeMem(afo->spec.name);
unsigned opFlags = opFlags;
if (opFlags & OPTION_MULTI)
{
switch (opFlags & OPTION_TYPE_MASK)
{
case OPTION_STRING:
slNameFreeList(&(afo->value));
break;
default:
errAbort("annoOptionFreeList: OPTION_MULTI implemented only for "
"OPTION_STRING (not 0x%x)", opFlags);
}
}
else
{
switch (opFlags & OPTION_TYPE_MASK)
{
// No need to free overloaded numeric values
case OPTION_DOUBLE:
case OPTION_FLOAT:
case OPTION_LONG_LONG:
case OPTION_INT:
case OPTION_BOOLEAN:
break;
case OPTION_STRING:
freeMem(afo->value);
break;
default:
errAbort("annoOptionFreeList: unrecognized op type 0x%x", opFlags);
}
}
freeMem(afo);
}
*pList = NULL;
}
struct grp *groupsFilterForTdbList(struct grp **grps,struct trackDb *tdbList)
{
struct grp *grpList = *grps;
*grps = NULL;
struct slName *tdbGroups = tdbListGetGroups(tdbList);
if (tdbList == NULL)
return *grps;
while (grpList != NULL)
{
struct grp *grp = slPopHead(&grpList);
if (slNameInList(tdbGroups,grp->name))
slAddHead(grps,grp);
}
slNameFreeList(&tdbGroups);
slReverse(grps);
return *grps;
}
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);
}
struct slName *randomVcfIds(char *table, struct sqlConnection *conn, int count, boolean isTabix)
/* Return some semi-random IDs from a VCF file. */
{
/* Read 10000 items from vcf file, or if they ask for a big list, then 4x what they ask for. */
struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
char *fileName = vcfFileName(tdb, conn, table, hDefaultChrom(database));
struct lineFile *lf = isTabix ? lineFileTabixMayOpen(fileName, TRUE) :
lineFileMayOpen(fileName, TRUE);
if (lf == NULL)
noWarnAbort();
int orderedCount = count * 4;
if (orderedCount < 100)
orderedCount = 100;
struct slName *idList = NULL;
char *words[4];
int i;
for (i = 0; i < orderedCount && lineFileChop(lf, words); i++)
{
// compress runs of identical ID, in case most are placeholder
if (i == 0 || !sameString(words[2], idList->name))
slAddHead(&idList, slNameNew(words[2]));
}
lineFileClose(&lf);
/* Shuffle list and trim it to count if necessary. */
shuffleList(&idList);
struct slName *sl;
for (sl = idList, i = 0; sl != NULL; sl = sl->next, i++)
{
if (i+1 >= count)
{
slNameFreeList(&(sl->next));
break;
}
}
freez(&fileName);
return idList;
}
struct slPair *mdbSelectPairs(struct cart *cart, struct slPair *mdbVars)
// Returns the current mdb vars and vals in the table of drop down selects
{
// figure out how many metadata selects are visible.
int numMetadataSelects = 0;
struct slPair *mdbSelectPairs = NULL;
if (mdbVars == NULL)
return 0;
// Get the current number of rows in the table of mdb selects
for (;;)
{
char buf[256];
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
char *str = cartOptionalString(cart, buf);
if (isEmpty(str))
break;
else
numMetadataSelects++;
}
// Requesting to add or delete any?
int delSearchSelect = cartUsualInt(cart, TRACK_SEARCH_DEL_ROW, 0); // 1-based row to delete
int addSearchSelect = cartUsualInt(cart, TRACK_SEARCH_ADD_ROW, 0); // 1-based row to insert after
if (delSearchSelect)
numMetadataSelects--;
if (addSearchSelect)
numMetadataSelects++;
if (numMetadataSelects)
{
int ix;
char buf[256];
for (ix = 0; ix < numMetadataSelects; ix++)
{
int offset; // used to handle additions/deletions
if (addSearchSelect > 0 && ix >= addSearchSelect)
offset = 0; // do nothing to offset (i.e. copy data from previous row)
else if (delSearchSelect > 0 && ix + 1 >= delSearchSelect)
offset = 2;
else
offset = 1;
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, ix + offset);
char *var = cartOptionalString(cart, buf);
char *val = NULL;
// We need to make sure var is valid in this assembly; if it isn't, reset it to "cell".
if (slPairFindVal(mdbVars,var) == NULL)
var = "cell";
else
{
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, ix + offset);
enum cvSearchable searchBy = cvSearchMethod(var);
if (searchBy == cvSearchByMultiSelect)
{
// Multi-selects as comma delimited list of values
struct slName *vals = cartOptionalSlNameList(cart,buf);
if (vals)
{
val = slNameListToString(vals,','); // A comma delimited list of values
slNameFreeList(&vals);
}
}
else if (searchBy == cvSearchBySingleSelect
|| searchBy == cvSearchByFreeText
|| searchBy == cvSearchByWildList)
val = cloneString(cartUsualString(cart, buf,ANYLABEL));
//else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
// {
// // TO BE IMPLEMENTED
// }
if (val != NULL && sameString(val, ANYLABEL))
val = NULL;
}
slPairAdd(&mdbSelectPairs,var,val); // val already cloned
}
if (delSearchSelect > 0)
{
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
}
}
else
{
// create defaults
slPairAdd(&mdbSelectPairs,"cell", NULL);
slPairAdd(&mdbSelectPairs,"antibody",NULL);
}
slReverse(&mdbSelectPairs);
return mdbSelectPairs;
}
void verifyGreatAssemblies()
{
// First read in the assembly name and description information into name lists
struct slName* supportedAssemblies = NULL;
struct lineFile *lf = lineFileOpen(greatData, TRUE);
int fieldCount = 1;
char* row[fieldCount];
int wordCount;
while ((wordCount = lineFileChopTab(lf, row)) != 0)
{
if (wordCount != fieldCount)
errAbort("The %s file is not properly formatted.\n", greatData);
slNameAddHead(&supportedAssemblies, row[0]);
}
lineFileClose(&lf);
boolean invalidAssembly = TRUE;
struct slName* currAssembly;
for (currAssembly = supportedAssemblies; currAssembly != NULL; currAssembly = currAssembly->next)
{
if (!hDbIsActive(currAssembly->name))
{
errAbort("Assembly %s in supported assembly file is not an active assembly.\n", currAssembly->name);
}
if (sameOk(database, currAssembly->name))
{
invalidAssembly = FALSE;
break;
}
}
if (invalidAssembly)
{
slReverse(&supportedAssemblies);
currAssembly = supportedAssemblies;
struct dyString* dy = dyStringNew(0);
addAssemblyToSupportedList(dy, currAssembly->name);
currAssembly = currAssembly->next;
while (currAssembly != NULL)
{
dyStringAppend(dy, ", ");
if (currAssembly->next == NULL)
dyStringAppend(dy, "and ");
addAssemblyToSupportedList(dy, currAssembly->name);
currAssembly = currAssembly->next;
}
hPrintf("<script type='text/javascript'>\n");
hPrintf("function logSpecies() {\n");
hPrintf("try {\n");
hPrintf("var r = new XMLHttpRequest();\n");
hPrintf("r.open('GET', 'http://great.stanford.edu/public/cgi-bin/logSpecies.php?species=%s');\n", database);
hPrintf("r.send(null);\n");
hPrintf("} catch (err) { }\n");
hPrintf("}\n");
hPrintf("window.onload = logSpecies;\n");
hPrintf("</script>\n");
errAbort("GREAT only supports the %s assemblies."
"\nPlease go back and ensure that one of those assemblies is chosen.",
dyStringContents(dy));
htmlClose();
dyStringFree(&dy);
}
slNameFreeList(&supportedAssemblies);
}
void submitRefToFiles(struct sqlConnection *conn, struct sqlConnection *conn2, struct sqlConnection *connSp,
char *ref, char *fileRoot, char *inJax)
/* Create a .ra and a .tab file for given reference. */
{
/* Initially the tab file will have some duplicate lines, so
* write to temp file, and then filter. */
char raName[PATH_LEN], tabName[PATH_LEN], capName[PATH_LEN];
FILE *ra = NULL, *tab = NULL, *cap = NULL;
struct dyString *query = dyStringNew(0);
struct sqlResult *sr;
char **row;
char *pubMed;
struct slName *list, *el;
boolean gotAny = FALSE;
struct hash *uniqImageHash = newHash(0);
struct hash *captionHash = newHash(0);
int imageWidth = 0, imageHeight = 0;
char path[PATH_LEN];
struct dyString *caption = dyStringNew(0);
struct dyString *copyright = dyStringNew(0);
struct dyString *probeNotes = dyStringNew(0);
boolean lookedForCopyright = FALSE;
safef(raName, sizeof(raName), "%s.ra", fileRoot);
safef(tabName, sizeof(tabName), "%s.tab", fileRoot);
safef(capName, sizeof(capName), "%s.txt", fileRoot);
tab = mustOpen(tabName, "w");
cap = mustOpen(capName, "w");
sqlDyStringPrintf(query, "select authors,journal,title,year from BIB_Refs where ");
sqlDyStringPrintf(query, "_Refs_key = '%s'", ref);
sr = sqlGetResultVerbose(conn, query->string);
row = sqlNextRow(sr);
if (row == NULL)
errAbort("Can't find _Refs_key %s in BIB_Refs", ref);
/* Make ra file with stuff common to whole submission set. */
ra = mustOpen(raName, "w");
fprintf(ra, "submissionSource MGI\n");
fprintf(ra, "acknowledgement Thanks to the Gene Expression Database group at "
"Mouse Genome Informatics (MGI) for collecting, annotating and sharing "
"this image. The MGI images were last updated in VisiGene on March 28, 2006. "
"Additional and more up to date annotations and images may be available "
"directly at <A HREF='http://www.informatics.jax.org' target='_blank'>MGI.</A>\n");
fprintf(ra, "submitSet jax%s\n", ref);
fprintf(ra, "taxon 10090\n"); /* Mus musculus taxon */
fprintf(ra, "fullDir http://hgwdev.gi.ucsc.edu/visiGene/full/inSitu/Mouse/jax\n");
fprintf(ra, "thumbDir http://hgwdev.gi.ucsc.edu/visiGene/200/inSitu/Mouse/jax\n");
fprintf(ra, "setUrl http://www.informatics.jax.org/\n");
fprintf(ra, "itemUrl http://www.informatics.jax.org/searches/image.cgi?%%s\n");
fprintf(ra, "abUrl http://www.informatics.jax.org/searches/antibody.cgi?%%s\n");
fprintf(ra, "journal %s\n", row[1]);
fprintf(ra, "publication %s\n", row[2]);
fprintf(ra, "year %s\n", row[3]);
/* The contributor (author) list is in format Kent WJ; Haussler DH; format in
* Jackson. We convert it to Kent W.J.,Haussler D.H., format for visiGene. */
fprintf(ra, "contributor ");
list = charSepToSlNames(row[0], ';');
for (el = list; el != NULL; el = el->next)
{
char *lastName = skipLeadingSpaces(el->name);
char *initials = strrchr(lastName, ' ');
if (initials == NULL)
initials = "";
else
*initials++ = 0;
fprintf(ra, "%s", lastName);
if (initials[0] != 0)
{
char c;
fprintf(ra, " ");
while ((c = *initials++) != 0)
fprintf(ra, "%c.", c);
}
fprintf(ra, ",");
}
fprintf(ra, "\n");
slNameFreeList(&list);
sqlFreeResult(&sr);
/* Add in link to PubMed record on publication. */
dyStringClear(query);
sqlDyStringPrintf(query,
"select ACC_Accession.accID from ACC_Accession,ACC_LogicalDB "
"where ACC_Accession._Object_key = %s "
"and ACC_Accession._LogicalDB_key = ACC_LogicalDB._LogicalDB_key "
"and ACC_LogicalDB.name = 'PubMed'", ref);
pubMed = sqlQuickStringVerbose(conn, query->string);
if (pubMed != NULL)
fprintf(ra, "pubUrl https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=%s\n", pubMed);
freez(&pubMed);
dyStringClear(query);
sqlDyStringPrintf(query,
"select distinct MRK_Marker.symbol as gene,"
"GXD_Specimen.sex as sex,"
"GXD_Specimen.age as age,"
"GXD_Specimen.ageMin as ageMin,"
"GXD_Specimen.ageMax as ageMax,"
"IMG_ImagePane.paneLabel as paneLabel,"
"ACC_Accession.numericPart as fileKey,"
"IMG_Image._Image_key as imageKey,"
"GXD_Assay._ProbePrep_key as probePrepKey,"
"GXD_Assay._AntibodyPrep_key as antibodyPrepKey,"
"GXD_Assay._ReporterGene_key as reporterGeneKey,"
"GXD_FixationMethod.fixation as fixation,"
"GXD_EmbeddingMethod.embeddingMethod as embedding,"
"GXD_Assay._Assay_key as assayKey,"
"GXD_Specimen.hybridization as sliceType,"
"GXD_Specimen._Genotype_key as genotypeKey,"
"IMG_ImagePane._ImagePane_key as imagePaneKey\n"
"from MRK_Marker,"
"GXD_Assay,"
"GXD_Specimen,"
"GXD_InSituResult,"
"GXD_InSituResultImage,"
"GXD_FixationMethod,"
"GXD_EmbeddingMethod,"
"IMG_ImagePane,"
"IMG_Image,"
"ACC_Accession\n"
"where MRK_Marker._Marker_key = GXD_Assay._Marker_key "
"and GXD_Assay._Assay_key = GXD_Specimen._Assay_key "
"and GXD_Specimen._Specimen_key = GXD_InSituResult._Specimen_key "
"and GXD_InSituResult._Result_key = GXD_InSituResultImage._Result_key "
"and GXD_InSituResultImage._ImagePane_key = IMG_ImagePane._ImagePane_key "
"and GXD_FixationMethod._Fixation_key = GXD_Specimen._Fixation_key "
"and GXD_EmbeddingMethod._Embedding_key = GXD_Specimen._Embedding_key "
"and IMG_ImagePane._Image_key = IMG_Image._Image_key "
"and IMG_Image._Image_key = ACC_Accession._Object_key "
"and ACC_Accession.prefixPart = 'PIX:' "
"and GXD_Assay._ImagePane_key is NULL "
);
sqlDyStringPrintf(query, "and GXD_Assay._Refs_key = '%s'", ref);
sr = sqlGetResultVerbose(conn, query->string);
fprintf(tab, "#");
fprintf(tab, "gene\t");
fprintf(tab, "probeColor\t");
fprintf(tab, "sex\t");
fprintf(tab, "age\t");
fprintf(tab, "ageMin\t");
fprintf(tab, "ageMax\t");
fprintf(tab, "paneLabel\t");
fprintf(tab, "fileName\t");
fprintf(tab, "submitId\t");
fprintf(tab, "fPrimer\t");
fprintf(tab, "rPrimer\t");
fprintf(tab, "abName\t");
fprintf(tab, "abTaxon\t");
fprintf(tab, "abSubmitId\t");
fprintf(tab, "fixation\t");
fprintf(tab, "embedding\t");
fprintf(tab, "bodyPart\t");
fprintf(tab, "sliceType\t");
fprintf(tab, "genotype\t");
fprintf(tab, "strain\t");
fprintf(tab, "priority\t");
fprintf(tab, "captionId\t");
fprintf(tab, "imageWidth\t");
fprintf(tab, "imageHeight\n");
while ((row = sqlNextRow(sr)) != NULL)
{
char *gene = row[0];
char *sex = row[1];
char *age = row[2];
char *ageMin = row[3];
char *ageMax = row[4];
char *paneLabel = row[5];
char *fileKey = row[6];
char *imageKey = row[7];
char *probePrepKey = row[8];
char *antibodyPrepKey = row[9];
char *reporterGeneKey = row[10];
char *fixation = row[11];
char *embedding = row[12];
char *assayKey = row[13];
char *sliceType = row[14];
char *genotypeKey = row[15];
char *imagePaneKey = row[16];
double calcAge = -1;
char *probeColor = "";
char *bodyPart = "";
char *abName = NULL;
char *rPrimer = NULL, *fPrimer = NULL;
char *genotype = NULL;
char *strain = NULL;
char *priority = NULL;
char abTaxon[32];
char *captionId = "";
char *abSubmitId = NULL;
verbose(3, " "); dumpRow(row, 16);
if (age == NULL)
continue;
if (!lookedForCopyright)
{
struct sqlResult *sr = NULL;
char **row;
lookedForCopyright = TRUE;
dyStringClear(query);
sqlDyStringPrintf(query,
"select note from MGI_NoteChunk,MGI_Note,MGI_NoteType,ACC_MGIType "
"where MGI_Note._Object_key = %s "
"and ACC_MGIType.name = 'Image' "
"and ACC_MGIType._MGIType_key = MGI_Note._MGIType_key "
"and MGI_NoteType.noteType='Copyright' "
"and MGI_Note._NoteType_key = MGI_NoteType._NoteType_key "
"and MGI_Note._Note_key = MGI_NoteChunk._Note_key "
"order by sequenceNum"
, imageKey);
sr = sqlGetResultVerbose(conn2, query->string);
while ((row = sqlNextRow(sr)) != NULL)
dyStringAppend(copyright, row[0]);
sqlFreeResult(&sr);
verbose(2,"imageKey=%s\n",imageKey);
if (copyright->stringSize != 0)
{
fprintf(ra, "copyright %s\n", copyright->string);
}
}
/* Massage sex */
{
if (sameString(sex, "Male"))
sex = "male";
else if (sameString(sex, "Female"))
sex = "female";
else
sex = "";
}
/* Massage age */
{
char *embryoPat = "embryonic day ";
char *newbornPat = "postnatal newborn";
char *dayPat = "postnatal day ";
char *weekPat = "postnatal week ";
char *adultPat = "postnatal adult";
double calcMinAge = atof(ageMin);
double calcMaxAge = atof(ageMax);
double mouseBirthAge = 21.0;
//double mouseAdultAge = 63.0; /* Relative to conception, not birth */
if (age[0] == 0)
{
warn("age null, ageMin %s, ageMax %s\n", ageMin, ageMax);
calcAge = (calcMinAge + calcMaxAge) * 0.5;
}
else if (startsWith(embryoPat, age))
calcAge = atof(age+strlen(embryoPat));
else if (sameString(newbornPat, age))
calcAge = mouseBirthAge;
else if (startsWith(dayPat, age))
calcAge = atof(age+strlen(dayPat)) + mouseBirthAge;
else if (startsWith(weekPat, age))
calcAge = 7.0 * atof(age+strlen(weekPat)) + mouseBirthAge;
else if (sameString(adultPat, age) && calcMaxAge - calcMinAge > 1000
&& calcMinAge < 365)
calcAge = 365; /* Most adult mice are relatively young */
else
{
warn("Calculating age from %s", age);
calcAge = (calcMinAge + calcMaxAge) * 0.5;
}
if (calcAge < calcMinAge)
calcAge = calcMinAge;
if (calcAge > calcMaxAge)
calcAge = calcMaxAge;
}
/* Massage probeColor */
{
if (!isStrNull(reporterGeneKey))
{
/* Fixme: make sure that reporterGene's end up in probeType table. */
char *name = NULL;
dyStringClear(query);
sqlDyStringPrintf(query,
"select term from VOC_Term where _Term_key = %s",
reporterGeneKey);
name = sqlQuickStringVerbose(conn2, query->string);
if (name == NULL)
warn("Can't find _ReporterGene_key %s in VOC_Term",
reporterGeneKey);
else if (sameString(name, "GFP"))
probeColor = "green";
else if (sameString(name, "lacZ"))
probeColor = "blue";
else
warn("Don't know color of reporter gene %s", name);
freez(&name);
}
if (!isStrNull(probePrepKey))
{
char *name = NULL;
dyStringClear(query);
sqlDyStringPrintf(query,
"select GXD_VisualizationMethod.visualization "
"from GXD_VisualizationMethod,GXD_ProbePrep "
"where GXD_ProbePrep._ProbePrep_key = %s "
"and GXD_ProbePrep._Visualization_key = GXD_VisualizationMethod._Visualization_key"
, probePrepKey);
name = sqlQuickStringVerbose(conn2, query->string);
if (name == NULL)
warn("Can't find visualization from _ProbePrep_key %s", probePrepKey);
probeColor = colorFromLabel(name, gene);
freez(&name);
if (probeColor[0] == 0)
{
dyStringClear(query);
sqlDyStringPrintf(query,
"select GXD_Label.label from GXD_Label,GXD_ProbePrep "
"where GXD_ProbePrep._ProbePrep_key = %s "
"and GXD_ProbePrep._Label_key = GXD_Label._Label_key"
, probePrepKey);
name = sqlQuickStringVerbose(conn2, query->string);
if (name == NULL)
warn("Can't find label from _ProbePrep_key %s",
probePrepKey);
probeColor = colorFromLabel(name, gene);
}
freez(&name);
}
if (!isStrNull(antibodyPrepKey) && probeColor[0] == 0 )
{
char *name = NULL;
dyStringClear(query);
sqlDyStringPrintf(query,
"select GXD_Label.label from GXD_Label,GXD_AntibodyPrep "
"where GXD_AntibodyPrep._AntibodyPrep_key = %s "
"and GXD_AntibodyPrep._Label_key = GXD_Label._Label_key"
, antibodyPrepKey);
name = sqlQuickStringVerbose(conn2, query->string);
if (name == NULL)
warn("Can't find label from _AntibodyPrep_key %s", antibodyPrepKey);
probeColor = colorFromLabel(name, gene);
freez(&name);
}
}
/* Get abName, abTaxon, abSubmitId */
abTaxon[0] = 0;
if (!isStrNull(antibodyPrepKey))
{
struct sqlResult *sr = NULL;
int orgKey = 0;
char **row;
dyStringClear(query);
sqlDyStringPrintf(query,
"select antibodyName,_Organism_key,GXD_Antibody._Antibody_key "
"from GXD_AntibodyPrep,GXD_Antibody "
"where GXD_AntibodyPrep._AntibodyPrep_key = %s "
"and GXD_AntibodyPrep._Antibody_key = GXD_Antibody._Antibody_key"
, antibodyPrepKey);
sr = sqlGetResultVerbose(conn2, query->string);
row = sqlNextRow(sr);
if (row != NULL)
{
abName = cloneString(row[0]);
orgKey = atoi(row[1]);
abSubmitId = cloneString(row[2]);
}
sqlFreeResult(&sr);
if (orgKey > 0)
{
char *latinName = NULL, *commonName = NULL;
int spTaxon = 0;
dyStringClear(query);
sqlDyStringPrintf(query, "select latinName from MGI_Organism "
"where _Organism_key = %d", orgKey);
latinName = sqlQuickStringVerbose(conn2, query->string);
if (latinName != NULL
&& !sameString(latinName, "Not Specified")
&& !sameString(latinName, "Not Applicable"))
{
char *e = strchr(latinName, '/');
if (e != NULL)
*e = 0; /* Chop off / and after. */
spTaxon = spBinomialToTaxon(connSp, latinName);
}
else
{
dyStringClear(query);
sqlDyStringPrintf(query, "select commonName from MGI_Organism "
"where _Organism_key = %d", orgKey);
commonName = sqlQuickStringVerbose(conn2, query->string);
if (commonName != NULL
&& !sameString(commonName, "Not Applicable")
&& !sameString(commonName, "Not Specified"))
{
spTaxon = spCommonToTaxon(connSp, commonName);
}
}
if (spTaxon != 0)
safef(abTaxon, sizeof(abTaxon), "%d", spTaxon);
freez(&latinName);
freez(&commonName);
}
}
if (abName == NULL)
abName = cloneString("");
if (abSubmitId == NULL)
abSubmitId = cloneString("");
/* Get rPrimer, lPrimer */
if (!isStrNull(probePrepKey))
{
struct sqlResult *sr = NULL;
char **row;
dyStringClear(query);
sqlDyStringPrintf(query,
"select primer1sequence,primer2sequence "
"from PRB_Probe,GXD_ProbePrep "
"where PRB_Probe._Probe_key = GXD_ProbePrep._Probe_key "
"and GXD_ProbePrep._ProbePrep_key = %s"
, probePrepKey);
sr = sqlGetResultVerbose(conn2, query->string);
row = sqlNextRow(sr);
if (row != NULL)
{
fPrimer = cloneString(row[0]);
rPrimer = cloneString(row[1]);
}
sqlFreeResult(&sr);
}
/* Note Jackson database actually stores the primers very
* erratically. In all the cases I can find for in situs
* the primers are actually stored in free text in the PRB_Notes
* e.g. ... primers CGCGGATCCAGGGGAAACAGAAGGGCTGCG and CCCAAGCTTAGACTGTACAGGCTGAGCC ...
*/
if (fPrimer == NULL || fPrimer[0]==0)
{
struct sqlResult *sr = NULL;
char **row;
dyStringClear(query);
sqlDyStringPrintf(query,
"select PRB_Notes.note from GXD_ProbePrep, PRB_Notes"
" where GXD_ProbePrep._ProbePrep_key = %s"
" and GXD_ProbePrep._Probe_key = PRB_Notes._Probe_key"
" order by PRB_Notes.sequenceNum"
, probePrepKey);
sr = sqlGetResultVerbose(conn2, query->string);
dyStringClear(probeNotes);
while ((row = sqlNextRow(sr)) != NULL)
dyStringAppend(probeNotes, row[0]);
sqlFreeResult(&sr);
if (probeNotes->stringSize > 0)
{
char f[256];
char r[256];
int i = 0;
char *s = strstr(probeNotes->string," primers ");
if (s)
{
s += strlen(" primers ");
i = 0;
while (strchr("ACGT",*s) && (i<sizeof(f)))
f[i++] = *s++;
f[i]=0;
if (strstr(s," and ")==s)
{
s += strlen(" and ");
i = 0;
while (strchr("ACGT",*s) && (i<sizeof(r)))
r[i++] = *s++;
r[i]=0;
if (strlen(f) >= 10 && strlen(r) >= 10)
{
fPrimer = cloneString(f);
rPrimer = cloneString(r);
}
else
{
verbose(1, "bad primer parse:_ProbePrep_key=%s fPrimer=[%s], rPrimer=[%s]\n",
probePrepKey,f,r);
}
}
}
}
}
if (fPrimer == NULL)
fPrimer = cloneString("");
if (rPrimer == NULL)
rPrimer = cloneString("");
fixation = blankOutUnknown(fixation);
embedding = blankOutUnknown(embedding);
/* Massage body part and slice type. We only handle whole mounts. */
if (sameString(sliceType, "whole mount"))
{
bodyPart = "whole";
priority = "100";
}
else
{
sliceType = "";
priority = "1000";
}
genotypeAndStrainFromKey(genotypeKey, conn2, &genotype, &strain);
if (isStrNull(paneLabel))
paneLabel = cloneString(""); /* trying to suppress nulls in output */
stripChar(paneLabel, '"'); /* Get rid of a difficult quote to process. */
/* Fetch image dimensions from file. */
imageWidth=0;
imageHeight=0;
safef(path, sizeof(path), "%s/%s.jpg", inJax, fileKey);
if (fileExists(path))
jpegSize(path,&imageWidth,&imageHeight); /* will errAbort if no valid .jpeg exists */
else
warn("Picture Missing! %s ",path);
/* Deal caption if any. Most of the work only happens the
* first time see the image. */
if (!hashLookup(uniqImageHash, imageKey))
{
struct sqlResult *sr = NULL;
char **row;
hashAdd(uniqImageHash, imageKey, NULL);
dyStringClear(caption);
dyStringClear(query);
sqlDyStringPrintf(query,
"select note from MGI_NoteChunk,MGI_Note,MGI_NoteType,ACC_MGIType "
"where MGI_Note._Object_key = %s "
"and ACC_MGIType.name = 'Image' "
"and ACC_MGIType._MGIType_key = MGI_Note._MGIType_key "
"and MGI_NoteType.noteType='Caption' "
"and MGI_Note._NoteType_key = MGI_NoteType._NoteType_key "
"and MGI_Note._Note_key = MGI_NoteChunk._Note_key "
"order by sequenceNum"
, imageKey);
sr = sqlGetResultVerbose(conn2, query->string);
while ((row = sqlNextRow(sr)) != NULL)
dyStringAppend(caption, row[0]);
sqlFreeResult(&sr);
if (caption->stringSize > 0)
{
subChar(caption->string, '\t', ' ');
subChar(caption->string, '\n', ' ');
fprintf(cap, "%s\t%s\n", imageKey, caption->string);
hashAdd(captionHash, imageKey, imageKey);
}
}
if (hashLookup(captionHash, imageKey))
captionId = imageKey;
else
captionId = "";
fprintf(tab, "%s\t", gene);
fprintf(tab, "%s\t", probeColor);
fprintf(tab, "%s\t", sex);
fprintf(tab, "%3.2f\t", calcAge);
fprintf(tab, "%s\t", ageMin);
fprintf(tab, "%s\t", ageMax);
fprintf(tab, "%s\t", paneLabel); /* may have to change NULL to empty string or "0" ? */
fprintf(tab, "%s.jpg\t", fileKey);
fprintf(tab, "%s\t", imageKey);
fprintf(tab, "%s\t", fPrimer);
fprintf(tab, "%s\t", rPrimer);
fprintf(tab, "%s\t", abName);
fprintf(tab, "%s\t", abTaxon);
fprintf(tab, "%s\t", abSubmitId);
fprintf(tab, "%s\t", fixation);
fprintf(tab, "%s\t", embedding);
fprintf(tab, "%s\t", bodyPart);
fprintf(tab, "%s\t", sliceType);
fprintf(tab, "%s\t", genotype);
fprintf(tab, "%s\t", strain);
fprintf(tab, "%s\t", priority);
fprintf(tab, "%s\t", captionId);
fprintf(tab, "%d\t", imageWidth);
fprintf(tab, "%d\n", imageHeight);
printExpression(tab, conn2, imagePaneKey, assayKey);
gotAny = TRUE;
freez(&genotype);
freez(&abName);
freez(&abSubmitId);
freez(&rPrimer);
freez(&fPrimer);
}
sqlFreeResult(&sr);
carefulClose(&ra);
carefulClose(&tab);
carefulClose(&cap);
if (!gotAny)
{
remove(raName);
remove(capName);
remove(tabName);
}
dyStringFree(&probeNotes);
dyStringFree(©right);
dyStringFree(&caption);
dyStringFree(&query);
hashFree(&uniqImageHash);
hashFree(&captionHash);
}
int palOutPredList(struct sqlConnection *conn, struct cart *cart,
struct genePred *list)
/* output a list of genePreds in pal format */
{
if (list == NULL)
return 0;
char *mafTable = cartString(cart, hgtaCGIGeneMafTable);
char *database = sqlGetDatabase(conn);
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
struct wigMafSpecies *wmSpecies;
int groupCnt;
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
/* this queries the state of the getSpecies dialog */
wigMafGetSpecies(cart, maftdb, maftdb->track, database, &wmSpecies, &groupCnt);
/* since the species selection dialog doesn't list
* the reference species, we just automatically include
* it */
struct slName *includeList = slNameNew(database);
/* now make a list of all species that are on */
for(; wmSpecies; wmSpecies = wmSpecies->next)
{
if (wmSpecies->on)
{
struct slName *newName = slNameNew(wmSpecies->name);
slAddHead(&includeList, newName);
}
}
slReverse(&includeList);
boolean inExons = cartUsualBoolean(cart, hgtaCGIGeneExons , FALSE);
boolean noTrans = cartUsualBoolean(cart, hgtaCGIGeneNoTrans, FALSE);
boolean outBlank = cartUsualBoolean(cart, hgtaCGIGeneOutBlank, FALSE);
boolean outTable = cartUsualBoolean(cart, hgtaCGIOutTable, FALSE);
boolean truncHeader = cartUsualBoolean(cart, hgtaCGITruncHeader, FALSE);
int numCols = cartUsualInt(cart, hgtaCGINumColumns, 20);
unsigned options = 0;
if (inExons) options |= MAFGENE_EXONS;
if (noTrans) options |= MAFGENE_NOTRANS;
if (outBlank) options |= MAFGENE_OUTBLANK;
if (outTable) options |= MAFGENE_OUTTABLE;
if (!truncHeader)
numCols = -1;
/* send out the alignments */
int outCount = 0;
for( ; list ; list = list->next)
{
if (list->cdsStart != list->cdsEnd)
{
outCount++;
mafGeneOutPred(stdout, list, database, mafTable,
includeList, options, numCols);
}
}
slNameFreeList(&includeList);
return outCount;
}
void bedListExpRecordAverage(struct bed **pBedList, struct expRecord **pERList, int extrasIndex)
/* This is a mildy complicated function to make the details page have the */
/* same data as the track when the UI option "Tissue averages" is selected. */
/* This is done by hacking the bed and expRecord lists in place and keeping */
/* the original code for the most part. */
{
struct bed *bed = NULL;
struct expRecord *er, *newERList = NULL;
struct slName *extras = NULL, *oneSlName;
int M, N, i, columns;
int *mapping;
if (!pBedList || !pERList || !*pBedList || !*pERList)
return;
er = *pERList;
if ((extrasIndex < 0) || (extrasIndex >= er->numExtras))
return;
/* Build up a unique list of words from the specific "extras" column. */
for (er = *pERList; er != NULL; er = er->next)
slNameStore(&extras, er->extras[extrasIndex]);
slReverse(&extras);
M = slCount(extras);
N = slCount(*pERList);
columns = N + 1;
/* M rows, reserve first column for counts. */
mapping = needMem(sizeof(int) * M * columns);
/* Create the mapping array: */
/* each row corresponds to one of the groupings. The first column is the number of */
/* things in the original list in the group (k things), and the next k elements on */
/* that row are indeces. */
for (er = *pERList, i = 0; er != NULL && i < N; er = er->next, i++)
{
int ix = slNameFindIx(extras, er->extras[extrasIndex]) * columns;
mapping[ix + ++mapping[ix]] = er->id;
}
/* Make a new expRecord list. */
for (oneSlName = extras, i = 0; oneSlName != NULL && i < M; oneSlName = oneSlName->next, i++)
{
struct expRecord *newER = basicExpRecord(oneSlName->name, i, extrasIndex);
slAddHead(&newERList, newER);
}
slReverse(&newERList);
expRecordFreeList(pERList);
*pERList = newERList;
/* Go through each bed and change it. */
for (bed = *pBedList; bed != NULL; bed = bed->next)
{
float *newExpScores = needMem(sizeof(float) * M);
int *newExpIds = needMem(sizeof(int) * M);
/* Calculate averages. */
for (i = 0; i < M; i++)
{
int ix = i * columns;
int size = mapping[ix];
int j;
double sum = 0;
for (j = 1; j < size + 1; j++)
sum += (double)bed->expScores[mapping[ix + j]];
newExpScores[i] = (float)(sum/size);
newExpIds[i] = i;
}
bed->expCount = M;
freeMem(bed->expIds);
bed->expIds = newExpIds;
freeMem(bed->expScores);
bed->expScores = newExpScores;
}
/* Free stuff. */
slNameFreeList(&extras);
freez(&mapping);
}
