| Potential Off-targets | \n");
+
+ printf("\n");
+ char *coords[65536];
+ int coordCount = chopByChar(val, '|', coords, ArraySize(coords));
+ int i;
+
+ struct subText *subList = NULL;
+ slSafeAddHead(&subList, subTextNew("ig:", "intergenic "));
+ slSafeAddHead(&subList, subTextNew("ex:", "exon "));
+ slSafeAddHead(&subList, subTextNew("in:", "intron "));
+ slSafeAddHead(&subList, subTextNew("|", "-"));
+
+ struct sqlConnection *conn = hAllocConn(database);
+
+ boolean hasLocus = sqlTableExists(conn, "locusName");
+
+ printf("\n");
+ printf("\n"
+ "| Mismatched nucleotides | \n"
+ "CFD Score | \n");
+ if (hasLocus)
+ printf("Locus | \n");
+ printf("Position | \n");
+
+ boolean collapsed = FALSE;
+ for (i=0; i10)
+ {
+ collapsed = TRUE;
+ printf("\n");
+ }
+ else
+ printf(" \n");
+
+ // parse single coordinate string
+ // chr15;63615585-;71 = chrom;startPosStrand;scoreAsInt
+ char *parts[3];
+ chopByChar(coords[i], ';', parts, 3);
+ char* chrom = parts[0];
+ char* posStrand = parts[1];
+ char* scoreStr = parts[2];
+
+ // get score and strand
+ char strand = *(posStrand+strlen(posStrand)-1);
+ int pos = atol(posStrand);
+ int scoreInt = atoi(scoreStr);
+ float score = (float)scoreInt/1000;
+
+ // get the DNA sequence - this is slow! twoBit currently does not cache
+ // if the input is not sorted and this list is sorted by off-target score (CFD)
+ struct dnaSeq *seq = hDnaFromSeq(database, chrom, pos, pos+23, dnaUpper);
+ if (strand=='-')
+ reverseComplement(seq->dna, seq->size);
+ char *guideSeq = (char*)slPairFindVal(extraFields, "guideSeq");
+ // PAM = the last three chars of the off-target
+ char *pam = seq->dna+20;
+
+ // print sequence + PAM
+ printf("| ");
+ printMismatchString(guideSeq, seq->dna);
+ printf(" %s", pam);
+ printf(" | \n");
+
+ // print score of off-target
+ printf("%0.3f | ", score);
+
+ // print name of this locus
+ if (hasLocus)
+ {
+ struct sqlResult *sr = hRangeQuery(conn, "locusName", chrom, pos, pos+23, NULL, 0);
+ char **row;
+ row = sqlNextRow(sr);
+ if (row != NULL)
+ {
+ char *desc = row[4];
+ char *descLong = subTextString(subList, desc);
+ printf("%s | ", descLong);
+ freeMem(descLong);
+ }
+ sqlFreeResult(&sr);
+ }
+
+ // print link to location
+ printf("%s:%d (%c) | \n",
+ hgTracksPathAndSettings(), database,
+ chrom, pos+1, pos+23, chrom, pos+1, strand);
+
+ printf(" \n");
+ }
+ hFreeConn(&conn);
+ printf("\n");
+ printf(" \n");
+ if (collapsed)
+ {
+ printf(""
+ "Show all %d off-targets...\n", coordCount);
+ // inline .js is bad style but why pollute our global .js files for such a rare
+ // case? Maybe we should have a generic "collapsible" class, like bootstrap?
+ printf("\n");
+ }
+ }
+}
+
+static void seekAndPrintTable(char *url, off_t offset, struct slPair *extraFields)
+/* seek to 0 at url, get headers, then seek to offset, read tab-sep fields and output
+ * (extraFields are needed for some special field handlers) */
+{
+char *detailsUrl = replaceChars(url, "$db", database);
+
+// open the URL
+struct lineFile *lf = lineFileUdcMayOpen(detailsUrl, FALSE);
+if (lf==NULL)
+ {
+ printf("Error: Could not open the URL referenced in detailsTabUrls, %s", detailsUrl);
+ return;
+ }
+
+// get the headers
+char *headLine;
+int lineSize;
+lineFileNext(lf, &headLine, &lineSize);
+char *headers[1024];
+int headerCount = chopTabs(headLine, headers);
+
+lineFileSeek(lf, offset, SEEK_SET);
+
+// read a line
+char *detailsLine;
+lineFileNext(lf, &detailsLine, &lineSize);
+if (!detailsLine || isEmpty(detailsLine))
+ return;
+char *fields[1024];
+int fieldCount = chopTabs(detailsLine, fields);
+
+if (fieldCount!=headerCount)
+ {
+ printf("Error encountered when reading %s:
", detailsUrl);
+ printf("The header line of the tab-sep file has a different number of fields compared ");
+ printf("with the line pointed to by offset %lld in the bigBed file.
", (long long int)offset);
+ printf("Number of headers: %d", headerCount);
+ printf("Number of fields at offset: %d", fieldCount);
+ return;
+ }
+
+// print the table for all external extra fields
+printf("
\n");
+
+lineFileClose(&lf);
+freez(&detailsUrl);
+}
+
+static void printAllExternalExtraFields(struct trackDb *tdb, struct slPair *extraFields)
+/* handle the "detailsTabUrls" trackDb setting:
+ * For each field, print a separate html table with all field names and values
+ * from the external tab-sep file */
+
+{
+char *detailsUrlsStr = trackDbSetting(tdb, "detailsTabUrls");
+if (!detailsUrlsStr)
+ return;
+
+struct slPair *detailsUrls = slPairListFromString(detailsUrlsStr, TRUE);
+if (!detailsUrls)
+ {
+ printf("Problem when parsing trackDb setting detailsTabUrls
\n");
+ printf("Expected: a space-separated key=val list, like 'fieldName1=URL1 fieldName2=URL2'
\n");
+ printf("But got: '%s'
", detailsUrlsStr);
+ return;
+ }
+
+struct slPair *pair;
+for (pair = detailsUrls; pair != NULL; pair = pair->next)
+ {
+ char *fieldName = pair->name;
+ char *detailsUrl = pair->val;
+
+ // get extra bigBed field (=the offset) and seek to it
+ void *p = slPairFindVal(extraFields, fieldName);
+ if (p==NULL)
+ {
+ printf("Error when parsing trackDb detailsTabUrls statement:
\n");
+ printf("Cannot find extra bigBed field with name %s\n", fieldName);
+ return;
+ }
+ char *offsetStr = (char*)p;
+
+ if (offsetStr==NULL || sameWord(offsetStr, "0"))
+ // empty or "0" value in bigBed means that the lookup should not be performed
+ continue;
+ off_t offset = atoll(offsetStr);
+
+ seekAndPrintTable(detailsUrl, offset, extraFields);
+ }
+slPairFreeValsAndList(&detailsUrls);
+}
+
static void bigBedClick(char *fileName, struct trackDb *tdb,
char *item, int start, int end, int bedSize)
/* Handle click in generic bigBed track. */
{
boolean showUrl = FALSE;
char *chrom = cartString(cart, "c");
/* Open BigWig file and get interval list. */
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct lm *lm = lmInit(0);
int ivStart = start, ivEnd = end;
if (start == end)
{
// item is an insertion; expand the search range from 0 bases to 2 so we catch it:
ivStart = max(0, start-1);
ivEnd++;
}
struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
/* Get bedSize if it's not already defined. */
if (bedSize == 0)
{
bedSize = bbi->definedFieldCount;
showUrl = TRUE;
}
char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL);
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
/* Find particular item in list - matching start, and item if possible. */
boolean found = FALSE;
boolean firstTime = TRUE;
struct bigBedInterval *bb;
for (bb = bbList; bb != NULL; bb = bb->next)
{
if (!(bb->start == start && bb->end == end))
continue;
if (bedSize > 3)
{
char *name = cloneFirstWordByDelimiterNoSkip(bb->rest, '\t');
boolean match = (isEmpty(name) && isEmpty(item)) || sameOk(name, item);
freez(&name);
if (!match)
continue;
}
found = TRUE;
if (firstTime)
printf("
\n");
int seq1Seq2Fields = 0;
// check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign)
boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2");
if (seq1Seq2 && bedSize == 6)
seq1Seq2Fields = 2;
char *fields[bedSize+seq1Seq2Fields];
char startBuf[16], endBuf[16];
char *rest = cloneString(bb->rest);
int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields,
bedSize+seq1Seq2Fields);
if (bbFieldCount != bedSize+seq1Seq2Fields)
{
errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)",
bedSize, fileName, bbFieldCount);
}
struct bed *bed = bedLoadN(fields, bedSize);
if (bedSize >= 6 && scoreFilter && bed->score < minScore)
continue;
if (showUrl && (bedSize >= 4))
printCustomUrl(tdb, item, TRUE);
bedPrintPos(bed, bedSize, tdb);
// display seq1 and seq2
if (seq1Seq2 && bedSize+seq1Seq2Fields == 8)
printf("| Sequence 1 | Sequence 2 |
|---|
"
"| %s | %s |
", fields[6], fields[7]);
else if (isNotEmpty(rest))
{
char *restFields[256];
int restCount = chopTabs(rest, restFields);
int restBedFields = bedSize - 3;
if (restCount > restBedFields)
{
- if (0 == extraFieldsPrint(tdb,NULL,restFields + restBedFields,restCount - restBedFields))
+ char **extraFields = (restFields + restBedFields);
+ int extraFieldCount = restCount - restBedFields;
+ int printCount = extraFieldsPrint(tdb,NULL,extraFields, extraFieldCount);
+
+ struct slPair* extraFieldPairs = getExtraFields(tdb, extraFields, extraFieldCount);
+ printAllExternalExtraFields(tdb, extraFieldPairs);
+
+ if (printCount == 0)
{
int i;
char label[20];
safef(label, sizeof(label), "nonBedFieldsLabel");
printf("%s ",
trackDbSettingOrDefault(tdb, label, "Non-BED fields:"));
for (i = restBedFields; i < restCount; i++)
printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]);
printf("
\n");
}
}
if (sameString(tdb->type, "bigGenePred"))
bigGenePredLinks(tdb->track, item);
}
+
+
if (isCustomTrack(tdb->track))
{
time_t timep = bbiUpdateTime(bbi);
printBbiUpdateTime(&timep);
}
}
if (!found)
{
printf("No item %s starting at %d\n", emptyForNull(item), start);
}
lmCleanup(&lm);
bbiFileClose(&bbi);
}
void genericBigBedClick(struct sqlConnection *conn, struct trackDb *tdb,
char *item, int start, int end, int bedSize)
/* Handle click in generic bigBed track. */
{
char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
bigBedClick(fileName, tdb, item, start, end, bedSize);
}
void bigBedCustomClick(struct trackDb *tdb)
/* Display details for BigWig custom tracks. */
{
char *fileName = trackDbSetting(tdb, "bigDataUrl");
char *item = cartOptionalString(cart, "i");
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
bigBedClick(fileName, tdb, item, start, end, 0);
}
|