fbdc691703e4bc2d98fcdb2014fe6fa19771c104
braney
Fri Feb 10 17:05:10 2017 -0800
make building a custom track with blat results an option on the hgBlat
page. Add some features to bigPsl click support to get the same kind
of UI that hgBlat provides.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index be8b9f3..9c58a17 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -244,30 +244,31 @@
#include "parClick.h"
#include "mdb.h"
#include "yaleGencodeAssoc.h"
#include "itemDetailsHtml.h"
#include "trackVersion.h"
#include "numtsClick.h"
#include "geneReviewsClick.h"
#include "bigBed.h"
#include "bigPsl.h"
#include "bedTabix.h"
#include "longRange.h"
#include "hmmstats.h"
#include "aveStats.h"
#include "trix.h"
#include "bPlusTree.h"
+#include "customFactory.h"
static char *rootDir = "hgcData";
#define LINESIZE 70 /* size of lines in comp seq feature */
struct cart *cart; /* User's settings. */
char *seqName; /* Name of sequence we're working on. */
int winStart, winEnd; /* Bounds of sequence. */
char *database; /* Name of mySQL database. */
char *organism; /* Colloquial name of organism. */
char *genome; /* common name, e.g. Mouse, Human */
char *scientificName; /* Scientific name of organism. */
struct hash *trackHash; /* A hash of all tracks - trackDb valued */
@@ -2969,41 +2970,54 @@
char *item, int start, int end)
/* Handle click in big psl track. */
{
struct psl* pslList = NULL;
char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
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++;
}
+boolean showEvery = sameString(item, "PrintAllSequences");
boolean showAll = trackDbSettingOn(tdb, "showAll");
unsigned seqTypeField = bbExtraFieldIndex(bbi, "seqType");
-struct bigBedInterval *bb, *bbList;
+struct bigBedInterval *bb, *bbList = NULL;
// If showAll is on, show all alignments with this qName, not just the
// selected one.
-if (showAll)
+if (showEvery)
+ {
+ struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
+ for (chrom = chromList; chrom != NULL; chrom = chrom->next)
+ {
+ char *chromName = chrom->name;
+ int start = 0, end = chrom->size;
+ int itemsLeft = 0; // Zero actually means no limit....
+ struct bigBedInterval *intervalList = bigBedIntervalQuery(bbi, chromName,
+ start, end, itemsLeft, lm);
+ slCat(&bbList, intervalList);
+ }
+ }
+else if (showAll)
{
int fieldIx;
struct bptFile *bpt = bigBedOpenExtraIndex(bbi, "name", &fieldIx);
- struct lm *lm = lmInit(0);
bbList = bigBedNameQuery(bbi, bpt, fieldIx, item, lm);
}
else
bbList = bigBedIntervalQuery(bbi, seqName, ivStart, ivEnd, 0, lm);
/* print out extra fields */
for (bb = bbList; bb != NULL; bb = bb->next)
{
char *restFields[256];
int restCount = chopTabs(cloneString(bb->rest), restFields);
if (sameString(restFields[0], item))
{
int bedSize = 25;
int restBedFields = bedSize - 3;
@@ -3017,39 +3031,45 @@
}
}
char *bedRow[32];
char startBuf[16], endBuf[16];
int lastChromId = -1;
char chromName[bbi->chromBpt->keySize+1];
for (bb = bbList; bb != NULL; bb = bb->next)
{
bbiCachedChromLookup(bbi, bb->chromId, lastChromId, chromName, sizeof(chromName));
lastChromId=bb->chromId;
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, 4);
- if (sameString(bedRow[3], item))
+ if (showEvery || sameString(bedRow[3], item))
{
struct psl *psl= pslFromBigPsl(chromName, bb, seqTypeField, NULL, NULL);
slAddHead(&pslList, psl);
}
}
+char *sort = cartUsualString(cart, "sort", pslSortList[0]);
+pslSortListByVar(&pslList, sort);
+
+if (showEvery)
+ printf("Genomic Alignments
");
+else
printf("%s/Genomic Alignments
", item);
-if (pslIsProtein(pslList))
+if (showEvery || pslIsProtein(pslList))
printAlignmentsSimple(pslList, start, "htcBigPslAli", tdb->table, item);
else
printAlignmentsExtra(pslList, start, "htcBigPslAli", "htcBigPslAliInWindow",
tdb->table, item);
pslFreeList(&pslList);
printItemDetailsHtml(tdb, item);
}
void genericPslClick(struct sqlConnection *conn, struct trackDb *tdb,
char *item, int start, char *subType)
/* Handle click in generic psl track. */
{
struct psl* pslList = getAlignments(conn, tdb->table, item);
/* check if there is an alignment available for this sequence. This checks
@@ -5868,51 +5888,55 @@
*/
{
return ((psl->tStart == startFirst) && sameString(psl->tName, seqName)) == isClicked;
}
void printAlignmentsSimple(struct psl *pslList, int startFirst, char *hgcCommand,
char *tableName, char *itemIn)
/* Print list of mRNA alignments, don't add extra textual link when
* doesn't honor hgcCommand. */
{
struct psl *psl;
int aliCount = slCount(pslList);
boolean isClicked;
if (pslList == NULL || tableName == NULL)
return;
+boolean showEvery = sameString(itemIn, "PrintAllSequences");
-if (aliCount > 1)
+if (!showEvery && (aliCount > 1))
printf("The alignment you clicked on is first in the table below.
\n");
printf("");
if (startsWith("chr", pslList->tName))
printf("BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END QUERY START END TOTAL\n");
else
printf("BROWSER | SIZE IDENTITY SCAFFOLD STRAND START END QUERY START END TOTAL\n");
printf("-----------------------------------------------------------------------------------------------------\n");
for (isClicked = 1; isClicked >= 0; isClicked -= 1)
{
for (psl = pslList; psl != NULL; psl = psl->next)
{
if (isPslToPrintByClick(psl, startFirst, isClicked))
{
char otherString[512];
+ char *qName = itemIn;
+ if (sameString(itemIn, "PrintAllSequences"))
+ qName = psl->qName;
safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, tableName);
printf("browser | ",
hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd);
- hgcAnchorWindow(hgcCommand, itemIn, psl->tStart, psl->tEnd, otherString, psl->tName);
+ hgcAnchorWindow(hgcCommand, qName, psl->tStart, psl->tEnd, otherString, psl->tName);
printf("%5d %5.1f%% %9s %s %9d %9d %20s %5d %5d %5d",
psl->match + psl->misMatch + psl->repMatch,
100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
skipChr(psl->tName), psl->strand, psl->tStart + 1, psl->tEnd,
psl->qName, psl->qStart+1, psl->qEnd, psl->qSize);
printf("\n");
}
}
}
printf("");
}
void printAlignmentsExtra(struct psl *pslList, int startFirst, char *hgcCommand, char *hgcCommandInWindow,
char *tableName, char *itemIn)
/* Print list of mRNA alignments with special "in window" alignment function. */
@@ -25111,30 +25135,111 @@
while (*c != 0)
{
if ((*c=='&') || (*c=='<'))
doNotBreak = TRUE;
if (*c==';' || (*c =='>'))
doNotBreak = FALSE;
printf("%c", *c);
if (i % distance == 0 && ! doNotBreak)
printf("");
c++;
i++;
}
}
+static char *replaceSuffix(char *input, char *newSuffix)
+/* Given a filename with a suffix, replace existing suffix with a new suffix. */
+{
+char buffer[4096];
+safecpy(buffer, sizeof buffer, input);
+char *dot = strrchr(buffer, '.');
+safecpy(dot+1, sizeof buffer - 1 - (dot - buffer), newSuffix);
+return cloneString(buffer);
+}
+
+static void makeBigPsl(char *pslName, char *faName, char *db, char *outputBigBed)
+/* Make a bigPsl with the blat results. */
+{
+char *bigPslFile = replaceSuffix(outputBigBed, "bigPsl");
+
+char cmdBuffer[4096];
+safef(cmdBuffer, sizeof(cmdBuffer), "loader/pslToBigPsl %s -fa=%s stdout | sort -k1,1 -k2,2n > %s", pslName, faName, bigPslFile);
+system(cmdBuffer);
+char buf[4096];
+char *twoBitDir;
+if (trackHubDatabase(db))
+ {
+ struct trackHubGenome *genome = trackHubGetGenome(db);
+ twoBitDir = genome->twoBitPath;
+ }
+else
+ {
+ safef(buf, sizeof(buf), "/gbdb/%s", db);
+ twoBitDir = hReplaceGbdbSeqDir(buf, db);
+ safef(buf, sizeof(buf), "%s%s.2bit", twoBitDir, db);
+ twoBitDir = buf;
+ }
+
+safef(cmdBuffer, sizeof(cmdBuffer), "loader/bedToBigBed -verbose=0 -udcDir=%s -extraIndex=name -sizesIs2Bit -tab -as=loader/bigPsl.as -type=bed9+16 %s %s %s",
+ udcDefaultDir(), bigPslFile, twoBitDir, outputBigBed);
+system(cmdBuffer);
+unlink(bigPslFile);
+}
+
+static void buildBigPsl(char *fileNames)
+/* Build a custom track with a bigPsl file out of blat results.
+ * Bring up the bigPsl detail page with all the alignments. */
+{
+char *trackName = cartString(cart, "trackName");
+char *trackDescription = cartString(cart, "trackDescription");
+char *pslName, *faName, *qName;
+parseSs(fileNames, &pslName, &faName, &qName);
+
+struct tempName bigBedTn;
+trashDirDateFile(&bigBedTn, "hgBlat", "bp", ".bb");
+char *bigBedFile = bigBedTn.forCgi;
+makeBigPsl(pslName, faName, database, bigBedFile);
+
+char* host = getenv("HTTP_HOST");
+char* reqUrl = cloneString(getenv("REQUEST_URI"));
+// delete arguements to the url
+char *e = strchr(reqUrl+1, '?');
+if (e) *e = 0;
+// remove the cgi name
+e = strchr(reqUrl+1, '/');
+if (e) *e = 0;
+
+char *customTextTemplate = "track type=bigPsl indelDoubleInsert=on indelQueryInsert=on pslFile=%s visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s%s/%s name=\"%s\" description=\"%s\"\n";
+char *extraForMismatch = "showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases";
+
+boolean isProt = FALSE;
+if (isProt)
+ extraForMismatch = "";
+char buffer[4096];
+safef(buffer, sizeof buffer, customTextTemplate, bigBedTn.forCgi, host, extraForMismatch, host, reqUrl, bigBedTn.forCgi, trackName, trackDescription);
+
+struct customTrack *ctList = getCtList();
+struct customTrack *newCts = customFactoryParse(database, buffer, FALSE, NULL);
+theCtList = customTrackAddToList(ctList, newCts, NULL, FALSE);
+
+customTracksSaveCart(database, cart, theCtList);
+
+cartSetString(cart, "i", "PrintAllSequences");
+hgCustom(newCts->tdb->track, NULL);
+}
+
void doMiddle()
/* Generate body of HTML. */
{
char *track = cartString(cart, "g");
char *item = cloneString(cartOptionalString(cart, "i"));
char *parentWigMaf = cartOptionalString(cart, "parentWigMaf");
struct trackDb *tdb = NULL;
if (hIsGisaidServer())
{
validateGisaidUser(cart);
}
/* database and organism are global variables used in many places */
@@ -25266,30 +25371,34 @@
{
doGetDna1();
}
else if (sameWord(table, "htcGetDna2"))
{
doGetDna2();
}
else if (sameWord(table, "htcGetDna3"))
{
doGetDna3();
}
else if (sameWord(table, "htcGetDnaExtended1"))
{
doGetDnaExtended1();
}
+else if (sameWord(table, "buildBigPsl"))
+ {
+ buildBigPsl(item);
+ }
else if (sameWord(table, "htcListItemsAssayed"))
{
doPeakClusterListItemsAssayed();
}
/* Lowe Lab Stuff */
#ifdef LOWELAB
else if (loweLabClick(table, item, tdb))
{
/* do nothing, everything handled in loweLabClick */
}
#endif
else if (sameWord(table, G_DELETE_WIKI_ITEM))
{
doDeleteWikiItem(item, seqName, winStart, winEnd);