static void hgSeqDisplayOptions(struct cart *cart, boolean canDoUTR,
boolean canDoIntrons, boolean offerRevComp)
/* Print out HTML FORM entries for sequence display options. */
{
char *casing, *repMasking;
puts("\n<H3> Sequence Formatting Options: </H3>\n");
casing = cartCgiUsualString(cart, "hgSeq.casing", "exon");
if (canDoIntrons)
{
cgiMakeRadioButton("hgSeq.casing", "exon", sameString(casing, "exon"));
if (canDoUTR)
puts("Exons in upper case, everything else in lower case. <BR>");
else
puts("Blocks in upper case, everything else in lower case. <BR>");
}
if (canDoUTR)
{
if (sameString(casing, "exon") && !canDoIntrons)
casing = "cds";
cgiMakeRadioButton("hgSeq.casing", "cds", sameString(casing, "cds"));
puts("CDS in upper case, UTR in lower case. <BR>");
}
if ((sameString(casing, "exon") && !canDoIntrons) ||
(sameString(casing, "cds") && !canDoUTR))
casing = "upper";
cgiMakeRadioButton("hgSeq.casing", "upper", sameString(casing, "upper"));
puts("All upper case. <BR>");
cgiMakeRadioButton("hgSeq.casing", "lower", sameString(casing, "lower"));
puts("All lower case. <BR>");
cgiMakeCheckBox("hgSeq.maskRepeats",
cartCgiUsualBoolean(cart, "hgSeq.maskRepeats", FALSE));
puts("Mask repeats: ");
repMasking = cartCgiUsualString(cart, "hgSeq.repMasking", "lower");
cgiMakeRadioButton("hgSeq.repMasking", "lower",
sameString(repMasking, "lower"));
puts(" to lower case ");
cgiMakeRadioButton("hgSeq.repMasking", "N", sameString(repMasking, "N"));
puts(" to N <BR>");
if (offerRevComp)
{
cgiMakeCheckBox("hgSeq.revComp",
cartCgiUsualBoolean(cart, "hgSeq.revComp", FALSE));
puts("Reverse complement (get \'-\' strand sequence)");
}
}
static void showWiggleMergeOptions()
/* Show subtrack merge operation options for wiggle/bedGraph tables. */
{
char *setting = cartUsualString(cart, hgtaNextSubtrackMergeWigOp, "average");
makeWigOpButton("average", setting);
printf("Average (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("sum", setting);
printf("Sum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("product", setting);
printf("Product (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("min", setting);
printf("Minimum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("max", setting);
printf("Maximum (at each position) of all selected subtracks' scores<P>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeRequireAll,
cartUsualBoolean(cart, hgtaSubtrackMergeRequireAll, FALSE));
printf("Discard scores for positions at which one or more selected subtracks "
"have no data.<BR>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeUseMinScore,
cartUsualBoolean(cart, hgtaSubtrackMergeUseMinScore, FALSE));
printf("Discard scores less than \n");
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeMinScore, "0.0");
cgiMakeTextVar(hgtaNextSubtrackMergeMinScore, setting, 5);
printf(" after performing the above operation.<P>\n");
}
static void showBedMergeOptions()
/* Show subtrack merge operation options for tables that are distilled
* to BED (not wiggle/bedGraph). */
{
char *op = cartUsualString(cart, hgtaNextSubtrackMergeOp, "any");
char *setting = NULL;
hPrintf("These combinations will maintain the gene/alignment structure "
"(if any) of %s: <P>\n", curTable);
makeOpButton("any", op);
printf("All %s records that have any overlap with any other selected subtrack<BR>\n",
curTable);
makeOpButton("none", op);
printf("All %s records that have no overlap with any other selected subtrack<BR>\n",
curTable);
makeOpButton("more", op);
printf("All %s records that have at least ",
curTable);
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeMoreThreshold, "80");
cgiMakeTextVar(hgtaNextSubtrackMergeMoreThreshold, setting, 3);
printf(" %% overlap with any other selected subtrack<BR>\n");
makeOpButton("less", op);
printf("All %s records that have at most ",
curTable);
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeLessThreshold, "80");
cgiMakeTextVar(hgtaNextSubtrackMergeLessThreshold, setting, 3);
printf(" %% overlap with any other selected subtrack<BR>\n");
makeOpButton("cat", op);
printf("All %s records, as well as all records from all other selected subtracks<P>\n",
curTable);
printf("These combinations will discard the gene/alignment structure (if any) "
"of %s and produce a simple list of position ranges.<P>\n",
curTable);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and other selected subtracks<BR>\n",
curTable);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and other selected subtracks<P>\n",
curTable);
}
static void conservationStatsLink(struct trackDb *tdb,
char *label, char *table)
/* write link that to display statistics of phastCons table */
{
char *chrom = cartCgiUsualString(cart, "c", "chr7");
printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%d&db=%s"
"&parentWigMaf=%s\" TARGET=\"_blank\">%s</A>",
hgcPathAndSettings(), table, table, chrom,
winStart, winEnd, winStart, database, tdb->track, label);
}
struct liftOverChain *defaultChoices(struct liftOverChain *chainList,
char *cartDb)
/* Out of a list of liftOverChains and a cart, choose a
* list to display. */
{
char *fromOrg, *fromDb, *toOrg, *toDb, *cartOrg;
struct liftOverChain *choice = NULL;
struct hash *dbRank = hGetDatabaseRank();
double bestScore = -1;
struct liftOverChain *this = NULL;
/* Get the initial values. */
fromOrg = cartCgiUsualString(cart, HGLFT_FROMORG_VAR, "0");
fromDb = cartCgiUsualString(cart, HGLFT_FROMDB_VAR, "0");
toOrg = cartCgiUsualString(cart, HGLFT_TOORG_VAR, "0");
toDb = cartCgiUsualString(cart, HGLFT_TODB_VAR, "0");
cartOrg = hArchiveOrganism(cartDb);
if (sameWord(fromOrg,"0"))
fromOrg = NULL;
if (sameWord(fromDb,"0"))
fromDb = NULL;
if (sameWord(toOrg,"0"))
toOrg = NULL;
if (sameWord(toDb,"0"))
toDb = NULL;
if (sameWord(cartDb,"0"))
cartDb = NULL;
for (this = chainList; this != NULL; this = this->next)
{
double score = scoreLiftOverChain(this, fromOrg, fromDb, toOrg, toDb, cartOrg, cartDb, dbRank);
if (score > bestScore)
{
choice = this;
bestScore = score;
}
}
return choice;
}
boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt,
boolean doCtFile, boolean redirectToGb)
/* Actually output bed or custom track. Return TRUE unless no results. */
{
char *db = cloneString(database);
char *table = curTable;
struct hTableInfo *hti = getHti(db, table, conn);
struct featureBits *fbList = NULL, *fbPtr;
struct customTrack *ctNew = NULL;
boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE)
|| doCt || doCtFile);
char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
char *fbQual = fbOptionsToQualifier();
char fbTQ[128];
int fields = hTableInfoBedFieldCount(hti);
boolean gotResults = FALSE;
struct region *region, *regionList = getRegions();
boolean isBedGr = isBedGraph(curTable);
boolean isBgWg = isBigWigTable(curTable);
boolean needSubtrackMerge = anySubtrackMerge(database, curTable);
boolean doDataPoints = FALSE;
boolean isWig = isWiggle(database, table);
struct wigAsciiData *wigDataList = NULL;
struct dataVector *dataVectorList = NULL;
boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable));
if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt)
{
textOpen();
}
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType))
doDataPoints = TRUE;
for (region = regionList; region != NULL; region = region->next)
{
struct bed *bedList = NULL, *bed;
struct lm *lm = lmInit(64*1024);
struct dataVector *dv = NULL;
if (isWig && doDataPoints)
{
if (needSubtrackMerge)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else
{
int count = 0;
struct wigAsciiData *wigData = NULL;
struct wigAsciiData *asciiData;
struct wigAsciiData *next;
wigData = getWiggleAsData(conn, curTable, region);
for (asciiData = wigData; asciiData; asciiData = next)
{
next = asciiData->next;
if (asciiData->count)
{
slAddHead(&wigDataList, asciiData);
++count;
}
}
slReverse(&wigDataList);
}
}
else if (isBedGr && doDataPoints)
{
dv = bedGraphDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isBgWg && doDataPoints)
{
dv = bigWigDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isWig || isBgWg)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
bedList = dataVectorToBedList(dv);
dataVectorFree(&dv);
}
else if (isBedGr)
{
bedList = getBedGraphAsBed(conn, curTable, region);
}
else
{
bedList = cookedBedList(conn, curTable, region, lm, &fields);
}
/* this is a one-time only initial creation of the custom track
* structure to receive the results. gotResults turns it off after
* the first time.
*/
if (doCtHdr && !gotResults &&
((bedList != NULL) || (wigDataList != NULL) ||
(dataVectorList != NULL)))
{
ctNew = beginCustomTrack(table, fields,
doCt, (isWig || isBedGr || isBgWg), doDataPoints);
}
if (doDataPoints && (wigDataList || dataVectorList))
gotResults = TRUE;
else
{
if ((fbQual == NULL) || (fbQual[0] == 0))
{
for (bed = bedList; bed != NULL; bed = bed->next)
{
if (bed->name != NULL)
{
subChar(bed->name, ' ', '_');
}
if (doCt)
{
struct bed *dupe = cloneBed(bed); /* Out of local memory. */
slAddHead(&ctNew->bedList, dupe);
}
else
{
if (doRgb)
bedTabOutNitemRgb(bed, fields, stdout);
else
bedTabOutN(bed, fields, stdout);
}
gotResults = TRUE;
}
}
else
{
safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual);
fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE);
if (fields >= 6)
fields = 6;
else if (fields >= 4)
fields = 4;
else
fields = 3;
if (doCt && ctNew)
{
ctNew->fieldCount = fields;
safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1,
"bed %d", fields);
}
for (fbPtr=fbList; fbPtr != NULL; fbPtr=fbPtr->next)
{
if (fbPtr->name != NULL)
{
char *ptr = strchr(fbPtr->name, ' ');
if (ptr != NULL)
*ptr = 0;
}
if (doCt)
{
struct bed *fbBed = fbToBedOne(fbPtr);
slAddHead(&ctNew->bedList, fbBed );
}
else
{
if (fields >= 6)
hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name,
0, fbPtr->strand);
else if (fields >= 4)
hPrintf("%s\t%d\t%d\t%s\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name);
else
hPrintf("%s\t%d\t%d\n",
fbPtr->chrom, fbPtr->start, fbPtr->end);
}
gotResults = TRUE;
}
featureBitsFreeList(&fbList);
}
}
bedList = NULL;
lmCleanup(&lm);
}
if (!gotResults)
{
hPrintf(NO_RESULTS);
}
else if (doCt)
{
int wigDataSize = 0;
/* Load existing custom tracks and add this new one: */
struct customTrack *ctList = getCustomTracks();
removeNamedCustom(&ctList, ctNew->tdb->table);
if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL);
// TODO: see if can make prettier wig output here that
// doesn't necessarily have one value per base
}
else
{
struct wiggleDataStream *wds = NULL;
/* create an otherwise empty wds so we can print out the list */
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE);
#if defined(DEBUG) /* dbg */
/* allow file readability for debug */
chmod(ctNew->wigAscii, 0666);
#endif
wiggleDataStreamFree(&wds);
}
}
else
slReverse(&ctNew->bedList);
slAddHead(&ctList, ctNew);
/* Save the custom tracks out to file (overwrite the old file): */
customTracksSaveCart(db, cart, ctList);
/* Put up redirect-to-browser page. */
if (redirectToGb)
{
char browserUrl[256];
char headerText[512];
int redirDelay = 3;
safef(browserUrl, sizeof(browserUrl),
"%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database);
safef(headerText, sizeof(headerText),
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">",
redirDelay, browserUrl);
webStartHeader(cart, database, headerText,
"Table Browser: %s %s: %s", hOrganism(database),
freezeName, "get custom track");
if (doDataPoints)
{
hPrintf("There are %d data points in custom track. ", wigDataSize);
}
else
{
hPrintf("There are %d items in custom track. ",
slCount(ctNew->bedList));
}
hPrintf("You will be automatically redirected to the genome browser in\n"
"%d seconds, or you can \n"
"<A HREF=\"%s\">click here to continue</A>.\n",
redirDelay, browserUrl);
}
}
else if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL);
}
else
{
/* create an otherwise empty wds so we can print out the list */
struct wiggleDataStream *wds = NULL;
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wds->asciiOut(wds, db, "stdout", TRUE, FALSE);
wiggleDataStreamFree(&wds);
}
}
return gotResults;
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
void doIntersectMore(struct sqlConnection *conn)
/* Continue working in intersect page. */
{
struct trackDb *iTrack;
char *name = curTableLabel();
char *iName, *iTable;
char *onChange = onChangeEither();
char *op, *setting;
boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable));
// Note - bigWig is purposely left out of wigOptions. It supports more intersection options
// than wig does.
struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL;
htmlOpen("Intersect with %s", name);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE BORDER=0>\n");
/* Print group and track line. */
hPrintf("Select a group, track and table to intersect with:\n");
iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange,
hgtaNextIntersectTrack, onChange, conn);
iName = iTrack->shortLabel;
hPrintf("<TR><TD>\n");
iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE);
hti2 = maybeGetHti(database, iTable, conn);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
if (!wigOptions)
{
if (hti1 && hti1->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the exons/blocks will be considered.\n", name);
if (hti2 && hti2->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the bases covered by its exons/blocks will be "
"considered.\n", iName);
hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n",
name, iName);
hPrintf("These combinations will maintain the names and "
"gene/alignment structure (if any) of %s: <P>\n",
name);
}
else
hPrintf("<P>\n");
op = cartUsualString(cart, hgtaNextIntersectOp, "any");
jsTrackingVar("op", op);
makeOpButton("any", op);
printf("All %s records that have any overlap with %s <BR>\n",
name, iName);
makeOpButton("none", op);
printf("All %s records that have no overlap with %s <BR>\n",
name, iName);
if (!wigOptions)
{
makeOpButton("more", op);
printf("All %s records that have at least ",
name);
setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80");
cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3);
printf(" %% overlap with %s <BR>\n", iName);
makeOpButton("less", op);
printf("All %s records that have at most ",
name);
setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80");
cgiMakeTextVar(hgtaNextLessThreshold, setting, 3);
printf(" %% overlap with %s <P>\n", iName);
}
else
{
/* keep javaScript onClick happy */
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n");
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n");
hPrintf(" <P>\n");
}
if (!wigOptions)
{
boolean bigWig = isBigWigTable(curTable);
hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n",
name, iName);
if (!bigWig)
hPrintf("These combinations will discard the names and "
"gene/alignment structure (if any) of %s and produce a simple "
"list of position ranges.<P>\n",
name);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n",
name, iName);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and %s <P>\n",
name, iName);
hPrintf("Check the following boxes to complement one or both tables. "
"To complement a table means to include a base pair in the "
"intersection/union if it is <I>not</I> included in the table."
"<P>\n");
if (!bigWig)
{
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE);
printf("Complement %s before base-pair-wise intersection/union <BR>\n",
name);
}
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE);
printf("Complement %s before base-pair-wise intersection/union <P>\n",
iName);
}
else
{
/* keep javaScript onClick happy */
jsTrackingVar("op", op);
hPrintf("<SCRIPT>\n");
hPrintf("var invertTable=0;\n");
hPrintf("var invertTable2=0;\n");
hPrintf("</SCRIPT>\n");
hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name);
}
cgiMakeButton(hgtaDoIntersectSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(nextVars);
memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
saveVars[varCount] = hgtaDoIntersectMore;
jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
}
htmlClose();
}
static void hgSeqFeatureRegionOptions(struct cart *cart, boolean canDoUTR,
boolean canDoIntrons)
/* Print out HTML FORM entries for feature region options. */
{
char *exonStr = canDoIntrons ? " Exons" : "";
char *setting;
puts("\n<H3> Sequence Retrieval Region Options: </H3>\n");
if (canDoIntrons || canDoUTR)
{
cgiMakeCheckBox("hgSeq.promoter",
cartCgiUsualBoolean(cart, "hgSeq.promoter", FALSE));
puts("Promoter/Upstream by ");
setting = cartCgiUsualString(cart, "hgSeq.promoterSize", "1000");
cgiMakeTextVar("hgSeq.promoterSize", setting, 5);
puts("bases <BR>");
}
if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.utrExon5",
cartCgiUsualBoolean(cart, "hgSeq.utrExon5", TRUE));
printf("5' UTR%s <BR>\n", exonStr);
}
if (canDoIntrons)
{
cgiMakeCheckBox("hgSeq.cdsExon",
cartCgiUsualBoolean(cart, "hgSeq.cdsExon", TRUE));
if (canDoUTR)
printf("CDS Exons <BR>\n");
else
printf("Blocks <BR>\n");
}
else if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.cdsExon",
cartCgiUsualBoolean(cart, "hgSeq.cdsExon", TRUE));
printf("CDS <BR>\n");
}
else
{
cgiMakeHiddenVar("hgSeq.cdsExon", "1");
}
if (canDoUTR)
{
cgiMakeCheckBox("hgSeq.utrExon3",
cartCgiUsualBoolean(cart, "hgSeq.utrExon3", TRUE));
printf("3' UTR%s <BR>\n", exonStr);
}
if (canDoIntrons)
{
cgiMakeCheckBox("hgSeq.intron",
cartCgiUsualBoolean(cart, "hgSeq.intron", TRUE));
if (canDoUTR)
puts("Introns <BR>");
else
puts("Regions between blocks <BR>");
}
if (canDoIntrons || canDoUTR)
{
cgiMakeCheckBox("hgSeq.downstream",
cartCgiUsualBoolean(cart, "hgSeq.downstream", FALSE));
puts("Downstream by ");
setting = cartCgiUsualString(cart, "hgSeq.downstreamSize", "1000");
cgiMakeTextVar("hgSeq.downstreamSize", setting, 5);
puts("bases <BR>");
}
if (canDoIntrons || canDoUTR)
{
setting = cartCgiUsualString(cart, "hgSeq.granularity", "gene");
cgiMakeRadioButton("hgSeq.granularity", "gene",
sameString(setting, "gene"));
if (canDoUTR)
puts("One FASTA record per gene. <BR>");
else
puts("One FASTA record per item. <BR>");
cgiMakeRadioButton("hgSeq.granularity", "feature",
sameString(setting, "feature"));
if (canDoUTR)
puts("One FASTA record per region (exon, intron, etc.) with ");
else
puts("One FASTA record per region (block/between blocks) with ");
}
else
{
puts("Add ");
}
setting = cartCgiUsualString(cart, "hgSeq.padding5", "0");
cgiMakeTextVar("hgSeq.padding5", setting, 5);
puts("extra bases upstream (5') and ");
setting = cartCgiUsualString(cart, "hgSeq.padding3", "0");
cgiMakeTextVar("hgSeq.padding3", setting, 5);
puts("extra downstream (3') <BR>");
if (canDoIntrons && canDoUTR)
{
puts(" ");
cgiMakeCheckBox("hgSeq.splitCDSUTR",
cartCgiUsualBoolean(cart, "hgSeq.splitCDSUTR", FALSE));
puts("Split UTR and CDS parts of an exon into separate FASTA records");
}
puts("<BR>\n");
puts("Note: if a feature is close to the beginning or end of a chromosome \n"
"and upstream/downstream bases are added, they may be truncated \n"
"in order to avoid extending past the edge of the chromosome. <P>");
}
void webMain(struct liftOverChain *chain, char *dataFormat, boolean multiple)
/* set up page for entering data */
{
struct dbDb *dbList;
char *fromOrg = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb);
cgiParagraph(
"This tool converts genome coordinates and genome annotation files "
"between assemblies. "
"The input data can be pasted into the text box, or uploaded from a file. "
"If a pair of assemblies cannot be selected from the pull-down menus,"
" a direct lift between them is unavailable. "
"However, a sequential lift may be possible. "
"Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, "
"Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9. "
"");
/* create HMTL form */
puts("<FORM ACTION=\"../cgi-bin/hgLiftOver\" METHOD=\"POST\" "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
/* create HTML table for layout purposes */
puts("\n<TABLE WIDTH=\"100%%\">\n");
/* top two rows -- genome and assembly menus */
cgiSimpleTableRowStart();
cgiTableField("Original Genome: ");
cgiTableField("Original Assembly: ");
cgiTableField("New Genome: ");
cgiTableField("New Assembly: ");
cgiTableRowEnd();
cgiSimpleTableRowStart();
/* genome */
cgiSimpleTableFieldStart();
dbList = hGetLiftOverFromDatabases();
printSomeGenomeListHtmlNamed(HGLFT_FROMORG_VAR, chain->fromDb, dbList, onChange);
cgiTableFieldEnd();
/* from assembly */
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(chain->fromDb, dbList, HGLFT_FROMDB_VAR,
TRUE, onChange);
cgiTableFieldEnd();
/* to assembly */
cgiSimpleTableFieldStart();
dbDbFreeList(&dbList);
dbList = hGetLiftOverToDatabases(chain->fromDb);
printLiftOverGenomeList(HGLFT_TOORG_VAR, chain->toDb, dbList, onChange);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(chain->toDb, dbList, HGLFT_TODB_VAR, TRUE, "");
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
cgiParagraph(" ");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum ratio of bases that must remap:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeDoubleVar(HGLFT_MINMATCH,chain->minMatch,6);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum chain size in target:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeIntVar(HGLFT_MINSIZET,chain->minSizeT,4);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum hit size in query:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeIntVar(HGLFT_MINSIZEQ,chain->minSizeQ,4);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Allow multiple output regions:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeCheckBox(HGLFT_MULTIPLE,multiple);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Min ratio of alignment blocks/exons that must map:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeDoubleVar(HGLFT_MINBLOCKS,chain->minBlocks,6);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeCheckBox(HGLFT_FUDGETHICK,(chain->fudgeThick[0]=='Y') ? TRUE : FALSE);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* next row -- file format menu */
cgiParagraph(
" For descriptions of the supported data formats, see the bottom of this page.");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiTableField("Data Format: ");
cgiSimpleTableFieldStart();
cgiMakeDropList(HGLFT_DATAFORMAT_VAR,
formatList, sizeof(formatList)/sizeof (char*) - 1, dataFormat);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* text box and two buttons (submit, reset) */
cgiParagraph(" Paste in data:\n");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeTextArea(HGLFT_USERDATA_VAR, cartCgiUsualString(cart, HGLFT_USERDATA_VAR, NULL), 10, 80);
cgiTableFieldEnd();
/* right element of table is a nested table
* with two buttons stacked on top of each other */
cgiSimpleTableFieldStart();
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeSubmitButton();
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeClearButton("mainForm", HGLFT_USERDATA_VAR);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* next row -- file upload controls */
cgiParagraph(" Or upload data from a file:");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
printf("<TD><INPUT TYPE=FILE NAME=\"%s\"></TD>\n", HGLFT_DATAFILE_VAR);
puts("<TD><INPUT TYPE=SUBMIT NAME=SubmitFile VALUE=\"Submit File\"></TD>\n");
cgiTableRowEnd();
cgiTableEnd();
printf("<input type=\"hidden\" name=\"%s\" value=\"0\">\n",
HGLFT_REFRESHONLY_VAR);
puts("</FORM>\n");
cartSaveSession(cart);
puts("</FORM>");
freeMem(fromOrg);
freeMem(toOrg);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
/* struct liftOverChain *chainList = NULL, *chain; */
char *userData;
/* char *dataFile; */
char *dataFormat;
char *organism;
char *db;
float minBlocks, minMatch;
boolean multiple, fudgeThick;
int minSizeQ, minSizeT;
boolean refreshOnly = FALSE;
/* char *err = NULL; */
struct liftOverChain *chainList = NULL, *choice;
cart = theCart;
if (cgiOptionalString(HGLFT_ERRORHELP_VAR))
{
puts("<PRE>");
puts(liftOverErrHelp());
//system("/usr/bin/cal");
puts("</PRE>");
return;
}
/* Get data to convert - from userData variable, or if
* that is empty from a file. */
if (cartOptionalString(cart, "SubmitFile"))
userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
else
userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
dataFormat = cartCgiUsualString(cart, HGLFT_DATAFORMAT_VAR, DEFAULT_FORMAT);
cartWebStart(cart, NULL, "Lift Genome Annotations");
getDbAndGenome(cart, &db, &organism, oldVars);
chainList = liftOverChainListFiltered();
choice = defaultChoices(chainList, db);
if (choice == NULL)
errAbort("Sorry, no conversions available from this assembly\n");
minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
minSizeT = cartCgiUsualInt(cart, HGLFT_MINSIZET, choice->minSizeT);
minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);
fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE);
multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE);
refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0);
webMain(choice, dataFormat, multiple);
liftOverChainFreeList(&chainList);
if (!refreshOnly && userData != NULL && userData[0] != '\0')
{
struct hash *chainHash = newHash(0);
char *chainFile;
struct tempName oldTn, mappedTn, unmappedTn;
FILE *old, *mapped, *unmapped;
char *line;
int lineSize;
char *fromDb, *toDb;
int ct = 0, errCt = 0;
/* read in user data and save to file */
makeTempName(&oldTn, HGLFT, ".user");
old = mustOpen(oldTn.forCgi, "w");
fputs(userData, old);
fputs("\n", old); /* in case user doesn't end last line */
carefulClose(&old);
chmod(oldTn.forCgi, 0666);
/* setup output files -- one for converted lines, the other
* for lines that could not be mapped */
makeTempName(&mappedTn, HGLFT, ".bed");
makeTempName(&unmappedTn, HGLFT, ".err");
mapped = mustOpen(mappedTn.forCgi, "w");
chmod(mappedTn.forCgi, 0666);
unmapped = mustOpen(unmappedTn.forCgi, "w");
chmod(unmappedTn.forCgi, 0666);
fromDb = cgiString(HGLFT_FROMDB_VAR);
toDb = cgiString(HGLFT_TODB_VAR);
chainFile = liftOverChainFile(fromDb, toDb);
if (chainFile == NULL)
errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
fromDb, toDb);
readLiftOverMap(chainFile, chainHash);
if (sameString(dataFormat, WIGGLE_FORMAT))
/* TODO: implement Wiggle */
{}
else if (sameString(dataFormat, POSITION_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
/* ignore multiple, it must be false when position is used */
ct = liftOverPositions(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, FALSE, NULL, &errCt);
}
else if (sameString(dataFormat, BED_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
ct = liftOverBed(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
}
else
/* programming error */
errAbort("ERROR: Unsupported data format: %s\n", dataFormat);
webNewSection("Results");
if (ct)
{
/* some records succesfully converted */
cgiParagraph("");
printf("Successfully converted %d record", ct);
printf("%s: ", ct > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi);
}
if (errCt)
{
/* some records not converted */
cgiParagraph("");
printf("Conversion failed on %d record", errCt);
printf("%s. ", errCt > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>Display failure file</A> \n",
unmappedTn.forCgi);
printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR);
puts("<P>Failed input regions:\n");
struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
puts("<BLOCKQUOTE><PRE>\n");
while (lineFileNext(errFile, &line, &lineSize))
puts(line);
lineFileClose(&errFile);
puts("</PRE></BLOCKQUOTE>\n");
}
if (sameString(dataFormat, POSITION_FORMAT) && multiple)
{
puts("<BLOCKQUOTE><PRE>\n");
puts("Note: multiple checkbox ignored since it is not supported for position format.");
puts("</PRE></BLOCKQUOTE>\n");
}
carefulClose(&unmapped);
}
webDataFormats();
webDownloads();
cartWebEnd();
}
