6823728f16334d9b53bd595688c8f5780cf833fe braney Sun Feb 16 12:13:13 2025 -0800 ongoing work on quickLift. Added support for SQL beds diff --git src/hg/hgConvert/hgConvert.c src/hg/hgConvert/hgConvert.c index 197cf201578..0e3c59fddfd 100644 --- src/hg/hgConvert/hgConvert.c +++ src/hg/hgConvert/hgConvert.c @@ -1,444 +1,447 @@ /* hgConvert - CGI-script to convert browser window coordinates * using chain files */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "errAbort.h" #include "jksql.h" #include "linefile.h" #include "hCommon.h" #include "fa.h" #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hui.h" #include "cart.h" #include "web.h" #include "chain.h" #include "liftOver.h" #include "liftOverChain.h" #include "chromInfo.h" #include "net.h" #include "genark.h" #include "trackHub.h" +#include "hubConnect.h" #include "quickLift.h" -#include "exportedDataHubs.h" /* CGI Variables */ #define HGLFT_TOORG_VAR "hglft_toOrg" /* TO organism */ #define HGLFT_TODB_VAR "hglft_toDb" /* TO assembly */ #define HGLFT_DO_CONVERT "hglft_doConvert" /* Do the actual conversion */ /* Global Variables */ static struct cart *cart; /* CGI and other variables */ static struct hash *oldVars = NULL; static char *organism = NULL; static char *database = NULL; /* Javascript to support New Assembly pulldown when New Genome changes. */ /* Copies selected values to a hidden form */ char *onChangeToOrg = "document.mainForm.submit();"; static struct dbDb *matchingDb(struct dbDb *list, char *name) /* Find database of given name in list or die trying. */ { struct dbDb *db; for (db = list; db != NULL; db = db->next) { if (sameString(name, db->name)) return db; } errAbort("Can't find %s in matchingDb", name); return NULL; } static void askForDestination(struct liftOverChain *liftOver, char *fromPos, struct dbDb *fromDb, struct dbDb *toDb) /* set up page for entering data */ { struct dbDb *dbList; boolean askAboutQuickLift = FALSE; -if (exportedDataHubsEnabled()) +if (quickLiftEnabled()) askAboutQuickLift = TRUE; cartWebStart(cart, database, "Convert %s to New Assembly", fromPos); /* create HMTL form */ puts("
\n"); cartSaveSession(cart); /* create HTML table for layout purposes */ puts("\n\n"); /* top row -- labels */ cgiSimpleTableRowStart(); cgiTableField("Old genome: "); cgiTableField("Old assembly: "); cgiTableField("New genome: "); cgiTableField("New assembly: "); if (askAboutQuickLift) cgiTableField("QuickLift tracks: "); cgiTableField(" "); cgiTableRowEnd(); /* Next row -- data and controls */ cgiSimpleTableRowStart(); /* From organism and assembly. */ cgiTableField(fromDb->organism); cgiTableField(fromDb->description); /* Destination organism. */ cgiSimpleTableFieldStart(); dbList = hGetLiftOverToDatabases(liftOver->fromDb); printSomeGenomeListHtmlNamed(HGLFT_TOORG_VAR, liftOver->toDb, dbList, "change", onChangeToOrg); cgiTableFieldEnd(); /* Destination assembly */ cgiSimpleTableFieldStart(); printAllAssemblyListHtmlParm(liftOver->toDb, dbList, HGLFT_TODB_VAR, TRUE, NULL, NULL); cgiTableFieldEnd(); if (askAboutQuickLift) { cgiSimpleTableFieldStart(); boolean quickLift = cartUsualBoolean(cart, "doQuickLift", FALSE); cgiMakeCheckBoxWithId("doQuickLift", quickLift, "doQuickLift"); cgiTableFieldEnd(); } cgiSimpleTableFieldStart(); cgiMakeButton(HGLFT_DO_CONVERT, "Submit"); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); puts("\n"); cartWebEnd(); } static double scoreLiftOverChain(struct liftOverChain *chain, char *fromOrg, char *fromDb, char *toOrg, char *toDb, struct hash *dbRank ) /* Score the chain in terms of best match for cart settings */ { double score = 0; char *chainFromOrg = hOrganism(chain->fromDb); char *chainToOrg = hOrganism(chain->toDb); int fromRank = hashIntValDefault(dbRank, chain->fromDb, 0); int toRank = hashIntValDefault(dbRank, chain->toDb, 0); int maxRank = hashIntVal(dbRank, "maxRank"); if (sameOk(fromOrg,chainFromOrg) && sameOk(fromDb,chain->fromDb) && sameOk(toOrg,chainToOrg) && sameOk(toDb,chain->toDb)) score += 10000000; if (sameOk(fromOrg,chainFromOrg)) score += 2000000; if (sameOk(fromDb,chain->fromDb)) score += 1000000; if (sameOk(toOrg,chainToOrg)) score += 200000; if (sameOk(toDb,chain->toDb)) score += 100000; if (toRank == 0) // chains to db's that are not active shouldn't be considered return 0; score += 10*(maxRank-fromRank); score += (maxRank - toRank); return score; } static struct liftOverChain *defaultChoices(struct liftOverChain *chainList, char *fromOrg, char *fromDb) /* Out of a list of liftOverChains and a cart, choose a * list to display. */ { char *toOrg, *toDb; struct liftOverChain *choice = NULL; struct hash *dbRank = hGetDatabaseRank(); double bestScore = -1; struct liftOverChain *this = NULL; /* Get the initial values. */ toOrg = cartCgiUsualString(cart, HGLFT_TOORG_VAR, "0"); toDb = cartCgiUsualString(cart, HGLFT_TODB_VAR, "0"); if (sameWord(toOrg,"0")) toOrg = NULL; if (sameWord(toDb,"0")) toDb = NULL; for (this = chainList; this != NULL; this = this->next) { double score = scoreLiftOverChain(this, fromOrg, fromDb, toOrg, toDb, dbRank); if (score > bestScore) { choice = this; bestScore = score; } } return choice; } static char *skipWord(char *s) /* Skip word, and any leading spaces before next word. */ { return skipLeadingSpaces(skipToSpaces(s)); } static long chainTotalBlockSize(struct chain *chain) /* Return sum of sizes of all blocks in chain */ { struct cBlock *block; long total = 0; for (block = chain->blockList; block != NULL; block = block->next) total += block->tEnd - block->tStart; return total; } static struct chain *chainLoadIntersecting(char *fileName, char *chrom, int start, int end) /* Load the chains that intersect given region. */ { struct lineFile *lf = netLineFileOpen(fileName); char *line; int chromNameSize = strlen(chrom); struct chain *chainList = NULL, *chain; #ifdef SOON /* Put in if we index. */ boolean gotChrom = FALSE; #endif /* SOON */ int chainCount = 0; while (lineFileNextReal(lf, &line)) { if (startsWith("chain", line) && isspace(line[5])) { ++chainCount; line = skipWord(line); /* Skip over 'chain' */ line = skipWord(line); /* Skip over chain score */ if (startsWith(chrom, line) && isspace(line[chromNameSize])) { #ifdef SOON /* Put in if we index. */ gotChrom = TRUE; #endif /* SOON */ lineFileReuse(lf); chain = chainReadChainLine(lf); if (rangeIntersection(chain->tStart, chain->tEnd, start, end) > 0) { chainReadBlocks(lf, chain); slAddHead(&chainList, chain); } else chainFree(&chain); } #ifdef SOON /* Put in if we index. */ else if (gotChrom) break; /* We assume file is sorted by chromosome, so we're done. */ #endif /* SOON */ } } lineFileClose(&lf); slReverse(&chainList); return chainList; } static struct chain *chainLoadAndTrimIntersecting(char *fileName, char *chrom, int start, int end) /* Load the chains that intersect given region, and trim them * to fit region. */ { struct chain *rawList, *chainList = NULL, *chain, *next; rawList = chainLoadIntersecting(fileName, chrom, start, end); for (chain = rawList; chain != NULL; chain = next) { struct chain *subChain, *chainToFree; next = chain->next; chainSubsetOnT(chain, start, end, &subChain, &chainToFree); if (subChain != NULL) slAddHead(&chainList, subChain); if (chainToFree != NULL) chainFree(&chain); } slSort(&chainList, chainCmpScore); return chainList; } static void doConvert(char *fromPos) /* Actually do the conversion */ { struct dbDb *fromDb = hDbDb(trackHubSkipHubName(database)), *toDb = hDbDb(cartString(cart, HGLFT_TODB_VAR)); char *fileName = liftOverChainFile(fromDb->name, toDb->name); fileName = hReplaceGbdbMustDownload(fileName); char *chrom; int start, end; int origSize; struct chain *chainList, *chain; struct dyString *visDy = NULL; cartWebStart(cart, database, "%s %s %s to %s %s", fromDb->organism, fromDb->description, fromPos, toDb->organism, toDb->description); if (!hgParseChromRange(database, fromPos, &chrom, &start, &end)) errAbort("position %s is not in chrom:start-end format", fromPos); origSize = end - start; boolean doQuickLift = cartUsualBoolean(cart, "doQuickLift", FALSE); +cartRemove(cart, "doQuickLift"); unsigned quickChain = 0; unsigned quickHub = 0; if (doQuickLift) { quickChain = quickLiftGetChain(fromDb->name, toDb->name); if (quickChain == 0) errAbort("can't find quickChain from %s to %s", fromDb->name, toDb->name); visDy = newDyString(1024); char *newHub = trackHubBuild(fromDb->name, cart, visDy); - if ((quickHub = registerExportedDataHub(fromDb->name, newHub)) == 0) - errAbort("can't register exportedDataHub %s\n", newHub); + char *error; + quickHub = hubFindOrAddUrlInStatusTable(cart, newHub, &error); + if (error != NULL) + errAbort("can't add quickLift hub"); } chainList = chainLoadAndTrimIntersecting(fileName, chrom, start, end); if (chainList == NULL) printf("Sorry this position couldn't be found in new assembly"); else { for (chain = chainList; chain != NULL; chain = chain->next) { int blockSize; int qStart, qEnd; if (chain->qStrand == '-') { qStart = chain->qSize - chain->qEnd; qEnd = chain->qSize - chain->qStart; } else { qStart = chain->qStart; qEnd = chain->qEnd; } blockSize = chainTotalBlockSize(chain); /* Check if the toDb database exists and if the chromosome sequence file (of the hgConvert result) exists in the location specified in chromInfo for the toDb. */ boolean chromSeqExists = (sqlDatabaseExists(toDb->name) && chromSeqFileExists(toDb->name, chain->qName)); /* Check if the toDb has active set to 1 in dbDb if the toDb database exists. If these conditions are met then print position link to browser for toDb, otherwise just print position without link. */ boolean startedAnchor = FALSE; if ((hDbIsActive(toDb->name) && chromSeqExists) || startsWith("hub:",toDb->nibPath)) { if (quickChain) printf("", hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain, visDy->string); else printf("", hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd); startedAnchor = TRUE; } else if (sameString(toDb->nibPath, "genark")) { char *hubUrl = genarkUrl(toDb->name); if (hubUrl) { startedAnchor = TRUE; if (quickChain) printf("", hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain); else printf("", hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd); } } printf("%s:%d-%d", chain->qName, qStart+1, qEnd); if (startedAnchor) printf(""); printf(" (%3.1f%% of bases, %3.1f%% of span)
\n", 100.0 * blockSize/origSize, 100.0 * (chain->tEnd - chain->tStart) / origSize); } } cartWebEnd(); } static struct liftOverChain *cleanLiftOverList(struct liftOverChain *list) /* eliminate from the list where toDb doesn't exist in dbDb */ { struct liftOverChain *cleanList = NULL; struct hash *dbDbHash = hDbDbHash(); struct liftOverChain *this = NULL; struct liftOverChain *next = NULL; for (this = list; this != NULL; this = next) { next = this->next; if (hashLookup(dbDbHash, this->toDb)) slAddHead(&cleanList, this); else liftOverChainFree(&this); } slReverse(&cleanList); return cleanList; } static void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { char *fromPos = cartString(theCart, "position"); cart = theCart; getDbAndGenome(cart, &database, &organism, oldVars); // Try to deal with virt chrom position used by hgTracks. if (startsWith( MULTI_REGION_CHROM, cartUsualString(cart, "position", "")) || startsWith(OLD_MULTI_REGION_CHROM, cartUsualString(cart, "position", ""))) cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", "")); if (cartVarExists(cart, HGLFT_DO_CONVERT)) doConvert(fromPos); else { struct liftOverChain *checkLiftOverList = liftOverChainListForDbFiltered(trackHubSkipHubName(database)); struct liftOverChain *liftOverList = cleanLiftOverList(checkLiftOverList); struct liftOverChain *choice = defaultChoices(liftOverList, organism, database); if (choice == NULL) errAbort("Sorry, no conversions available from this assembly."); struct dbDb *dbList, *fromDb, *toDb; dbList = hDbDbListMaybeCheck(FALSE); fromDb = matchingDb(dbList, choice->fromDb); toDb = matchingDb(dbList, choice->toDb); askForDestination(choice, fromPos, fromDb, toDb); liftOverChainFreeList(&liftOverList); } } /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = { "submit", HGLFT_DO_CONVERT, NULL}; int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); oldVars = hashNew(10); cgiSpoof(&argc, argv); cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars); cgiExitTime("hgConvert", enteredMainTime); return 0; }