void doPrintSelectedFields() /* Actually produce selected field output as text stream. */ { char *db = cartString(cart, hgtaDatabase); char *table = cartString(cart, hgtaTable); char *varPrefix = checkVarPrefix(); int varPrefixSize = strlen(varPrefix); struct hashEl *varList = NULL, *var; struct slName *fieldList = NULL, *field; textOpen(); /* Gather together field list for primary and linked tables from cart. */ varList = cartFindPrefix(cart, varPrefix); for (var = varList; var != NULL; var = var->next) { if (!sameString(var->val, "0")) { field = slNameNew(var->name + varPrefixSize); if (primaryOrLinked(field->name)) slAddHead(&fieldList, field); } } if (fieldList == NULL) errAbort("Please go back and select at least one field"); slReverse(&fieldList); /* Do output. */ tabOutSelectedFields(db, table, NULL, fieldList); /* Clean up. */ slFreeList(&fieldList); hashElFreeList(&varList); }
void doGenePredPal(struct sqlConnection *conn) /* Output genePred protein alignment. */ { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) { sendParamsToGalaxy(hgtaDoPalOut, "submit"); return; } /* get rid of pesky cookies that would bring us back here */ cartRemove(cart, hgtaDoPal); cartRemove(cart, hgtaDoPalOut); if (anyIntersection() && intersectionIsBpWise()) errAbort("Can't do CDS FASTA output when bit-wise intersection is on. " "Please go back and select another output type, or clear the intersection."); checkNoGenomeDisabled(database, curTable); struct lm *lm = lmInit(64*1024); int fieldCount; struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(), lm, &fieldCount); //lmCleanup(&lm); textOpen(); int outCount = palOutPredsInBeds(conn, cart, bedList, curTable); /* Do some error diagnostics for user. */ if (outCount == 0) explainWhyNoResults(NULL); }
void doTest(struct sqlConnection *conn) /* Put up a page to see what happens. */ { char *s = NULL; textOpen(); hPrintf("Doing test!\n"); s = filterClause("hg18", "knownGene", "chrX", NULL); if (s != NULL) hPrintf("%s\n", s); else hPrintf("%p\n", s); }
void doOutGff(char *table, struct sqlConnection *conn, boolean outputGtf) /* Save as GFF/GTF. */ { struct hTableInfo *hti = getHti(database, table, conn); struct bed *bedList; struct hash *chromHash = NULL; struct slName *exonFramesList = NULL; char source[HDB_MAX_TABLE_STRING]; int itemCount; struct region *region, *regionList = getRegions(); textOpen(); int efIdx = -1; safef(source, sizeof(source), "%s_%s", database, table); if (conn) { boolean simpleTableExists = sqlTableExists(conn, table); // simpleTable means not split table, not custom track // However it still can include bbi table with bam fileName path if (simpleTableExists) // no tables having exonFrames are split tables anyway efIdx = sqlFieldIndex(conn, table, "exonFrames"); itemCount = 0; int regionCount = slCount(regionList); // regionList can have many thousands of items e.g. rheMac3 has 34000 chroms! // This regionCount threshold should be just above the # chroms in the latest human assembly if (simpleTableExists && (regionCount > 500)) { chromHash = makeChromHashForTable(conn, table); } } // Note: code could be added here to extract exonFrames from bigGenePred // Process each region for (region = regionList; region != NULL; region = region->next) { if (chromHash && (!hashFindVal(chromHash, region->chrom))) continue; struct lm *lm = lmInit(64*1024); int fieldCount; bedList = cookedBedList(conn, table, region, lm, &fieldCount); // Use exonFrames field if available for better accuracy instead of calculating from coordinates if (efIdx != -1) exonFramesList = getExonFrames(table, conn, bedList); itemCount += bedToGffLines(bedList, exonFramesList, hti, fieldCount, source, outputGtf); lmCleanup(&lm); } if (itemCount == 0) hPrintf(NO_RESULTS); }
void doGenomicDna(struct sqlConnection *conn) /* Get genomic sequence (UI has already told us how). */ { struct region *region, *regionList = getRegions(); struct hTableInfo *hti = getHti(database, curTable, conn); int fieldCount; textOpen(); int resultCount = 0; for (region = regionList; region != NULL; region = region->next) { struct lm *lm = lmInit(64*1024); struct bed *bedList = cookedBedList(conn, curTable, region, lm, &fieldCount); if (bedList != NULL) resultCount += hgSeqBed(database, hti, bedList); lmCleanup(&lm); } if (!resultCount) hPrintf(NO_RESULTS); }
void doHalMaf(struct trackDb *parentTrack, char *table, struct sqlConnection *conn) /* Output regions as MAF. maf tables look bed-like enough for * cookedBedsOnRegions to handle intersections. */ { #ifdef USE_HAL struct region *region = NULL, *regionList = getRegions(); struct trackDb *tdb; if ((tdb = findTrackDb(parentTrack, table)) == NULL) errAbort("cannot find track named %s under %s\n", table, parentTrack->table); char *fileName = trackDbSetting(tdb, "bigDataUrl"); char *otherSpecies = trackDbSetting(tdb, "otherSpecies"); int handle = halOpenLOD(fileName); struct hal_species_t *speciesList = halGetSpecies(handle); for(; speciesList; speciesList = speciesList->next) { if (sameString(speciesList->name, otherSpecies)) break; } if (speciesList == NULL) errAbort("cannot find species %s in hal file %s\n", otherSpecies, fileName); speciesList->next = NULL; textOpen(); for (region = regionList; region != NULL; region = region->next) { halGetMAF(stdout, handle, speciesList, trackHubSkipHubName(database), region->chrom, region->start, region->end, FALSE); } #else // USE_HAL errAbort("hgTables not compiled with HAL support."); #endif // USE_HAL }
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; }
static void doOutWig(struct trackDb *track, char *table, struct sqlConnection *conn, enum wigOutputType wigOutType) { struct region *regionList = getRegions(), *region; int maxOut = 0, outCount, curOut = 0; char *shortLabel = table, *longLabel = table; if (track == NULL) errAbort("Sorry, can't find necessary track information for %s. " "If you reached this page by selecting \"All tables\" as the " "group, please go back and select the same table via a regular " "track group if possible.", table); maxOut = bigFileMaxOutput(); if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE)) fputs("#", stdout); else textOpen(); if (track != NULL) { if (!sameString(track->table, table) && track->subtracks != NULL) { struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks); struct slRef *tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *tdb = tdbRef->val; if (sameString(tdb->table, table)) { track = tdb; break; } } slFreeList(&tdbRefList); } shortLabel = track->shortLabel; longLabel = track->longLabel; } wigDataHeader(shortLabel, longLabel, NULL, wigOutType); for (region = regionList; region != NULL; region = region->next) { int curMaxOut = maxOut - curOut; if (anySubtrackMerge(database, table)) outCount = mergedWigOutRegion(table, conn, region, curMaxOut, wigOutType); else if (startsWithWord("bedGraph", track->type)) outCount = bedGraphOutRegion(table, conn, region, curMaxOut, wigOutType); else if (startsWithWord("mathWig", track->type)) outCount = mathWigOutRegion(track, table, conn, region, curMaxOut, wigOutType); else if (startsWithWord("bigWig", track->type)) outCount = bigWigOutRegion(table, conn, region, curMaxOut, wigOutType); else outCount = wigOutRegion(table, conn, region, curMaxOut, wigOutType, NULL, 0); curOut += outCount; if (curOut >= maxOut) break; } if (curOut >= maxOut) errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", curOut); }
void doGenePredNongenomic(struct sqlConnection *conn, int typeIx) /* Get mrna or protein associated with selected genes. */ { /* Note this does do the whole genome at once rather than one * chromosome at a time, but that's ok because the gene prediction * tracks this serves are on the small side. */ char *typeWords[3]; char *table; struct lm *lm = lmInit(64*1024); int fieldCount; struct bed *bed, *bedList = cookedBedsOnRegions(conn, curTable, getRegions(), lm, &fieldCount); int typeWordCount; textOpen(); /* Figure out which table to use. */ if (isRefGeneTrack(curTable)) { if (typeIx == 1) /* Protein */ doRefGeneProteinSequence(conn, bedList); else doRefGeneMrnaSequence(conn, bedList); } else { char *dupType = cloneString(findTypeForTable(database, curTrack, curTable, ctLookupName)); typeWordCount = chopLine(dupType, typeWords); if (typeIx >= typeWordCount) internalErr(); table = typeWords[typeIx]; if (sqlTableExists(conn, table)) { struct sqlResult *sr; char **row; char query[256]; struct hash *hash = newHash(18); boolean gotResults = FALSE; /* Make hash of all id's passing filters. */ for (bed = bedList; bed != NULL; bed = bed->next) hashAdd(hash, bed->name, NULL); /* Scan through table, outputting ones that match. */ sqlSafef(query, sizeof(query), "select name, seq from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (hashLookup(hash, row[0])) { hPrintf(">%s\n", row[0]); writeSeqWithBreaks(stdout, row[1], strlen(row[1]), 60); gotResults = TRUE; } } sqlFreeResult(&sr); hashFree(&hash); if (!gotResults) hPrintf(NO_RESULTS); } else { internalErr(); } freez(&dupType); } lmCleanup(&lm); }