b1c2fdec9a31078a56333427830a760757d22a51 angie Fri Jun 17 14:44:44 2016 -0700 Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216 diff --git src/hg/lib/hAnno.c src/hg/lib/hAnno.c index 71bdc5e..847d03f 100644 --- src/hg/lib/hAnno.c +++ src/hg/lib/hAnno.c @@ -1,373 +1,410 @@ /* hAnno -- helpers for creating anno{Streamers,Grators,Formatters,Queries} */ #include "common.h" #include "hAnno.h" #include "basicBed.h" #include "bigGenePred.h" #include "customTrack.h" #include "factorSource.h" #include "grp.h" #include "hdb.h" #include "hubConnect.h" #include "hui.h" #include "jksql.h" #include "pgSnp.h" #include "trackHub.h" #include "vcf.h" #include "annoGratorQuery.h" #include "annoGratorGpVar.h" #include "annoStreamBigBed.h" #include "annoStreamBigWig.h" #include "annoStreamDb.h" #include "annoStreamDbFactorSource.h" #include "annoStreamTab.h" #include "annoStreamVcf.h" #include "annoStreamTabix.h" #include "annoStreamWig.h" #include "annoGrateWigDb.h" #include "annoFormatTab.h" #include "annoFormatVep.h" //#*** duplicated in hgVarAnnoGrator and annoGratorTester struct annoAssembly *hAnnoGetAssembly(char *db) /* Make annoAssembly for db. */ { static struct annoAssembly *aa = NULL; if (aa == NULL) { if (trackHubDatabase(db)) { struct trackHubGenome *thg = trackHubGetGenome(db); char *url = thg->twoBitPath; aa = annoAssemblyNew(db, url); } else { char *nibOrTwoBitDir = hDbDbNibPath(db); if (nibOrTwoBitDir == NULL) errAbort("Can't find .2bit for db '%s'", db); char twoBitPath[HDB_MAX_PATH_STRING]; safef(twoBitPath, sizeof(twoBitPath), "%s/%s.2bit", nibOrTwoBitDir, db); char *path = hReplaceGbdb(twoBitPath); aa = annoAssemblyNew(db, path); freeMem(path); } } return aa; } static boolean columnsMatch(struct asObject *asObj, struct sqlFieldInfo *fieldList) /* Return TRUE if asObj's column names match the given SQL fields. */ { if (asObj == NULL) return FALSE; struct sqlFieldInfo *firstRealField = fieldList; if (sameString("bin", fieldList->field) && differentString("bin", asObj->columnList->name)) firstRealField = fieldList->next; boolean columnsMatch = TRUE; struct sqlFieldInfo *field = firstRealField; struct asColumn *asCol = asObj->columnList; for (; field != NULL && asCol != NULL; field = field->next, asCol = asCol->next) { if (!sameString(field->field, asCol->name)) { columnsMatch = FALSE; break; } } if (field != NULL || asCol != NULL) columnsMatch = FALSE; return columnsMatch; } static struct asObject *asObjectFromFields(char *name, struct sqlFieldInfo *fieldList, boolean skipBin) /* Make autoSql text from SQL fields and pass it to asParse. */ { struct dyString *dy = dyStringCreate("table %s\n" "\"Column names grabbed from mysql\"\n" " (\n", name); struct sqlFieldInfo *field; for (field = fieldList; field != NULL; field = field->next) { if (skipBin && field == fieldList && sameString("bin", field->field)) continue; char *sqlType = field->type; // hg19.wgEncodeOpenChromSynthGm12878Pk.pValue has sql type "float unsigned", // and I'd rather pretend it's just a float than work unsigned floats into autoSql. if (sameString(sqlType, "float unsigned")) sqlType = "float"; char *asType = asTypeNameFromSqlType(sqlType); if (asType == NULL) errAbort("No asTypeInfo for sql type '%s'!", field->type); dyStringPrintf(dy, " %s %s;\t\"\"\n", asType, field->field); } dyStringAppend(dy, " )\n"); return asParseText(dy->string); } struct asObject *hAnnoGetAutoSqlForDbTable(char *db, char *table, struct trackDb *tdb, boolean skipBin) /* Get autoSql for db.dbTable from tdb and/or db.tableDescriptions; * if it doesn't match columns, make one up from db.table sql fields. * Some subtleties are lost in translation from .as to .sql, that's why * we try tdb & db.tableDescriptions first. But ultimately we need to return * an asObj whose columns match all fields of the table. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlFieldInfo *fieldList = sqlFieldInfoGet(conn, table); struct asObject *asObj = NULL; if (tdb != NULL) asObj = asForTdb(conn, tdb); if (asObj == NULL) asObj = asFromTableDescriptions(conn, table); hFreeConn(&conn); if (columnsMatch(asObj, fieldList)) return asObj; else { // Special case for pgSnp, which includes its bin column in autoSql... struct asObject *pgSnpAsO = pgSnpAsObj(); if (columnsMatch(pgSnpAsO, fieldList)) return pgSnpAsO; return asObjectFromFields(table, fieldList, skipBin); } } static char *getBigDataFileName(char *db, struct trackDb *tdb, char *selTable, char *chrom) /* Get fileName from bigBed/bigWig/BAM/VCF database table, or bigDataUrl from custom track. */ { char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (isNotEmpty(bigDataUrl)) { return bigDataUrl; } else { struct sqlConnection *conn = hAllocConn(db); char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, selTable, chrom); hFreeConn(&conn); return fileOrUrl; } } static boolean dbTableMatchesAutoSql(char *db, char *table, struct asObject *asObj) /* Return true if table exists and its fields match the columns of asObj. */ { boolean matches = FALSE; struct sqlConnection *conn = hAllocConn(db); if (sqlTableExists(conn, table)) { struct sqlFieldInfo *fieldList = sqlFieldInfoGet(conn, table); matches = columnsMatch(asObj, fieldList); } hFreeConn(&conn); return matches; } +struct annoStreamer *hAnnoStreamerFromBigFileUrl(char *fileOrUrl, struct annoAssembly *assembly, + int maxOutRows, char *type) +/* Determine what kind of big data file/url we have and make streamer for it. + * If type is NULL, this will determine type using custom track type or file suffix. */ +{ +struct annoStreamer *streamer = NULL; +if (isEmpty(type)) + type = customTrackTypeFromBigFile(fileOrUrl); +if (type == NULL) + { + if (endsWith(fileOrUrl, "pgSnp") || endsWith(fileOrUrl, "pgsnp") || + endsWith(fileOrUrl, "pgSnp.gz") || endsWith(fileOrUrl, "pgsnp.gz") || + endsWith(fileOrUrl, "bed") || endsWith(fileOrUrl, "bed.gz")) + { + type = "pgSnp"; + } + else + errAbort("Unrecognized bigData type of file or url '%s'", fileOrUrl); + } +if (sameString(type, "bigBed") || sameString("bigGenePred", type)) + streamer = annoStreamBigBedNew(fileOrUrl, assembly, maxOutRows); +else if (sameString(type, "vcfTabix")) + streamer = annoStreamVcfNew(fileOrUrl, TRUE, assembly, maxOutRows); +else if (sameString(type, "vcf")) + streamer = annoStreamVcfNew(fileOrUrl, FALSE, assembly, maxOutRows); +else if (sameString(type, "bigWig")) + streamer = annoStreamBigWigNew(fileOrUrl, assembly); +else if (sameString(type, "pgSnp")) + streamer = annoStreamTabNew(fileOrUrl, assembly, pgSnpFileAsObj()); +else if (sameString(type, "bam")) + errAbort("Sorry, BAM is not yet supported"); +else + errAbort("Unrecognized bigData type %s of file or url '%s'", type, fileOrUrl); +return streamer; +} + struct annoStreamer *hAnnoStreamerFromTrackDb(struct annoAssembly *assembly, char *selTable, struct trackDb *tdb, char *chrom, int maxOutRows, struct jsonElement *config) /* Figure out the source and type of data and make an annoStreamer. */ { struct annoStreamer *streamer = NULL; char *db = assembly->name, *dataDb = db, *dbTable = selTable; if (chrom == NULL) chrom = hDefaultChrom(db); if (isCustomTrack(selTable)) { dbTable = trackDbSetting(tdb, "dbTableName"); if (dbTable != NULL) // This is really a database table, not a bigDataUrl CT. dataDb = CUSTOM_TRASH; } if (startsWithWord("wig", tdb->type)) streamer = annoStreamWigDbNew(dataDb, dbTable, assembly, maxOutRows); else if (sameString("longTabix", tdb->type)) { char *fileOrUrl = getBigDataFileName(dataDb, tdb, selTable, chrom); streamer = annoStreamTabixNew(fileOrUrl, assembly, maxOutRows); } else if (sameString("vcfTabix", tdb->type)) { char *fileOrUrl = getBigDataFileName(dataDb, tdb, selTable, chrom); streamer = annoStreamVcfNew(fileOrUrl, TRUE, assembly, maxOutRows); } else if (sameString("vcf", tdb->type)) { char *fileOrUrl = getBigDataFileName(dataDb, tdb, dbTable, chrom); streamer = annoStreamVcfNew(fileOrUrl, FALSE, assembly, maxOutRows); } else if (sameString("bam", tdb->type)) { warn("Sorry, BAM is not yet supported"); } else if (startsWith("bigBed", tdb->type) || sameString("bigGenePred", tdb->type)) { char *fileOrUrl = getBigDataFileName(dataDb, tdb, selTable, chrom); streamer = annoStreamBigBedNew(fileOrUrl, assembly, maxOutRows); } else if (startsWith("bigWig", tdb->type)) { char *fileOrUrl = getBigDataFileName(dataDb, tdb, selTable, chrom); streamer = annoStreamBigWigNew(fileOrUrl, assembly); //#*** no maxOutRows support } else if (sameString("factorSource", tdb->type) && dbTableMatchesAutoSql(dataDb, tdb->table, factorSourceAsObj())) { char *sourceTable = trackDbSetting(tdb, "sourceTable"); char *inputsTable = trackDbSetting(tdb, "inputTrackTable"); streamer = annoStreamDbFactorSourceNew(dataDb, tdb->track, sourceTable, inputsTable, assembly, maxOutRows); } else if (trackHubDatabase(db)) errAbort("Unrecognized type '%s' for hub track '%s'", tdb->type, tdb->track); if (streamer == NULL) { streamer = annoStreamDbNew(dataDb, dbTable, assembly, maxOutRows, config); } return streamer; } struct annoGrator *hAnnoGratorFromBigFileUrl(char *fileOrUrl, struct annoAssembly *assembly, int maxOutRows, enum annoGratorOverlap overlapRule) /* Determine what kind of big data file/url we have and make streamer & grator for it. */ { struct annoStreamer *streamer = NULL; struct annoGrator *grator = NULL; char *type = customTrackTypeFromBigFile(fileOrUrl); if (sameString(type, "bigBed") || sameString("bigGenePred", type)) streamer = annoStreamBigBedNew(fileOrUrl, assembly, maxOutRows); else if (sameString(type, "vcfTabix")) streamer = annoStreamVcfNew(fileOrUrl, TRUE, assembly, maxOutRows); else if (sameString(type, "bigWig")) grator = annoGrateBigWigNew(fileOrUrl, assembly, agwmAverage); else if (sameString(type, "bam")) errAbort("Sorry, BAM is not yet supported"); else errAbort("Unrecognized bigData type %s of file or url '%s'", type, fileOrUrl); if (grator == NULL) grator = annoGratorNew(streamer); grator->setOverlapRule(grator, overlapRule); return grator; } struct annoGrator *hAnnoGratorFromTrackDb(struct annoAssembly *assembly, char *selTable, struct trackDb *tdb, char *chrom, int maxOutRows, struct asObject *primaryAsObj, enum annoGratorOverlap overlapRule, struct jsonElement *config) /* Figure out the source and type of data, make an annoStreamer & wrap in annoGrator. * If not NULL, primaryAsObj is used to determine whether we can make an annoGratorGpVar. */ { struct annoGrator *grator = NULL; boolean primaryIsVariants = (primaryAsObj != NULL && (asObjectsMatch(primaryAsObj, pgSnpAsObj()) || + asObjectsMatch(primaryAsObj, pgSnpFileAsObj()) || asObjectsMatch(primaryAsObj, vcfAsObj()))); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl != NULL) { if (primaryIsVariants && sameString("bigGenePred", tdb->type)) { struct annoStreamer *streamer = annoStreamBigBedNew(bigDataUrl, assembly, maxOutRows); grator = annoGratorGpVarNew(streamer); } else grator = hAnnoGratorFromBigFileUrl(bigDataUrl, assembly, maxOutRows, overlapRule); } else if (startsWithWord("wig", tdb->type)) { char *dataDb = assembly->name; char *dbTable = selTable; if (isCustomTrack(selTable)) { dbTable = trackDbSetting(tdb, "dbTableName"); if (dbTable != NULL) // This is really a database table, not a bigDataUrl CT. dataDb = CUSTOM_TRASH; } grator = annoGrateWigDbNew(dataDb, dbTable, assembly, agwmAverage, maxOutRows); } else if (startsWithWord("bigWig", tdb->type)) { char *fileOrUrl = getBigDataFileName(assembly->name, tdb, tdb->table, chrom); grator = annoGrateBigWigNew(fileOrUrl, assembly, agwmAverage); } else { struct annoStreamer *streamer = hAnnoStreamerFromTrackDb(assembly, selTable, tdb, chrom, maxOutRows, config); if (primaryIsVariants && (asColumnNamesMatchFirstN(streamer->asObj, genePredAsObj(), 10) || asObjectsMatch(streamer->asObj, bigGenePredAsObj()))) grator = annoGratorGpVarNew(streamer); else grator = annoGratorNew(streamer); } grator->setOverlapRule(grator, overlapRule); return grator; } static struct asObject *getAutoSqlForType(char *db, char *chrom, struct trackDb *tdb) /* Return an asObject for tdb->type if recognized as a hub or custom track type. */ { struct asObject * asObj = NULL; if (startsWith("wig", tdb->type) || startsWith("bigWig", tdb->type)) asObj = annoStreamBigWigAsObject(); else if (startsWith("vcf", tdb->type)) asObj = vcfAsObj(); else if (startsWith("bigBed", tdb->type) || sameString("bigGenePred", tdb->type)) { char *fileOrUrl = getBigDataFileName(db, tdb, tdb->table, chrom); asObj = bigBedFileAsObjOrDefault(fileOrUrl); } else if (sameString("pgSnp", tdb->type)) asObj = pgSnpAsObj(); else if (sameString("bam", tdb->type) || sameString("maf", tdb->type)) warn("Sorry, %s is not yet supported", tdb->type); else if (startsWithWord("bed", tdb->type) && !strchr(tdb->type, '+')) { // BED with no + fields; parse bed field count out of type line. int bedFieldCount = 3; char typeCopy[PATH_LEN]; safecpy(typeCopy, sizeof(typeCopy), tdb->type); char *words[8]; int wordCount = chopLine(typeCopy, words); if (wordCount > 1) bedFieldCount = atoi(words[1]); asObj = asParseText(bedAsDef(bedFieldCount, bedFieldCount)); } else if (sameString("factorSource", tdb->type) && dbTableMatchesAutoSql(db, tdb->table, factorSourceAsObj())) { asObj = annoStreamDbFactorSourceAsObj(); } return asObj; } struct asObject *hAnnoGetAutoSqlForTdb(char *db, char *chrom, struct trackDb *tdb) /* If possible, return the asObj that a streamer for this track would use, otherwise NULL. */ { struct asObject *asObj = getAutoSqlForType(db, chrom, tdb); if (!asObj && !isHubTrack(tdb->track)) { // If none of the above, it must be a database table; deduce autoSql from sql fields. char *dataDb = db, *dbTable = tdb->table; if (isCustomTrack(tdb->track)) { dbTable = trackDbSetting(tdb, "dbTableName"); if (dbTable) dataDb = CUSTOM_TRASH; else return NULL; } char maybeSplitTable[HDB_MAX_TABLE_STRING]; if (!hFindSplitTable(dataDb, chrom, dbTable, maybeSplitTable, NULL)) errAbort("hAnnoGetAutoSqlForTdb: can't find table (or split table) for '%s.%s'", dataDb, dbTable); asObj = hAnnoGetAutoSqlForDbTable(dataDb, maybeSplitTable, tdb, TRUE); } return asObj; }