/* snpFinalTable - create chrN_snp tables from chrN_snpTmp tables. */ /* Also create exceptions table from exceptions files. */ /* Get chroms from UCSC chromInfo. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* Reorder columns. */ /* Add bin. */ /* Add 'rs' in front of snp_id. */ /* Orientation --> strandStrings. */ /* Add score for BED format (always 0). */ /* Expand validation_status. */ /* Drop refUCSCReverseComp. */ /* Not currently using outputFileHandle. */ #include "common.h" #include "dystring.h" #include "hdb.h" #include "jksql.h" #include "snp125.h" #include "snp125Exceptions.h" static char *snpDb = NULL; static int version = 0; FILE *outputFileHandle = NULL; char *strandStrings[] = { "+", "-", }; /* these are described in b125_mapping.doc */ /* Also snpFixed.LocTypeCode */ char *locTypeStrings[] = { "unknown", "range", "exact", "between", "rangeInsertion", "rangeSubstitution", "rangeDeletion", }; char *exceptionTables[] = { "snpCheckAlleles", "snpCheckClassAndObserved", "snpExpandAllele", "snpLocType", }; void usage() /* Explain usage and exit. */ { errAbort( "snpFinalTable - create chrN_snp tables from chrN_snpTmp tables.\n" "Also create exceptions table from exceptions files.\n" "usage:\n" " snpFinalTable snpDb version\n"); } char *validString(int validCode) /* These are from snpFixed.SnpValidationCode */ { switch (validCode) { case 0: return "unknown"; case 1: return "by-cluster"; case 2: return "by-frequency"; case 3: return "by-cluster,by-frequency"; case 4: return "by-submitter"; case 5: return "by-submitter,by-cluster"; case 6: return "by-submitter,by-frequency"; case 7: return "by-submitter"; case 8: return "by-2hit-2allele"; case 9: return "by-2hit-2allele,by-cluster"; case 10: return "by-2hit-2allele,by-frequency"; case 11: return "by-2hit-2allele,by-frequency,by-cluster"; case 12: return "by-2hit-2allele,by-submitter"; case 13: return "by-2hit-2allele,by-submitter,by-cluster"; case 14: return "by-2hit-2allele,by-submitter,by-frequency"; case 15: return "by-2hit-2allele,by-submitter,by-frequency,by-cluster"; case 16: return "by-hapmap"; case 17: return "by-hapmap,by-cluster"; case 18: return "by-hapmap,by-frequency"; case 19: return "by-hapmap,by-frequency,by-cluster"; case 20: return "by-hapmap,by-submitter"; case 21: return "by-hapmap,by-submitter,by-cluster"; case 22: return "by-hapmap,by-submitter,by-frequency"; case 23: return "by-hapmap,by-submitter,by-frequency,by-cluster"; case 24: return "by-hapmap,by-2hit-2allele"; case 25: return "by-hapmap,by-2hit-2allele,by-cluster"; case 26: return "by-hapmap,by-2hit-2allele,by-frequency"; case 27: return "by-hapmap,by-2hit-2allele,by-frequency,by-cluster"; case 28: return "by-hapmap,by-2hit-2allele,by-submitter"; case 29: return "by-hapmap,by-2hit-2allele,by-submitter,by-cluster"; case 30: return "by-hapmap,by-2hit-2allele,by-submitter,by-frequency"; case 31: return "by-hapmap,by-2hit-2allele,by-submitter,by-frequency,by-cluster"; default: return "unknown"; } } void processSnps(char *chromName, int version) /* read chrN_snpTmp */ /* write to chrN_snp.tab */ /* 0: snp_id int(11) */ /* 1: chromStart int(11) */ /* 2: chromEnd int(11) */ /* 3: loc_type tinyint(4) */ /* 4: class varchar(255) */ /* 5: orientation tinyint(4) */ /* 6: molType varchar(255) */ /* 7: fxn_class varchar(255) */ /* 8: validation_status tinyint(4) */ /* 9: avHet float */ /* 10: avHetSE float */ /* 11: allele blob */ /* 12: refUCSC blob */ /* 13: refUCSCReverseComp blob */ /* 14: observed blob */ /* 15: weight int */ { char tableName[64]; char fileName[64]; char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; int start = 0; int end = 0; int score = 0; int bin = 0; char *s; FILE *f; char *observedString = NULL; char *molTypeString = NULL; char *classString = NULL; char *alleleString = NULL; char *refUCSCString = NULL; char *functionString = NULL; safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); if (!hTableExists(tableName)) return; safef(fileName, ArraySize(fileName), "%s_snp%d.tab", chromName, version); f = mustOpen(fileName, "w"); sqlSafef(query, sizeof(query), "select * from %s", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { start = sqlUnsigned(row[1]); end = sqlUnsigned(row[2]); bin = hFindBin(start, end); /* 16 things to print. Start with 4x4. */ fprintf(f, "%d\t%s\t%d\t%d\trs%s\t", bin, chromName, start, end, row[0]); alleleString = cloneString(row[11]); refUCSCString = cloneString(row[12]); fprintf(f, "%d\t%s\t%s\t%s\t", score, strandStrings[sqlUnsigned(row[5])], alleleString, refUCSCString); s = validString(sqlUnsigned(row[8])); observedString = cloneString(row[14]); molTypeString = cloneString(row[6]); classString = cloneString(row[4]); fprintf(f, "%s\t%s\t%s\t%s\t", observedString, molTypeString, classString, s); functionString = cloneString(row[7]); fprintf(f, "%s\t%s\t%s\t%s\t", row[9], row[10], functionString, locTypeStrings[sqlUnsigned(row[3])]); fprintf(f, "%s\n", row[15]); } sqlFreeResult(&sr); hFreeConn(&conn); carefulClose(&f); } void loadDatabase(char *chromName, int version) { struct sqlConnection *conn = hAllocConn(); char fileName[64]; char tableName[64]; FILE *f; safef(tableName, ArraySize(tableName), "%s_snp%d", chromName, version); safef(fileName, ArraySize(fileName), "%s_snp%d.tab", chromName, version); snp125TableCreate(conn, tableName); f = mustOpen(fileName, "r"); hgLoadTabFile(conn, ".", tableName, &f); hFreeConn(&conn); } void doExceptions(int version) /* write snpExceptions table */ { struct sqlConnection *conn = hAllocConn(); int i = 0; FILE *exceptionFileHandle = NULL; char tableName[64]; char fileName[64]; safef(fileName, ArraySize(fileName), "snp%dExceptions", version); snp125ExceptionsTableCreate(conn); for (i = 0; i < ArraySize(exceptionTables); i++) { safef(tableName, ArraySize(tableName), "%s.tab", exceptionTables[i]); exceptionFileHandle = mustOpen(tableName, "r"); hgLoadNamedTabFile(conn, ".", fileName, exceptionTables[i], &exceptionFileHandle); } hFreeConn(&conn); } int main(int argc, char *argv[]) /* Query all chrN_snpTmp tables; write to snp.tab. */ { struct slName *chromList, *chromPtr; char tableName[64]; char fileName[64]; if (argc != 3) usage(); snpDb = argv[1]; hSetDb(snpDb); chromList = hAllChromNamesDb(snpDb); version = atoi(argv[2]); safef(fileName, ArraySize(fileName), "snp%d.tab", version); outputFileHandle = mustOpen(fileName, "w"); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; verbose(1, "chrom = %s\n", chromPtr->name); processSnps(chromPtr->name, version); } carefulClose(&outputFileHandle); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; loadDatabase(chromPtr->name, version); } doExceptions(version); return 0; }