int main(int argc, char *argv[]) /* hash subsnp_class and var_str from UniVariation */ /* read SNP for univar_id, lookup into univarHash */ /* store univarHash elements in snpHash */ /* read through chrN_snpTmp, rewrite with extensions to individual chrom tables */ { struct slName *chromList, *chromPtr; char tableName[64]; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); /* check for necessary tables */ if(!hTableExistsDb(snpDb, "SNP")) errAbort("missing SNP table"); if(!hTableExistsDb(snpDb, "UniVariation")) errAbort("missing UniVariation table"); chromList = hAllChromNamesDb(snpDb); errorFileHandle = mustOpen("snpClassAndObserved.errors", "w"); univarHash = getUnivarHash(); snpHash = getSNPHash(); 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); } carefulClose(&errorFileHandle); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; recreateDatabaseTable(chromPtr->name); verbose(1, "loading chrom = %s\n", chromPtr->name); loadDatabase(chromPtr->name); } return 0; }
int main(int argc, char *argv[]) /* read chrN_snpTmp, lookup in snpFasta, rewrite to individual chrom tables */ { struct slName *chromList, *chromPtr; char tableName[64]; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); chromList = hAllChromNamesDb(snpDb); if (chromList == NULL) { verbose(1, "couldn't get chrom info\n"); return 1; } errorFileHandle = mustOpen("snpSNP.errors", "w"); /* read into global hash */ verbose(1, "reading SNP table into hash...\n"); readSNP(); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; verbose(1, "processing chrom = %s\n", chromPtr->name); processSnps(chromPtr->name); } carefulClose(&errorFileHandle); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; recreateDatabaseTable(chromPtr->name); verbose(1, "loading chrom = %s\n", chromPtr->name); loadDatabase(chromPtr->name); } return 0; }
int main(int argc, char *argv[]) /* Read chromInfo into hash. */ /* Read ContigLocusIdCondense into hash. */ /* Recreate chrN_snpTmp, adding fxn_classes. */ { struct slName *chromList, *chromPtr; char tableName[64]; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); chromList = hAllChromNamesDb(snpDb); /* check for needed tables */ if(!hTableExistsDb(snpDb, "ContigLocusIdCondense")) errAbort("no ContigLocusIdCondense table in %s\n", snpDb); if(!hTableExistsDb(snpDb, "chromInfo")) errAbort("no chromInfo table in %s\n", snpDb); functionHash = createFunctionHash(); 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); addFunction(chromPtr->name); } for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; verbose(1, "loading chrom = %s\n", chromPtr->name); recreateDatabaseTable(chromPtr->name); loadDatabase(chromPtr->name); } return 0; }
int main(int argc, char *argv[]) { struct slName *chromList, *chromPtr; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); outputFileHandle = mustOpen("snpCheckFunction.out", "w"); getGeneHash(); getContigHash(); chromList = hAllChromNamesDb(snpDb); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) scanGenes(chromPtr->name); carefulClose(&outputFileHandle); return 0; }
int main(int argc, char *argv[]) /* hash snpFasta, read through chrN_snpTmp, rewrite with extensions to individual chrom tables */ { struct slName *chromList, *chromPtr; char tableName[64]; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); chromList = hAllChromNamesDb(snpDb); errorFileHandle = mustOpen("snpMoltype.errors", "w"); multiFastaHash = readFasta("chrMulti"); 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); chromFastaHash = readFasta(chromPtr->name); processSnps(chromPtr->name); } carefulClose(&errorFileHandle); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; recreateDatabaseTable(chromPtr->name); verbose(1, "loading chrom = %s\n", chromPtr->name); loadDatabase(chromPtr->name); } return 0; }