4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/snp/snpLoad/snpSNP.c src/hg/snp/snpLoad/snpSNP.c index 3a895c4..afefcd2 100644 --- src/hg/snp/snpLoad/snpSNP.c +++ src/hg/snp/snpLoad/snpSNP.c @@ -1,222 +1,222 @@ /* snpSNP - ninth step in dbSNP processing. * Read the chrN_snpTmp tables into memory. * Do lookups into SNP for validation status and heterozygosity. * Could combine this with earlier step snpClassAndObserved, which also uses the SNP table. * Report if missing. * Use UCSC chromInfo. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "hdb.h" struct snpData { int validation_status; char *avHet; char *avHetSE; }; static char *snpDb = NULL; FILE *errorFileHandle = NULL; static struct hash *snpDataHash = NULL; void usage() /* Explain usage and exit. */ { errAbort( "snpSNP - lookup validation status and heterozygosity in SNP\n" "recreate chrN_snpTmp\n" "usage:\n" " snpSNP snpDb \n"); } void readSNP() /* get validation status and heterozygosity from SNP table */ /* store in global snpDataHash */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; int validInt = 0; struct snpData *sel; /* could increase the default size */ snpDataHash = newHash(16); sqlSafef(query, sizeof(query), "select snp_id, validation_status, avg_heterozygosity, het_se from SNP"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { validInt = sqlUnsigned(row[1]); if (validInt > 31) { fprintf(errorFileHandle, "unexpected validation_status %d for snp_id %s\n", validInt, row[0]); validInt = 0; } AllocVar(sel); sel->validation_status = validInt; sel->avHet = cloneString(row[2]); sel->avHetSE = cloneString(row[3]); hashAdd(snpDataHash, cloneString(row[0]), sel); } sqlFreeResult(&sr); hFreeConn(&conn); } void processSnps(char *chromName) /* read through chrN_snpTmp tables */ /* lookup into snpDataHash */ /* write to output file */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; char tableName[64]; char fileName[64]; FILE *f; struct snpData *sel = NULL; safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName); f = mustOpen(fileName, "w"); sqlSafef(query, sizeof(query), "select snp_id, chromStart, chromEnd, loc_type, class, orientation, fxn_class, " "allele, refUCSC, refUCSCReverseComp, observed, weight from %s ", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { sel = hashFindVal(snpDataHash, row[0]); if (sel == NULL) { fprintf(f, "%s\t%s\t%s\t%s\t", row[0], row[1], row[2], row[3]); fprintf(f, "%s\t%s\t%s\t", row[4], row[5], row[6]); fprintf(f, "0\t0.0\t0.0\t"); fprintf(f, "%s\t%s\t%s\t%s\t%s\n", row[7], row[8], row[9], row[10], row[11]); fprintf(errorFileHandle, "no match for snp_id %s\n", row[0]); continue; } /* check here for avHet < 0 */ /* check here for class = "single" and isBiallelic(observed) and avHet <= .5 */ /* check here for class = "single" and isTriallelic(observed) and avHet <= .3333 */ /* check here for class = "single" and isQuadallelic(observed) and avHet <= .25 */ fprintf(f, "%s\t%s\t%s\t%s\t", row[0], row[1], row[2], row[3]); fprintf(f, "%s\t%s\t%s\t", row[4], row[5], row[6]); fprintf(f, "%d\t%s\t%s\t", sel->validation_status, sel->avHet, sel->avHetSE); fprintf(f, "%s\t%s\t%s\t%s\t%s\n", row[7], row[8], row[9], row[10], row[11]); } sqlFreeResult(&sr); hFreeConn(&conn); carefulClose(&f); } void recreateDatabaseTable(char *chromName) /* create a new chrN_snpTmp table with new definition */ { struct sqlConnection *conn = hAllocConn(); char tableName[64]; char *createString = "CREATE TABLE %s (\n" " snp_id int(11) not null,\n" " chromStart int(11) not null,\n" " chromEnd int(11) not null,\n" " loc_type tinyint(4) not null,\n" " class varchar(255) not null,\n" " orientation tinyint(4) not null,\n" " fxn_class varchar(255) not null,\n" " validation_status tinyint(4) not null,\n" " avHet float not null, \n" " avHetSE float not null, \n" " allele blob,\n" " refUCSC blob,\n" " refUCSCReverseComp blob,\n" " observed blob,\n" " weight int\n" ");\n"; struct dyString *dy = newDyString(1024); safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); sqlDyStringPrintf(dy, createString, tableName); sqlRemakeTable(conn, tableName, dy->string); dyStringFree(&dy); hFreeConn(&conn); } void loadDatabase(char *chromName) /* load one table into database */ { FILE *f; struct sqlConnection *conn = hAllocConn(); char tableName[64], fileName[64]; safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName); f = mustOpen(fileName, "r"); /* hgLoadTabFile closes the file handle */ hgLoadTabFile(conn, ".", tableName, &f); hFreeConn(&conn); } 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; }