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/makeDb/outside/hgJaxQtl/hgJaxQtl.c src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c index e79acf5..acdadb1 100644 --- src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c +++ src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c @@ -1,251 +1,251 @@ /* hgJaxQtl - generate the bed file for jaxQTL3 table using the mySQL table jaxQtlRaw as input. */ /* 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 "hCommon.h" #include "hdb.h" void usage() /* Explain usage and exit. */ { errAbort( "hgJaxQtl - generate bed file for jaxQTL3 table \n" " using the table jaxQtlRaw as input\n" " output file is jaxQTL3.tab.\n" "usage:\n" " hgJaxQtl xxxx\n" " xxxx is the database\n" "example: hgJaxQtl mm5\n"); } /* get valid identNo from stsMapMouseNew table, return NULL if not found */ char *getStsId(struct sqlConnection *conn3, char *database, char *stsName) { char cond_str[255]; char *identNo; sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", stsName); identNo = sqlGetField(database, "stsMapMouseNew", "identNo", cond_str); if (identNo == NULL) { /* check to see if stsAlias has it */ sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s'", stsName); identNo = sqlGetField(database, "stsAlias", "identNo", cond_str); /* now make sure that stsMapMouseNew has an entry for this identNo */ if (identNo != NULL) { sqlSafefFrag(cond_str, sizeof(cond_str), "identNo=%s", identNo); identNo = sqlGetField(database, "stsMapMouseNew", "identNo", cond_str); } } return(identNo); } int main(int argc, char *argv[]) { struct sqlConnection *conn2, *conn3; char query2[256], query3[256]; struct sqlResult *sr2, *sr3; char **row2, **row3; FILE *outF; char *database; char *mgiID, *name, *description, *flank1, *flank2, *peak; char *peakChrom, *peakChromStart, *peakChromEnd; char *identNo; char *flanks[2]; char *qtlChrom, *qtlChromStart, *qtlChromEnd, *qtlName, *qtlScore, *qtlStrand; char *qtlThickStart, *qtlThickEnd, *qtlMarker, *qtlMgiID, *qtlDescription, *qtlCMScore; char *flankChrom, *flankChromStart, *flankChromEnd; char na[10] = {""}; char zero[10] = {"0"}; int qtlValid; int pos; int iFlank; int regionStart, regionEnd; if (argc != 2) usage(); database = argv[1]; /* the following fields are not available yet */ qtlScore = strdup("0"); qtlCMScore = strdup("0"); qtlStrand = strdup("."); outF = fopen("jaxQTL3.tab", "w"); conn2= hAllocConn(database); conn3= hAllocConn(database); sqlSafef(query2, sizeof query2, "select * from %s.jaxQtlRaw", database); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { mgiID = row2[0]; name = row2[1]; description = row2[2]; flank1 = row2[4]; flank2 = row2[5]; peak = row2[6]; flanks[0] = flank1; flanks[1] = flank2; qtlValid = 0; /* this record is not valid until we found something to put out */ qtlMgiID = mgiID; qtlName = name; qtlDescription = description; /* set default values */ qtlChrom = strdup(na); qtlChromStart = zero; qtlChromEnd = zero; qtlThickStart = zero; qtlThickEnd = zero; qtlMarker = na; regionStart = 0; regionEnd = 0; peakChrom = strdup(na); /* process peak marker */ if (!sameWord(peak, "")) { identNo = getStsId(conn3, database, peak); /* if getStsId result is not NULL, there exist an entry in stsMapMouseNew */ if (identNo != NULL) { qtlValid = 1; sqlSafef(query3, sizeof query3, "select * from %s.stsMapMouseNew where identNo=%s", database, identNo); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); /* only a few markers have mulitple answers, so just grab the first one */ peakChrom = strdup(row3[0]); peakChromStart = strdup(row3[1]); peakChromEnd = strdup(row3[2]); qtlChrom = peakChrom; qtlChromStart = peakChromStart; qtlChromEnd = peakChromEnd; qtlThickStart = peakChromStart; qtlThickEnd = peakChromEnd; qtlMarker = peak; qtlValid = 1; sqlFreeResult(&sr3); } } else { /* printf("%s has no peak marker.\n", name);fflush(stdout); */ } /* process flanking markers to get regionStart and regionEnd if both flanking markers exist */ if (!sameWord(flank1, "") && !sameWord(flank2,"")) { for (iFlank=0; iFlank<2; iFlank++) { if (flanks[iFlank] != NULL) { qtlValid = 1; identNo = getStsId(conn3, database, flanks[iFlank]); if (identNo != NULL) { sqlSafef(query3, sizeof query3, "select * from %s.stsMapMouseNew where identNo=%s",database,identNo); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); /* only a few has mulitple answers, so just grab the first one */ flankChrom = row3[0]; flankChromStart = row3[1]; flankChromEnd = row3[2]; /* if this QTL does not have a peak, use flanking marker's chrom */ if (sameWord(qtlChrom,na)) qtlChrom = strdup(flankChrom); pos = sqlUnsigned(flankChromStart); /* initialize regionStart if not initialized */ if (regionStart == 0) regionStart = pos; if (pos < regionStart) regionStart = pos; if (pos > regionEnd) regionEnd = pos; pos = sqlUnsigned(flankChromEnd); if (pos < regionStart) regionStart = pos; if (pos > regionEnd) regionEnd = pos; sqlFreeResult(&sr3); } } } } /* set regionStart/End for those entries that does not have flanking markers */ if ((regionStart == 0) && !sameWord(qtlChromStart, zero)) { regionStart = atoi(qtlChromStart); } if ((regionEnd == 0) && !sameWord(qtlChromEnd, zero)) { regionEnd = atoi(qtlChromEnd); } /* fix problematic cases that thickStart/thickEnd are outside regionStart/regionEnd */ pos = atoi(qtlThickStart); if (! ((pos >= regionStart) && (pos <= regionEnd))) { qtlThickStart = strdup(zero); } pos = atoi(qtlThickEnd); if (! ((pos >= regionStart) && (pos <= regionEnd))) { qtlThickEnd = strdup(zero); } /* the following logic was used to check raw data vs processed data */ /* sprintf(chrCheck, "chr%s", chrom); if (!sameWord(chrCheck, qtlChrom))printf("=== "); if (!sameWord(peak, "") && !sameWord(peakPos, "0")) printf("%s\t%s\txx%dxx\t%s\t%s\n", name, peak, -(atoi(peakChromStart)-atoi(peakPos)), peakPos, peakChromStart);fflush(stdout); */ /* only put out valid entries */ if (qtlValid && !sameWord(qtlChrom, na)) fprintf(outF, "%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", qtlChrom, regionStart, regionEnd, qtlName, qtlScore, qtlStrand, qtlThickStart, qtlThickEnd, qtlMarker, qtlMgiID, qtlDescription, qtlCMScore, flank1, flank2); else { /* printf("%s\t%s\t%s\t%s\n", flank1, peak, flank2, qtlName);fflush(stdout); */ } row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn2); hFreeConn(&conn3); fclose(outF); return(0); }