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/protein/kgBestMrna2/kgPrepBestMrna2.c src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c index 572b5c4..7f4c029 100644 --- src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c +++ src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c @@ -1,210 +1,210 @@ /* * kgPrepBestMrna - prepare input files for blat run to * select best mRNA for each protein */ /* 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 <limits.h> #include "common.h" #include "hCommon.h" #include "hdb.h" char proteinName[20], mrnaName[20]; char mrnaNames[500][20]; int mrnaScore[500]; char proteinNameOld[20] = {""}; struct dnaSeq *seq; HGID id; bioSeq *mSeq, qSeq, *pSeq; extern int answer_for_kg; struct dnaSeq *untransList; char line[2000]; char line2[2000]; int mrnaCount; int proteinCount; char mrnaNames[500][20]; int mrnaScore[500]; int diffIdent[500]; char *proteinDataDate; char *kgTempDb; char *genomeDBname; char proteinsDB[100]; char spDB[100]; char gbTempDB[100]; char *clusterDir = "./clusterRun"; /* Explain usage and exit. */ void usage() { errAbort( "usage:\tkgPrepBestMrna YYMMDD db 2> jobList\n" "\tYYMMDD is the release date of SWISS-PROT data, eg: 031117\n" "\tdb is the genome under construction, eg: mm4\n" "kgPrepBestMrna - read a list of proteins from protein.lis and get\n" "\tcorresponding mRNAs from dbTemp.refMrna to prepare input files\n" "\tfor blat run. Creates files ./clusterRun/protN/[mp]NNNN.fa\n" "\tand result directories: ./out/protN/ (2000 results per directory)\n" "\tOutputs the jobList for 'para create jobList' to stderr"); } int cal_months(char *date) { int year, month, day; int months; sscanf(date, "%d-%d-%d", &year, &month, &day); months = (year - 1970)*12 + month - 1; return(months); } int main(int argc, char *argv[]) { char proteinID[20]; FILE *IN, *OUT; char line[2000]; int imrna; char dirName[1000]; char protName[1000]; char mrnaFile[1000]; char outName[1000]; char outDir[1000]; char blatCmd[1000]; struct sqlConnection *conn2, *conn3; char query2[256]; struct sqlResult *sr2; char **row2; char *mrnaID; FILE *aaOut, *mrnaOut; char *aaSeq, *mrnaSeq; char cond_str[200]; if (argc != 3) usage(); proteinDataDate = argv[1]; //genomeDb = argv[2]; kgTempDb = argv[2]; // make sure db connection goes to correct genome // hRnaSeqAndIdx() needs this. sprintf(spDB, "sp%s", proteinDataDate); sprintf(proteinsDB, "proteins%s", proteinDataDate); sprintf(gbTempDB, "%s", kgTempDb); IN = fopen("protein.lis", "r"); OUT = fopen("rawJobList", "w"); conn2= hAllocConn(kgTempDb); conn3= hAllocConn(kgTempDb); proteinCount = 0; snprintf(dirName, (size_t) sizeof(dirName), "./out" ); mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH ); snprintf(dirName, (size_t) sizeof(dirName), "%s", clusterDir ); mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH ); if (chdir(dirName)) errAbort("ERROR: Can not change dir to %s\n", dirName); while (fgets(line, 1000, IN) != NULL) { sscanf(line, "%s", proteinID); printf(">>%s\n", proteinID); sqlSafefFrag(cond_str, sizeof cond_str, "acc='%s'", proteinID); aaSeq = sqlGetField(spDB, "protein","val", cond_str); if (aaSeq == NULL) { aaSeq = sqlGetField(spDB, "varProtein","val", cond_str); } if (aaSeq == NULL) { printf("no seq found for %s in %s.\n", proteinID, spDB); fflush(stdout); exit(1); } /* 2000 results per output directory. 4000 input files for each * ./protN directory */ if ( 0 == (proteinCount % 2000) ) { snprintf(dirName, (size_t)sizeof(dirName), "../out/prot%05d", proteinCount); if (mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH )) { if (errno != EEXIST) errAbort("ERROR: Can not create dir %s\n", dirName); } snprintf(dirName, (size_t) sizeof(dirName), "prot%05d", proteinCount ); if (mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH )) { if (errno != EEXIST) errAbort("ERROR: Can not create dir %s\n", dirName); } snprintf(outDir, (size_t) sizeof(outDir), "out/prot%05d", proteinCount); } snprintf(protName, (size_t) sizeof(protName), \ "%s/p%05d.fa", dirName, proteinCount ); aaOut = fopen(protName, "w"); fprintf(aaOut, ">%s\n%s\n", proteinID, aaSeq); fclose(aaOut); sqlSafef(query2, sizeof query2, "select mrnaID from %s.spMrna where spID='%s';",kgTempDb, proteinID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); imrna = 0; snprintf(mrnaFile, (size_t) sizeof(mrnaFile), \ "%s/m%05d.fa", dirName, proteinCount ); mrnaOut = fopen(mrnaFile, "w"); while (row2 != NULL) { mrnaID = row2[0]; strcpy(mrnaNames[imrna], mrnaID); printf("%s\t%s\n", proteinID, mrnaID);fflush(stdout); sqlSafefFrag(cond_str, sizeof cond_str, "name='%s'", mrnaID); mrnaSeq = sqlGetField(gbTempDB,"mrnaSeq","seq", cond_str); fprintf(mrnaOut, ">%s\n%s\n", mrnaID, mrnaSeq); row2 = sqlNextRow(sr2); imrna++; } mrnaCount = imrna; fclose(mrnaOut); sqlFreeResult(&sr2); snprintf(outName, (size_t) sizeof(outName),"./%s/b%05d.out", outDir, proteinCount); snprintf(blatCmd, (size_t) sizeof(blatCmd), "blat {check in exists %s/%s} {check in exists %s/%s} {check out line %s} -noHead -t=dnax -q=prot", \ clusterDir, mrnaFile, clusterDir, protName, outName); fprintf(OUT, "%s\n", blatCmd); proteinCount++; } hFreeConn(&conn2); hFreeConn(&conn3); fclose(IN); fclose(OUT); return(0); }