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/spm7/spm7.c src/hg/protein/spm7/spm7.c index d185004..3ae354f 100644 --- src/hg/protein/spm7/spm7.c +++ src/hg/protein/spm7/spm7.c @@ -1,290 +1,290 @@ /* spm7 - Creates sorted list of mRNA-SP data file for further duplicates processing */ /* 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" char proteinName[20], mrnaName[20]; FILE *inf; char line_in[10000]; char line[10000]; char newInfo[10000], oldInfo[10000]; char *oldMrnaStr, *oldProteinStr, *oldAlignStr; char *mrnaStr, *proteinStr, *alignStr; int aaLen; int cdsLen; char cond_str[256]; char *aaStr; void usage() /* Explain usage and exit. */ { errAbort( "spm7 - Create sorted list of mRNA-SP data file for further duplicates processing\n" "usage:\n" " spm7 xxxx yyyy\n" " xxxx is the release date of SWISS-PROT data\n" " yyyy is the genome under construction\n" "example:\n" " spm7 072003 hg16\n"); } int main(int argc, char *argv[]) { char *skippedKgId; char *lastValidKgId; struct sqlConnection *conn2, *conn3; struct sqlResult *sr2; char query2[256]; char **row2; char *proteinID; FILE *o3, *o7; char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd, *exonCount, *exonStarts, *exonEnds; char *alignID; char *chp; int i, j; int isDuplicate; char *genomeDBname; char *proteinDataDate; char proteinsDB[40]; char spDB[40]; char *acc; #define MAX_EXON 1000 int exStart[MAX_EXON], exEnd[MAX_EXON]; int exCount; int aaStart[MAX_EXON], aaEnd[MAX_EXON]; char *sp, *ep; int aalen; int cdsS, cdsE; int eS, eE; if (argc != 3) usage(); proteinDataDate = argv[1]; genomeDBname = argv[2]; safef(spDB, sizeof(spDB), "sp%s", proteinDataDate); safef(proteinsDB, sizeof(proteinsDB), "proteins%s", proteinDataDate); o3 = fopen("j.dat", "w"); o7 = fopen("jj.dat", "w"); conn2= hAllocConn(genomeDBname); conn3= hAllocConn(genomeDBname); inf = mustOpen("sorted.lis", "r"); strcpy(oldInfo, ""); skippedKgId = cloneString(""); lastValidKgId = cloneString(""); isDuplicate = 0; oldMrnaStr = cloneString(""); oldAlignStr = cloneString(""); oldProteinStr = cloneString(""); mrnaStr = cloneString(""); proteinStr = cloneString(""); alignStr = cloneString(""); while (fgets(line_in, 10000, inf) != NULL) { strcpy(line, line_in); chp = strstr(line, "\t"); /* chrom */ chp ++; chp = strstr(chp, "\t"); /* cds block start position */ chp ++; chp = strstr(chp, "\t"); /* cds block end position */ *chp = '\0'; chp++; strcpy(newInfo, line); if (sameString(oldInfo, newInfo)) { isDuplicate = 1; } else { /* remember previous record as old only if it is not a duplicate */ if (!isDuplicate) { oldMrnaStr = mrnaStr; oldProteinStr = proteinStr; oldAlignStr = alignStr; } strcpy(oldInfo, newInfo); isDuplicate = 0; } chp = strstr(chp, "\t"); /* priority score */ chp ++; chp = strstr(chp, "\t"); /* mRNA transcription length */ chp ++; chp = strstr(chp, "\t"); /* mRNA date */ chp ++; mrnaStr = chp; chp = strstr(chp, "\t"); /* mRNA ID */ *chp = '\0'; chp ++; mrnaStr = cloneString(mrnaStr); proteinStr = chp; chp = strstr(chp, "\t"); /* protein ID */ *chp = '\0'; chp ++; proteinStr = cloneString(proteinStr); alignID = chp; /* get rid of "end-of-line" character at the end of the string */ alignStr = trimSpaces(alignID); if (isDuplicate) { /* only put out records for valid KG entries */ if (!sameString(oldMrnaStr, skippedKgId) || sameString(oldMrnaStr, lastValidKgId)) { fprintf(o7, "%s\t%s\t%s\t%s\n", oldMrnaStr, oldProteinStr, mrnaStr, proteinStr); } } else { sqlSafef(query2, sizeof(query2), "select * from %sTemp.knownGene0 where alignID='%s';", genomeDBname, alignID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { name = row2[0]; chrom = row2[1]; strand = row2[2]; txStart = row2[3]; txEnd = row2[4]; cdsStart = row2[5]; cdsEnd = row2[6]; exonCount = row2[7]; exonStarts = row2[8]; exonEnds = row2[9]; proteinID = row2[10]; alignID = row2[11]; sscanf(exonCount, "%d", &exCount); sp = cloneString(exonStarts); ep = cloneString(exonEnds); sscanf(cdsStart, "%d", &cdsS); sscanf(cdsEnd, "%d", &cdsE); aalen = 0; j=0; for (i=0; i<exCount; i++) { chp = strstr(sp, ","); *chp = '\0'; sscanf(sp, "%d", &(exStart[i])); chp++; sp = chp; chp = strstr(ep, ","); *chp = '\0'; sscanf(ep, "%d", &(exEnd[i])); eS = exStart[i]; eE = exEnd[i]; if (cdsS > eS) { eS = cdsS; } if (cdsE < eE) { eE = cdsE; } if (eS > eE) { eS = 0; eE = 0; } if (eS != eE) { aaStart[j] = aalen; aaEnd[j] = aaStart[j] + (eE- eS +1)/3 -1; aalen = aalen + (eE- eS +1)/3; j++; } chp++; ep = chp; } cdsLen = aalen; sqlSafefFrag(cond_str, sizeof(cond_str), "val='%s'", proteinID); acc = sqlGetField(spDB, "displayId", "acc", cond_str); sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", acc); aaStr=sqlGetField(spDB, "protein", "val", cond_str); aaLen = strlen(aaStr); if ((cdsLen > 50) || ((cdsLen * 100)/aaLen > 50)) { fprintf(o3,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, proteinID, alignID); lastValidKgId = cloneString(name); } else { printf("skipping %s %d \n", name, cdsLen); skippedKgId = cloneString(name); } row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); } } hFreeConn(&conn2); hFreeConn(&conn3); fclose(o3); fclose(o7); mustSystem("cat j.dat|sort|uniq >knownGene.tab"); mustSystem("cat jj.dat|sort|uniq >duplicate.tab"); mustSystem("rm j.dat"); mustSystem("rm jj.dat"); return(0); }