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/spm6/spm6.c src/hg/protein/spm6/spm6.c index c9c7a65..1b9ba1b 100644 --- src/hg/protein/spm6/spm6.c +++ src/hg/protein/spm6/spm6.c @@ -1,293 +1,293 @@ /* spm6 - generates sorted.lis and knownGene0.tab for further KG 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" #define PDB_YES 90000 #define SWISSPROT_YES 8000 #define REFSEQREVIWED 700 #define REFSEQPROVISIONAL 60 FILE *o3, *o4, *o5; int exStart[500], exEnd[500]; int aaStart[500], aaEnd[500]; void usage() /* Explain usage and exit. */ { errAbort( "spm6 - generates sorted.lis and knownGene0.tab for further duplicates processing\n" "usage:\n" " spm6 xxxx db ro_db\n" " xxxx is the release date of SWISS-PROT data\n" " db is the genome under construction, e.g.: kgDB\n" " ro_db is the target genome to read data from\n" "example:\n" " spm6 040115 kgDB hg16\n"); } void getCDS(char *cdsStart, char *cdsEnd, char *exonCount, char *exonStarts_in, char *exonEnds_in) { int exCount; char *sp, *ep; char *chp; int i, j; int aalen; int cdsS, cdsE; int eS, eE; int estLen; char *exonStarts, *exonEnds; estLen = 0; exonStarts = strdup(exonStarts_in); exonEnds = strdup(exonEnds_in); sscanf(exonCount, "%d", &exCount); sp = exonStarts; ep = 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; } estLen = estLen + (eE-eS+1); if (eS != eE) { aaStart[j] = aalen; aaEnd[j] = aaStart[j] + (eE- eS +1)/3 -1; aalen = aalen + (eE- eS +1)/3; j++; } else { } chp++; ep = chp; } for (i=0; i<exCount; i++) { if (exEnd[i] < cdsS) { // exon is outside of CDS at right // do nothing } else { if ((exStart[i] <= cdsS) && (cdsS <= exEnd[i])) { fprintf(o4, "%d,", cdsS); } else { if (exStart[i] <= cdsE) { fprintf(o4, "%d,", exStart[i]); } } } } fprintf(o4, "\t"); for (i=0; i<exCount; i++) { if (exEnd[i] < cdsS) { // exon is outside of CDS at right // do nothing } else { if ((exStart[i] <= cdsE) && (cdsE <= exEnd[i])) { fprintf(o4, "%d,", cdsE); } else { if (cdsE > exEnd[i]) { fprintf(o4, "%d,", exEnd[i]); } } } } fprintf(o4, "\t"); } int main(int argc, char *argv[]) { struct sqlConnection *conn2; char proteinName[40], mrnaName[40]; char query2[256]; char cond_str[500]; FILE *inf; char line[1000]; int alignmentID; struct sqlResult *sr2; char **row2; char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd, *exonCount, *exonStarts, *exonEnds; char *mrnaDate; char *pdbID; char *genomeDBname; char *genomeReadOnly; char *proteinDataDate; char proteinsDB[40]; char *proteinDbSource; int itxStart, itxEnd; int transcriptLength; int priority; if (argc != 4) usage(); proteinDataDate = argv[1]; genomeDBname = argv[2]; genomeReadOnly = argv[3]; o3 = fopen("j.dat", "w"); o4 = fopen("jj.dat", "w"); o5 = fopen("align.lis", "w"); conn2= hAllocConn(genomeReadOnly); inf = mustOpen("best.lis", "r"); alignmentID = 0; while (fgets(line, 1000, inf) != NULL) { sscanf(line, "%s\t%s", proteinName, mrnaName); priority = 0; sqlSafefFrag(cond_str, sizeof cond_str, "sp='%s'", proteinName); sprintf(proteinsDB, "proteins%s", proteinDataDate); pdbID= sqlGetField(proteinsDB, "pdbSP", "pdb", cond_str); if (pdbID != NULL) { priority = priority + PDB_YES; } sqlSafefFrag(cond_str, sizeof cond_str, "displayID='%s'", proteinName); proteinDbSource = sqlGetField(proteinsDB, "spXref2", "biodatabaseID", cond_str); if (proteinDbSource == NULL) { printf("No proteinDbSource found for %s, skipping it ... \n", proteinName); break; } if (strcmp(proteinDbSource, "1") == 0) { priority = priority + SWISSPROT_YES; } // get mRNA date if ((mrnaDate = hGenbankModDate(mrnaName, conn2)) == NULL) { fprintf(stderr, "%s could not be found!!!\n", mrnaName); exit(1); } sqlSafef(query2, sizeof query2, "select * from %sTemp.mrnaGene where name='%s';", genomeDBname, mrnaName); 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]; fprintf(o4, "%s\t", chrom); getCDS(cdsStart, cdsEnd, exonCount, exonStarts, exonEnds); sscanf(txStart, "%d", &itxStart); sscanf(txEnd, "%d", &itxEnd); transcriptLength = itxEnd - itxStart; fprintf(o4, "%d\t%010d\t%s\t%s\t%s\t%d\n", priority, transcriptLength, mrnaDate, name, proteinName, alignmentID); fprintf(o5, "%d\t%d\t%s\t%s\t%s\n", alignmentID, priority, name, proteinName, proteinDbSource); fprintf(o3,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\n", name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, proteinName, alignmentID); alignmentID++; row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); } hFreeConn(&conn2); fclose(o3); fclose(o4); fclose(o5); mustSystem("cat j.dat|sort|uniq >knownGene0.tab"); mustSystem("rm j.dat"); mustSystem("cat jj.dat|sort -r |uniq >sorted.lis"); mustSystem("rm jj.dat"); return(0); }