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/pbCalDistGlobal/pbCalDistGlobal.c src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c index de727cf..8b9a6ac 100644 --- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c +++ src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c @@ -1,299 +1,299 @@ /* pbCalDistGlobal - Create tab delimited data files to be used by Proteome Browser stamps */ /* 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 "hCommon.h" #include "hdb.h" #include "spDb.h" #include "linefile.h" #define MAX_PROTEIN_CNT 10000000 void usage() /* Explain usage and exit. */ { errAbort( "pbCalDistGlobal- Create tab delimited data files to be used by Proteome Browser stamps.\n" "usage:\n" " pbCalDistGlobal spDb protsDb\n" " spDb is the name of SWISS-PROT database\n" " protsDb is the name of proteinsXXXXXX database\n" "Example: pbCalDistGlobal sp040915 proteins040915\n"); } int calDist(double *measure, int nInput, int nDist, double xMin, double xDelta, char *oFileName) /* calculate histogram distribution of a double array of nInput elements */ { int distCnt[1000]; double xDist[1000]; FILE *o3; int i,j; int highestCnt, totalCnt; int lowCnt, hiCnt; printf("processing %s\n", oFileName);fflush(stdout); assert(nDist < ArraySize(distCnt)); o3 = mustOpen(oFileName, "w"); for (j=0; j<=(nDist+1); j++) { distCnt[j] = 0; xDist[j] = xMin + xDelta * (double)j; } lowCnt = 0; hiCnt = 0; for (i=0; i<nInput; i++) { /* count values below xmin */ if (measure[i] < xDist[0]) { lowCnt++; } for (j=0; j<nDist; j++) { if ((measure[i] >= xDist[j]) && (measure[i] < xDist[j+1])) { distCnt[j]++; } } /* count values above xmax */ if (measure[i] >= xDist[nDist]) { hiCnt++; } } highestCnt = 0; totalCnt = 0; for (j=0; j<nDist; j++) { if (distCnt[j] > highestCnt) highestCnt = distCnt[j]; totalCnt = totalCnt + distCnt[j]; } printf("\tdisplayedCnt=%d lowCnt=%d hiCnt=%d total=%d\n", totalCnt, lowCnt, hiCnt, totalCnt + hiCnt + lowCnt);fflush(stdout); totalCnt = totalCnt + hiCnt + lowCnt; if (totalCnt != nInput) errAbort("nInput %d is not equal totalCnt %d, aborting ...\n", nInput, totalCnt); for (j=0; j<nDist; j++) { fprintf(o3, "%f\t%d\n", xDist[j], distCnt[j]); } carefulClose(&o3); return(highestCnt); } int hashCountMatches(struct hash *hash, char *key) /* Return numbers of hits to key in hash. */ { int count = 0; struct hashEl *hel; for (hel = hashLookup(hash, key); hel != NULL; hel = hashLookupNext(hel)) ++count; return count; } double molWt[MAX_PROTEIN_CNT]; double pI[MAX_PROTEIN_CNT]; double aaLenDouble[MAX_PROTEIN_CNT]; double avgHydro[MAX_PROTEIN_CNT]; double cCountDouble[MAX_PROTEIN_CNT]; double exonCountDouble[MAX_PROTEIN_CNT]; double pfamCountDouble[MAX_PROTEIN_CNT]; double interProCountDouble[MAX_PROTEIN_CNT]; int main(int argc, char *argv[]) { struct sqlConnection *conn2, *conn3; char query2[256]; struct sqlResult *sr2; char **row2; char *proteinDatabaseName; /* example: sp031112 */ char *protDbName; /* example: proteins031112 */ FILE *o2; char *accession; char *aaSeq; char *chp; int i, j, len; int cCnt; double hydroSum; int aaResCnt[30]; double aaResCntDouble[30]; char aaAlphabet[30]; int aaResFound; int totalResCnt; int molWtCnt; int pIcnt; char *database; int aaSize; double aa_hydro[256]; int icnt, jExon, pcnt; int ipcnt={0}; int interProCount; if (argc != 3) usage(); strcpy(aaAlphabet, "WCMHYNFIDQKRTVPGEASLXZB"); /* Ala: 1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500 */ aa_hydro['A'] = 1.800; aa_hydro['R'] = -4.500; aa_hydro['N'] = -3.500; aa_hydro['D'] = -3.500; aa_hydro['C'] = 2.500; aa_hydro['Q'] = -3.500; /* Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900 */ aa_hydro['E'] = -3.500; aa_hydro['G'] = -0.400; aa_hydro['H'] = -3.200; aa_hydro['I'] = 4.500; aa_hydro['L'] = 3.800; aa_hydro['K'] = -3.900; /* Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900 */ aa_hydro['M'] = 1.900; aa_hydro['F'] = 2.800; aa_hydro['P'] = -1.600; aa_hydro['S'] = -0.800; aa_hydro['T'] = -0.700; aa_hydro['W'] = -0.900; /* Tyr: -1.300 Val: 4.200 Asx: -3.500 Glx: -3.500 Xaa: -0.490 */ aa_hydro['Y'] = -1.300; aa_hydro['V'] = 4.200; proteinDatabaseName = argv[1]; protDbName = argv[2]; database = argv[2]; o2 = mustOpen("pepResDist.tab", "w"); conn2 = sqlConnect(database); conn3 = sqlConnect(protDbName); for (j=0; j<23; j++) { aaResCnt[j] = 0; } icnt = jExon = pcnt = 0; pIcnt = 0; molWtCnt = 0; /* Build up hash of swInterPro accessions. We'll use this to count domains. */ struct hash *swInterProHash = hashNew(23); { struct sqlResult *sr = sqlGetResult(conn3, NOSQLINJ "select accession from swInterPro"); char **row; while ((row = sqlNextRow(sr)) != NULL) hashAdd(swInterProHash, row[0], NULL); sqlFreeResult(&sr); } sqlSafef(query2, sizeof(query2), "select info.acc, molWeight, aaSize, protein.val, Pi from %s.info, %s.protein, %s.pepPi where info.acc=protein.acc and pepPi.accession=protein.acc", proteinDatabaseName, proteinDatabaseName, database); sr2 = sqlMustGetResult(conn2, query2); while ((molWtCnt < MAX_PROTEIN_CNT) && (row2 = sqlNextRow(sr2)) != NULL) { accession = row2[0]; molWt[molWtCnt] = (double)(atof(row2[1])); molWtCnt++; aaSize = atoi(row2[2]); aaSeq = row2[3]; pI[pIcnt] = (double)(atof(row2[4])); pIcnt++; /* count InterPro domains */ int interProDomains = hashCountMatches(swInterProHash, accession); interProCount += interProDomains; interProCountDouble[ipcnt] = interProDomains; ++ipcnt; len = aaSize; chp = aaSeq; for (i=0; i<len; i++) { aaResFound = 0; for (j=0; j<23; j++) { if (*chp == aaAlphabet[j]) { aaResFound = 1; aaResCnt[j] ++; } } if (!aaResFound) { verbose(2, "%c %d not a valid AA residue in %s:\n%s\n", *chp, *chp, accession, aaSeq); } chp++; } /* calculate hydrophobicity */ chp = aaSeq; cCnt = 0; hydroSum = 0; for (i=0; i<len; i++) { hydroSum = hydroSum + aa_hydro[(int)(*chp)]; /* count Cysteines */ if ((*chp == 'C') || (*chp == 'c')) { cCnt ++; } chp++; } aaLenDouble[icnt] = len; cCountDouble[icnt] = (double)cCnt; avgHydro[icnt] = hydroSum/(double)len; icnt++; if (icnt >= MAX_PROTEIN_CNT) errAbort("Too many proteins - please set MAX_PROTEIN_CNT to be more than %d\n", MAX_PROTEIN_CNT); if ((icnt % 10000) == 0) { printf("%d done.\n", icnt); } } sqlFreeResult(&sr2); sqlDisconnect(&conn2); sqlDisconnect(&conn3); totalResCnt = 0; for (i=0; i<23; i++) { totalResCnt = totalResCnt + aaResCnt[i]; } /* write out residue count distribution */ for (i=0; i<20; i++) { aaResCntDouble[i] = ((double)aaResCnt[i])/((double)totalResCnt); fprintf(o2, "%d\t%f\n", i+1, (float)aaResCntDouble[i]); } fprintf(o2, "%d\t%f\n", i+1, 0.0); carefulClose(&o2); /* calculate and write out various distributions */ calDist(molWt, molWtCnt, 21, 0.0, 10000.0,"pepMolWtDist.tab"); calDist(pI, pIcnt, 61, 3.0, 0.2, "pepPiDist.tab"); calDist(avgHydro, icnt, 41, -2.0, 0.1, "pepHydroDist.tab"); calDist(cCountDouble, icnt, 51, 0.0, 1.0, "pepCCntDist.tab"); calDist(interProCountDouble,ipcnt, 16, 0.0, 1.0, "pepIPCntDist.tab"); return(0); }