src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c 1.8
1.8 2009/09/23 18:42:24 angie
Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
Index: src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c 23 Jul 2008 20:55:15 -0000 1.7
+++ src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c 23 Sep 2009 18:42:24 -0000 1.8
@@ -1,300 +1,300 @@
/* pbCalDistGlobal - Create tab delimited data files to be used by Proteome Browser stamps */
#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, "select accession from swInterPro");
char **row;
while ((row = sqlNextRow(sr)) != NULL)
hashAdd(swInterProHash, row[0], NULL);
sqlFreeResult(&sr);
}
safef(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 ((row2 = sqlNextRow(sr2)) != NULL)
{
if (molWtCnt >= MAX_PROTEIN_CNT)
errAbort("Too many proteins - please set MAX_PROTEIN_CNT to be more than %d\n",
MAX_PROTEIN_CNT);
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)
{
warn("%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);fflush(stdout);
- system("date");
+ mustSystem("date");
}
}
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);
}