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/pbCalResStd/pbCalResStd.c src/hg/protein/pbCalResStd/pbCalResStd.c
index f2a07fd..57d2968 100644
--- src/hg/protein/pbCalResStd/pbCalResStd.c
+++ src/hg/protein/pbCalResStd/pbCalResStd.c
@@ -1,334 +1,334 @@
 /* pbCalResStd- Calculate the avg frequency and standard deviation of each AA residue for the proteins in a specific genome*/
 
 /* 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. */
 
 #define MAXN 1000000
 #define MAXRES 23
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "spDb.h"
 #include "math.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "pbCalResStd calculates the avg frequency and standard deviation of every AA residues of the proteins in a specific genome\n"
   "usage:\n"
   "   pbCalResStd spDb taxNum gDb\n"
   "      spDb is the SWISS-PROT database name\n"
   "      taxNumis the taxnomy number of the genome\n"
   "      gDb is the genome database name\n"
   "Example: pbCalResStd sp050415 9606 hg17\n"
   );
 }
 
 double measure[MAXN];
 double freq[MAXN][MAXRES];
 double avg[MAXRES];
 double sumJ[MAXRES];
 double sigma[MAXRES];
 double sumJ[MAXRES];
 
 int recordCnt;
 double recordCntDouble;
 double lenDouble;
 double sum;
 
 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;
 
 assert(nDist < ArraySize(distCnt));
 
 o3 = mustOpen(oFileName, "w");
 for (j=0; j<=nDist; j++)
     {
     distCnt[j] = 0;
     xDist[j] = xMin + xDelta * (double)j;
     }
 
 for (i=0; i<nInput; i++)
     {
     if (measure[i] <= xDist[0])
 	{
 	distCnt[0]++;
 	}
     for (j=1; j<nDist; j++)
 	{
 	if ((measure[i] > xDist[j-1]) && (measure[i] <= xDist[j]))
  	    {
 	    distCnt[j]++;
 	    }
 	}
     if (measure[i] > xDist[nDist-1])
 	{
 	distCnt[nDist]++;
 	}
     }
 
 highestCnt = 0;
 totalCnt   = 0;
 for (j=0; j<=nDist; j++)
     {
     if (distCnt[j] > highestCnt) highestCnt = distCnt[j];
     totalCnt = totalCnt + distCnt[j];
     }
     
 if (totalCnt != nInput)
     errAbort("nInput %d is not equal totalCnt %d, aborting ...\n", nInput, totalCnt);
    
 /* do not print out count of the last inteval, which is everything beyond xMax */
 for (j=0; j<nDist; j++)
     {
     fprintf(o3, "%f\t%d\n", xDist[j], distCnt[j]);
     }
 carefulClose(&o3);
    
 return(highestCnt);
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 char cond_str[255];
 char *proteinDatabaseName;
 FILE *o1, *o2, *o3;
 FILE *fh[23];
 char temp_str[1000];;
 char *accession;
 char *aaSeq;
 char *chp;
 int i, j, len;
 int ihi, ilow;
 char *answer;
 char *protDisplayId;
 int aaResCnt[30];
 char aaAlphabet[30];
 int aaResFound;
 float fvalue1, fvalue2;
 float p1, p2;
 int icnt, jcnt;
 char *taxon;
 char *database;
 int sortedCnt;
 
 if (argc != 4) usage();
 
 strcpy(aaAlphabet, "WCMHYNFIDQKRTVPGEASLXZB");
 
 proteinDatabaseName = argv[1];
 taxon = argv[2];
 database = argv[3];
 
 o2 = mustOpen("pbResAvgStd.tab", "w");
 
 for (i=0; i<20; i++)
     {
     safef(temp_str, sizeof(temp_str), "%c.txt", aaAlphabet[i]);
     fh[i] = mustOpen(temp_str, "w");
     }
 
 conn  = hAllocConn(hDefaultDb());
 conn2 = hAllocConn(hDefaultDb());
 
 sqlSafef(query2, sizeof(query2), "select proteinID from %s.knownGene;", database);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 icnt = 0;
 jcnt = 0;
 
 for (j=0; j<MAXRES; j++)
     {
     sumJ[j] = 0;
     }
 
 while (row2 != NULL)
     {
     protDisplayId = row2[0];   
     sqlSafefFrag(cond_str, sizeof(cond_str),  "val='%s'", protDisplayId);
     accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);
 
     if (accession == NULL)
 	{
         sqlSafefFrag(cond_str, sizeof(cond_str),  "acc='%s'", protDisplayId);
     	accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);
 	if (accession == NULL)
 	    {
 	    verbose(2, "'%s' not found.\n", protDisplayId);
 	    goto skip;
 	    }
 	}
     
     sqlSafefFrag(cond_str, sizeof(cond_str),  "accession='%s'", accession);
     answer = sqlGetField("proteins040115", "spXref2", "biodatabaseID", cond_str);
     if (answer == NULL)
 	{
 	/* this protein might be a variant splice protein, and then it won't be in spXref2 */
 	goto skip;
 	}
     if (answer[0] != '1')
 	{
 	/* printf("%s not in SWISS-PROT\n", protDisplayId);fflush(stdout); */
 	goto skip;
 	}
     
     sqlSafefFrag(cond_str, sizeof(cond_str),  "acc='%s'", accession);
     aaSeq = sqlGetField(proteinDatabaseName, "protein", "val", cond_str);
     if (aaSeq == NULL)
 	{
 	printf("Can't find peptide sequence for %s, exiting ...\n", protDisplayId);
 	fflush(stdout);
 	exit(1);
 	}
 
     len  = strlen(aaSeq);
     if (len < 100) goto skip;
 
     lenDouble = (double)len;
 
     for (j=0; j<MAXRES; j++)
     	{
     	aaResCnt[j] = 0;
 	}
 
     chp = aaSeq;
     for (i=0; i<len; i++)
 	{
 	aaResFound = 0;
 	for (j=0; j<MAXRES; j++)
 	    {
 	    if (*chp == aaAlphabet[j])
 		{
 		aaResFound = 1;
 		aaResCnt[j] ++;
 		}
 	    }
 	if (!aaResFound)
 	    {
 	    fprintf(stderr, "%c %d not a valid AA residue.\n", *chp, *chp);
 	    }
 	chp++;
 	}
 
     for (j=0; j<MAXRES; j++)
 	{	
 	freq[icnt][j] = (double)aaResCnt[j]/lenDouble;
 	sumJ[j] = sumJ[j] + freq[icnt][j];
 	}
 
     for (j=0; j<20; j++)
 	{
 	fprintf(fh[j], "%15.7f\t%s\n", freq[icnt][j], accession);fflush(fh[j]);
 	}
     icnt++;
     if (icnt >= MAXN)
 	errAbort("Too many proteins - please set MAXN to be more than %d\n", MAXN);
 		
 skip:
     row2 = sqlNextRow(sr2);
     }
 
 recordCnt = icnt;
 recordCntDouble = (double)recordCnt;
 
 for (j=0; j<20; j++)
     {
     carefulClose(&(fh[j]));
     }
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 for (j=0; j<MAXRES; j++)
     {
     avg[j] = sumJ[j]/recordCntDouble;
     }
 
 for (j=0; j<20; j++)
     {
     sum = 0.0;
     for (i=0; i<recordCnt; i++)
      	{
 	sum = sum + (freq[i][j] - avg[j]) * (freq[i][j] - avg[j]);
 	}
     sigma[j] = sqrt(sum/(double)(recordCnt-1));
     fprintf(o2, "%c\t%f\t%f\n", aaAlphabet[j], avg[j], sigma[j]);
     }
 
 carefulClose(&o2);
 
 o1 = mustOpen("pbAnomLimit.tab", "w");
 for (j=0; j<20; j++)
     {
     safef(temp_str, sizeof(temp_str), "cat %c.txt|sort|uniq > %c.srt",  aaAlphabet[j], aaAlphabet[j]);
     mustSystem(temp_str);
 
     /* figure out how many unique entries */
     safef(temp_str, sizeof(temp_str), "wc %c.srt > %c.tmp",  aaAlphabet[j], aaAlphabet[j]);
     mustSystem(temp_str);
     safef(temp_str, sizeof(temp_str), "%c.tmp",  aaAlphabet[j]);
     o3 = mustOpen(temp_str, "r");
     mustGetLine(o3, temp_str, 1000);
     chp = temp_str;
     while (*chp == ' ') chp++;
     while (*chp != ' ') chp++;
     *chp = '\0';
     sscanf(temp_str, "%d", &sortedCnt);
     safef(temp_str, sizeof(temp_str), "rm %c.tmp", aaAlphabet[j]);
     mustSystem(temp_str);
 
     /* cal hi and low cutoff threshold */
     ilow = (int)((float)sortedCnt * 0.025);
     ihi  = (int)((float)sortedCnt * 0.975);
     
     safef(temp_str, sizeof(temp_str), "%c.srt",  aaAlphabet[j]);
     o2 = mustOpen(temp_str, "r");
     i=0;
     for (i=0; i<ilow; i++)
 	{
 	mustGetLine(o2, temp_str, 1000);
 	}
     sscanf(temp_str, "%f", &fvalue1);
 
     mustGetLine(o2, temp_str, 1000);
     sscanf(temp_str, "%f", &fvalue2);
     p1 = (fvalue1 + fvalue2)/2.0;
 
     for (i=ilow+1; i<ihi; i++)
 	{
 	mustGetLine(o2, temp_str, 1000);
 	}
     sscanf(temp_str, "%f", &fvalue1);
 
     mustGetLine(o2, temp_str, 1000);
     sscanf(temp_str, "%f", &fvalue2);
     p2 = (fvalue1 + fvalue2)/2.0;
     carefulClose(&o2);
 
     fprintf(o1, "%c\t%f\t%f\n", aaAlphabet[j], p1, p2);fflush(stdout);
 
     for (i=0; i<recordCnt; i++)
 	{
 	measure[i] = freq[i][j]; 
 	}
     safef(temp_str, sizeof(temp_str), "pbAaDist%c.tab", aaAlphabet[j]);
     calDist(measure,  recordCnt,    51,     0.0, 0.005, temp_str);
     }
     
 carefulClose(&o1);
 
 return(0);
 }