-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-#include <time.h>
-#include <math.h>
-#include "fisher2.h"
-void testp(double *permuted_ttests,int *B,double *permuted,double
- *Imatrix,int *nc,int *nr,int *g,double *Tinitial,double *ps);
-void permute_matrix(double *Imatrix,int *nc,int *nr,double
- *permuted,int *g,double *trial_ts,double *Tinitial,double
- *counter);
-void permute_array(int *array, int n);
-void calc_twosample_ts(double *Pmatrix,int *g,int *nc,int *nr,double
- *Ts,double *Tinitial,double *counter1);
-void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *storage);
-void start(double *Imatrix,int *g,int *nr,int *nc,double *testing,
- double storage[][9]);
+#include "metastats.h"
-int main (int argc, char *argv[]){
+int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int secondGroupingStart){
- int col=-1, row=-1, size,g=0,c=0,i=0,j=0,k,counter=0,lines=0, B=10000;
- double placeholder=0,min=0, thresh=0.05;
-
- char arr[10000], str[51], a;
- char location[41]="jobj.txt", output[41]="out.txt";
-
- for(i=0;i<10000;i++){
- arr[i]='q';
- }
+ int size,c=0,i=0,j=0,k,counter=0, bflag=0;
+ int B=numPermutations;
+ int row = numRows;
+ int col = numCols;
+ int g = secondGroupingStart;
+ double thresh=threshold;
+ double placeholder=0,min=0;
-int u,rflag=0,cflag=0, bflag=0;
-char *filename;
-int numbers;
-double numb;
-extern char *optarg;
-extern int optind, optopt, opterr;
-
-while ((u = getopt(argc, argv, ":r:c:g:b:t:f:o:")) != -1) {
- switch(u) {
- case 'r':
- numbers = atoi(optarg);
- printf("The number of features/rows is %d.\n", numbers);
- row = numbers;
- rflag = 1;
- break;
- case 'c':
- numbers = atoi(optarg);
- printf("The number of samples/columns is %d.\n", numbers);
- col = numbers;
- cflag = 1;
- break;
- case 'g':
- numbers = atoi(optarg);
- printf("Your g-value is %d.\n", numbers);
- g = numbers;
- break;
- case 'b':
- numbers = atoi(optarg);
- printf("The number of permutations is %d\n", numbers);
- B = numbers;
- break;
- case 't':
- numb = atof(optarg);
- printf("Threshold is is %lf\n", numb);
- thresh = numb;
- break;
- case 'f':
- filename = optarg;
- printf("filename input is %s\n", filename);
- strcpy(location,filename);
- break;
- case 'o':
- filename = optarg;
- printf("filename output %s\n", filename);
- strcpy(output,filename);
- break;
- case ':':
- printf("-%c without filename\n", optopt);
- break;
- case '?':
- printf("unknown arg %c\n", optopt);
- break;
- }
-}
-
- FILE *jobj, *out;
- jobj=fopen(location,"r");
-
- if(jobj == NULL){
- printf("Please don't forget to save your matrix in the active");
- printf(" directory as \"%s\".\n",location);
- return 0;
- }
-
- // Gets the first line of samples names and checks for user error.
- fgets(arr,10000,jobj);
-
- for(i=0;i<10000;i++){
- if(isspace(arr[i])){
- counter++; }
- }
-
- if (cflag == 0) {
- printf("You didn't tell us how many subjects there are!\n");
- printf("But we'll still do the analysis as if there are %d subjects.\n\n",col=counter-1);
- }
- if (cflag == 1) {
- if (col != counter-1){
- printf("We would expect %d subjects, but you said %d.\n",counter-1,col);
- }
- }
-
- while((a = fgetc(jobj)) != EOF){
- if(a == '\n'){
- lines++; }
- }
+ char output[1024];
+ strcpy(output, outputFileName);
+ FILE *out;
- if (rflag == 0) {
- printf("You didn't specify the number of features!\n");
- printf("But we'll still do the analysis assuming %d features.\n\n", row=lines-1);
- }
- if (rflag == 1) {
- if ( lines-1 != row ){
- printf("We would expect %d features, but you said %d.\n",lines-1,row);
- }
- }
-
if (g>=col || g<=0){
printf("Check your g value\n");
}
storage[i][j]=0;
}
}
- // Reset file below and create a separate matrix.
- rewind(jobj);
- fgets(arr,10000,jobj);
-
+
for(i=0; i<row; i++){
- fscanf(jobj,"%s",str);
for(j=0; j<col;j++){
- fscanf(jobj,"%lf",&placeholder);
- matrix[i][j]=placeholder;
- if(isalnum(placeholder)!=0){ // check for ""
- printf("Your matrix isn't set up properly!\n");
- return 0;
- }
+ matrix[i][j]=data[i][j];
pmatrix[c]=0; // initializing to zero
permuted[c]=0;
c++;
}
}
-
- fclose(jobj);
-
// Produces the sum of each column
double total[col],total1=0,total2=0;
t = time(NULL);
local = localtime(&t);
- jobj= fopen(location,"r");
- fgets(arr,10000,jobj);
-
- out = fopen(output,"a+");
+ out = fopen(output,"w");
fprintf(out,"Local time and date of test: %s\n", asctime(local));
fprintf(out,"# rows = %d, # col = %d, g = %d\n\n",row,col,g);
if (bflag == 1){
fprintf(out,"%d permutations\n\n",B);
}
+
+ //output column headings - not really sure... documentation labels 9 columns, there are 10 in the output file
+ //storage 0 = meanGroup1 - line 529, 1 = varGroup1 - line 532, 2 = err rate1 - line 534, 3 = mean of counts group1?? - line 291, 4 = meanGroup2 - line 536, 5 = varGroup2 - line 539, 6 = err rate2 - line 541, 7 = mean of counts group2?? - line 292, 8 = pvalues - line 293
+ fprintf(out, "OTU\tmean(group1)\tvariance(group1)\tstderr(group1)\tmean_of_counts(group1)\tmean(group2)\tvariance(group2)\tstderr(group2)\tmean_of_counts(group1)\tp-value\n");
+
for(i=0; i<row; i++){
- fscanf(jobj,"%s",str);
- fprintf(out,"%s",str);
- for(k=0;k<col;k++){
- fscanf(jobj,"%*lf",&placeholder);
- }
+ fprintf(out,"%d",(i+1));
+
for(j=0; j<9;j++){
fprintf(out,"\t%.12lf",storage[i][j]);
}
fprintf(out,"\n \n");
- fclose(jobj);
+ // fclose(jobj);
fclose(out);
return 0;
initial[i]=fabs(xbardiff/denom);
}
}
+
+
+
+
projects / mothur.git / blobdiff