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dotur.cpp
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dotur.cpp
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//
//
#include "otu.h"
#include "richness.h"
#include <iostream>
#include <fstream>
#include <iomanip>
#include <vector>
#include <string>
#include <sstream>
#include <list>
#include <ctime>
using namespace std;
/**************************************************************************************************/
void usageError(char *name)
{
cerr << "Usage: " << name << " [-i Iterations (<1000>)] [-c ClusterMethod (<f>, n, a)] [-p Precision (10, <100>, 1000, 10000)] [-l] [-j] <file>" << endl;
cerr << "Options:\n";
cerr << " -i: Number of iterations (default = 1000)\n";
cerr << " -c: Clustering method - (f) furthest neighbor, (n) nearest neighbor,\n";
cerr << " (a) average neighbor (default = f)\n";
cerr << " -p: Precision of distances for output, increasing can dramatically\n";
cerr << " lengthen execution times - 10, 100, 1000, 10000 (default = 100)\n";
cerr << " -l: Input file is lower triangular (default = square matrix)\n";
cerr << " -r: Calculates rarefaction curves for each parameter, can dramatically\n";
cerr << " lengthen execution times. Simple rarefaction curve always calculated.\n";
cerr << " -stop: Stops clustering when cutoff has been reached.\n";
cerr << " -wrep: Samples with replacement.\n";
cerr << " -jumble: Jumble the order of the distance matrix.\n";
cerr << " -sim: Converts similarity score to distance (D=1-S).\n";
exit(1);
}
/**************************************************************************************************/
void init_files(string fname, int rarefy, int sample, vector<string>& r_names, vector<string>& c_names){
r_names.push_back(fname + ".rarefaction");
if(sample == 1){
r_names.push_back(fname + ".wr_rarefaction");
}
c_names.push_back(fname + ".collect");
c_names.push_back(fname + ".c_chao");
c_names.push_back(fname + ".c_ace");
c_names.push_back(fname + ".c_jack");
c_names.push_back(fname + ".c_boot");
c_names.push_back(fname + ".c_simpson");
c_names.push_back(fname + ".c_shannon");
for(int i=0;i<c_names.size();i++){
ofstream cfile(c_names[i].c_str(), ios::trunc);
}
if(rarefy){
r_names.push_back(fname + ".r_chao");
r_names.push_back(fname + ".r_ace");
r_names.push_back(fname + ".r_jack");
r_names.push_back(fname + ".r_boot");
r_names.push_back(fname + ".r_simpson");
r_names.push_back(fname + ".r_shannon");
}
for(int i=0;i<r_names.size();i++){
ofstream rfile(r_names[i].c_str(), ios::trunc);
}
}
/**************************************************************************************************/
int main(int argc, char *argv[])
{
// srand(54321);
srand( (unsigned)time( NULL ) );
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
cerr.setf(ios::fixed, ios::floatfield);
cerr.setf(ios::showpoint);
DistanceMatrix dist;
OTUMatrix otu;
string filename = "";
char cmethod = 'f';
otu.rarefy = 0;
dist.cutoff = 1000;
int matrix = 1;
int precise = 100;
otu.iter = 1000;
otu.sample = 0;
dist.jumble = 0;
dist.similarity = 0;
string otuname, listname, indexname, fbase;
char **p;
if(argc>1){
for(p=argv+1;p<argv+argc;p++){
if(strcmp(*p, "-c")==0){
if(++p>=argv+argc)
usageError(argv[0]);
istringstream f(*p);
if(!(f >> cmethod))
usageError(argv[0]);
}
else if(strcmp(*p, "-l")==0){
if(p>=argv+argc)
usageError(argv[0]);
matrix=2; //lower triangle
}
else if(strcmp(*p, "-r")==0){
if(p>=argv+argc)
usageError(argv[0]);
otu.rarefy=1; //calculate rarefaction for parameters
}
else if(strcmp(*p, "-stop")==0){
if(++p>=argv+argc)
usageError(argv[0]);
istringstream f(*p);
if(!(f >> dist.cutoff))
usageError(argv[0]);
}
else if(strcmp(*p, "-wrep")==0){
if(p>=argv+argc)
usageError(argv[0]);
otu.sample=1; //sample with replacement
}
else if(strcmp(*p, "-jumble") == 0){
if(p>=argv+argc)
usageError(argv[0]);
dist.jumble=1;
}
else if(strcmp(*p, "-sim") == 0){
if(p>=argv+argc)
usageError(argv[0]);
dist.similarity=1;
}
else if(strcmp(*p, "-p")==0){
if(++p>=argv+argc)
usageError(argv[0]);
istringstream f(*p);
if(!(f >> precise))
usageError(argv[0]);
}
else if(strcmp(*p, "-i")==0){
if(++p>=argv+argc)
usageError(argv[0]);
istringstream f(*p);
if(!(f >> otu.iter))
usageError(argv[0]);
}
else {
istringstream f(*p);
if(!(f >> filename))
usageError(argv[0]);
}
}
fbase = filename;
if(fbase.find_last_of(".")!=string::npos){
fbase.erase(fbase.find_last_of(".")+1);
}
else{
fbase += ".";
}
dist.read(filename, matrix);
otuname = fbase + cmethod + "n.otu";
listname = fbase + cmethod + "n.list";
indexname = fbase + cmethod + "n.index";
ofstream otu_file(otuname.c_str(), ios::trunc);
ofstream list_file(listname.c_str(), ios::trunc);
ofstream index_file(indexname.c_str(), ios::trunc);
}
else
usageError(argv[0]);
cout << endl;
cout << "|-------------------------------------------------------|" << endl;
cout << "| | % Complete |" << endl;
cout << "| Progress | 10 20 30 40 50 60 70 80 90 100 |" << endl;
cout << "|-------------------------------------------------------|" << endl;
cout << "| OTU Ident |";
cout.flush();
dist.initw();
vector<float> dnames(1);
otu.distances = 0;
int incr = dist.rank/10;
int check = incr;
int z = 0;
while(dist.rank > 1){
dist.small_element();
dist.cluster(cmethod);
dist.merge();
if(dist.print_nonred_w(otuname, listname, indexname, precise, otu.distances, dnames) == 1){ break; }
if(z==check) {
cout << "****";
cout.flush();
check += incr;
}
z++;
}
cout << " |\n";
string fname = fbase+cmethod+ "n";
vector<string> r_names;
vector<string> c_names;
otu.rank_abundance(fname);
init_files(fname,otu.rarefy, otu.sample, r_names, c_names);
otu.binomial();
otu.file_root = fname;
cout << "| Collectors |";
cout.flush();
otu.readlist(dist.orig_name_list);
cout << "| Rarefaction |";
cout.flush();
otu.readotu();
cout << "|-------------------------------------------------------|" << endl << endl;
cout << "Cleaning up..." << endl;
cout.flush();
for(int i=0;i<r_names.size();i++){ otu.output("no", r_names[i]); }
for(int i=0;i<c_names.size();i++){ otu.output("yes", c_names[i]); }
return(0);
}