bscampp 1.0.1__py3-none-any.whl

bscampp/tools/hamming_distance/src/homology.cpp

@@ -0,0 +1,179 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+#include <omp.h>
+
+
+int main( int argc, char **argv ){
+    if( argc <= 6 ){
+        std::cerr << "Usage: "<<argv[0]<<" [ref infile] [nbr ref records] [query infile] [nbr query records] [outfile] [nbr of leaves returned]" << std::endl;
+        return -1;
+    }
+ 
+    // read in the reference sequences first
+    std::ifstream input_q(argv[1]);
+    if(!input_q.good()){
+        std::cerr << "Error opening '"<<argv[1]<<"'. Bailing out." << std::endl;
+        return -1;
+    }
+
+    //std::string name_arr[std::stoi(argv[2])];
+    //std::string seq_arr[std::stoi(argv[2])];
+    int ref_size = std::stoi(argv[2]) + 3;
+    int count1 = 0;
+    std::vector<std::string> name_arr(ref_size);
+    std::vector<std::string> seq_arr(ref_size);
+    std::string line, name, content;
+
+    while( std::getline( input_q, line ).good() ){
+        if( line.empty() || line[0] == '>' ){ // Identifier marker
+            if( !name.empty() ){ // Print out what we read from the last entry
+
+                name_arr[count1] = name.c_str();
+                seq_arr[count1] = content.c_str();
+                name.clear();
+
+                count1++;
+            }
+            if( !line.empty() ){
+                name = line.substr(1);
+            }
+            content.clear();
+        } else if( !name.empty() ){
+            if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed
+                name.clear();
+                content.clear();
+            } else {
+                content += line;
+            }
+        }
+    }
+    
+    if( !name.empty() ){ // Print out what we read from the last entry
+        //std::cout << name << " : " << content << std::endl;        
+        name_arr[count1] = name;
+        seq_arr[count1] = content;
+        count1++;
+    }
+  
+    // read in query sequences second
+    std::ifstream input(argv[3]);
+    if(!input.good()){
+        std::cerr << "Error opening '"<<argv[3]<<"'. Bailing out." << std::endl;
+        return -1;
+    }
+
+    int q_size = std::stoi(argv[4]) + 3;
+    int count2 = 0;
+    //std::string q_name_arr[std::stoi(argv[4])+3];
+    //std::string q_seq_arr[std::stoi(argv[4])+3];
+    std::vector<std::string> q_name_arr(q_size);
+    std::vector<std::string> q_seq_arr(q_size);
+    name = "";
+
+    while( std::getline( input, line ).good() ){
+        if( line.empty() || line[0] == '>' ){ // Identifier marker
+            if( !name.empty() ){ // Print out what we read from the last entry
+                //std::cout << name << " : " << content << std::endl;
+                q_name_arr[count2] = name.c_str();
+                q_seq_arr[count2] = content.c_str();
+                name.clear();
+                //std::cout << count2 << " : " << q_name_arr[count2] <<std::endl;
+                count2++;
+            }
+            if( !line.empty() ){
+                name = line.substr(1);
+            }
+            content.clear();
+        } else if( !name.empty() ){
+            if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed
+                name.clear();
+                content.clear();
+            } else {
+                content += line;
+            }
+        }
+
+    }
+    
+
+    if( !name.empty() ){ // Print out what we read from the last entry
+        //std::cout << name << " : " << content << std::endl;        
+        q_name_arr[count2] = name;
+        q_seq_arr[count2] = content;
+        count2++;
+    }
+
+    //std::cout << "ref count: "<< count1 <<" query count2: " <<count2 << std::endl;
+
+    std::ofstream outFile(argv[5]);
+
+    // find n (size) closest reference sequences by Hamming distance to each query 
+    // print this to outfile with the one query per line followed by the n closest
+    // reference sequences separated by a comma, with their requisite Hamming
+    // distances separated with a semicolon.
+    
+    #pragma omp parallel for 
+    for (int c2=0; c2<count2; c2++){ //query seq array
+    
+        int size = std::stoi(argv[6]);
+
+        int best_homolog[size];
+        int best_homolog_index[size];
+        int furthest_homolog_index = 0;
+
+        for (int i=0; i<size; i++){
+            best_homolog_index[i] = 0;
+            best_homolog[i] = 999999999;
+        }
+        
+        int q_len = q_seq_arr[c2].length();
+        int q_hom_idx_arr[q_len];
+        int hom_nbr = 0;
+        for (int i=0; i < q_len; i++) {
+            if (q_seq_arr[c2][i] != '-') {
+                q_hom_idx_arr[hom_nbr] = i;
+                hom_nbr++;
+            }
+        }
+        
+        for (int c1=0; c1<count1 ; c1++) { //ref seq array
+            int count = 0;
+            int non_hom_count = 0;
+            int len = seq_arr[c1].length();
+            for(int i=0; i < hom_nbr; i++) {
+                if(seq_arr[c1][q_hom_idx_arr[i]] != q_seq_arr[c2][q_hom_idx_arr[i]]) {
+                    non_hom_count++;
+                    if (non_hom_count > best_homolog[furthest_homolog_index]) {
+                        break;
+                    }
+                }
+            }
+            //std::cout << "here" << std::endl;
+            if (non_hom_count <= best_homolog[furthest_homolog_index]) {
+                best_homolog[furthest_homolog_index] = non_hom_count;
+                best_homolog_index[furthest_homolog_index] = c1;
+                int high_homolog = 0;
+                int high_hom_index = 0;
+                for (int i=0; i<size; i++){
+                    if (best_homolog[i] > high_homolog){
+                        high_homolog = best_homolog[i];
+                        high_hom_index = i;
+                    }
+                furthest_homolog_index = high_hom_index;
+                }
+            }
+        }
+        #pragma omp critical
+        {   
+            outFile << q_name_arr[c2] << ":" << hom_nbr;
+            for (int i=0; i<size; i++){
+                outFile << "," << name_arr[best_homolog_index[i]] << ":" << best_homolog[i];
+            }
+            outFile << std::endl;
+        }
+    }
+    outFile.close();
+    return 0;
+}

bscampp/tools/hamming_distance/src/new_hamming.cpp

@@ -0,0 +1,161 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+#include <omp.h>
+
+
+int main( int argc, char **argv ){
+    if( argc <= 6 ){
+        std::cerr << "Usage: "<<argv[0]<<" [ref infile] [nbr ref records] [query infile] [nbr query records] [outfile] [nbr of leaves returned]" << std::endl;
+        return -1;
+    }
+ 
+    std::ifstream input_q(argv[1]);
+    if(!input_q.good()){
+        std::cerr << "Error opening '"<<argv[1]<<"'. Bailing out." << std::endl;
+        return -1;
+    }
+    //std::cout << argv[2] << std::endl;
+    int ref_size = std::stoi(argv[2]) + 3;
+    int count1 = 0;
+    std::vector<std::string> name_arr(ref_size);
+    std::vector<std::string> seq_arr(ref_size);
+    std::string line, name, content;
+
+    while( std::getline( input_q, line ).good() ){
+        if( line.empty() || line[0] == '>' ){ // Identifier marker
+            if( !name.empty() ){ // Print out what we read from the last entry
+                //std::cout << name << " : " << content << std::endl;
+                name_arr[count1] = name.c_str();
+                seq_arr[count1] = content.c_str();
+                name.clear();
+                //std::cout << count1<< " : " << name_arr[count1] <<std::endl;
+                count1++;
+            }
+            if( !line.empty() ){
+                name = line.substr(1);
+            }
+            content.clear();
+        } else if( !name.empty() ){
+            if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed
+                name.clear();
+                content.clear();
+            } else {
+                content += line;
+            }
+        }
+
+    }
+    
+    //std::cout << "here" << std::endl;
+    
+    if( !name.empty() ){ // Print out what we read from the last entry
+        //std::cout << name << " : " << content << std::endl;        
+        name_arr[count1] = name;
+        seq_arr[count1] = content;
+        count1++;
+    }
+  
+  
+    std::ifstream input(argv[3]);
+    if(!input.good()){
+        std::cerr << "Error opening '"<<argv[3]<<"'. Bailing out." << std::endl;
+        return -1;
+    }
+    //std::cout << argv[4] << std::endl;
+    int q_size = std::stoi(argv[4]) + 3;
+    int count2 = 0;
+    //std::string q_name_arr[std::stoi(argv[4])+3];
+    //std::string q_seq_arr[std::stoi(argv[4])+3];
+    std::vector<std::string> q_name_arr(q_size);
+    std::vector<std::string> q_seq_arr(q_size);
+    name = "";
+    while( std::getline( input, line ).good() ){
+        if( line.empty() || line[0] == '>' ){ // Identifier marker
+            if( !name.empty() ){ // Print out what we read from the last entry
+                //std::cout << name << " : " << content << std::endl;
+                q_name_arr[count2] = name.c_str();
+                q_seq_arr[count2] = content.c_str();
+                name.clear();
+                //std::cout << count2 << " : " << q_name_arr[count2] <<std::endl;
+                count2++;
+            }
+            if( !line.empty() ){
+                name = line.substr(1);
+            }
+            content.clear();
+        } else if( !name.empty() ){
+            if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed
+                name.clear();
+                content.clear();
+            } else {
+                content += line;
+            }
+        }
+
+    }
+    
+
+    if( !name.empty() ){ // Print out what we read from the last entry
+        //std::cout << name << " : " << content << std::endl;        
+        q_name_arr[count2] = name;
+        q_seq_arr[count2] = content;
+        count2++;
+    }
+
+    //std::cout << "ref count: "<< count1 <<" query count2: " <<count2 << std::endl;
+
+    std::ofstream outFile(argv[5]);
+
+    #pragma omp parallel for 
+    for (int c2=0; c2<count2; c2++){ //query seq array
+    
+        int size = std::stoi(argv[6]);
+        int best_hamming[size];
+        int best_index[size];
+        int furthest_index = 0;
+
+        for (int i=0; i<size; i++){
+            best_index[i] = 0;
+            best_hamming[i] = 999999999;
+        }
+
+        for (int c1=0; c1<count1 ; c1++) { //ref seq array
+            int count = 0;
+            int len = seq_arr[c1].length();
+            for(int i=0; i < len; i++) {
+                if(seq_arr[c1][i] != q_seq_arr[c2][i]) {
+                    count++;
+                    if (count > best_hamming[furthest_index]) {
+                        break;
+                    }
+                }
+            }
+            //std::cout << "here" << std::endl;
+            if (count <= best_hamming[furthest_index]) {
+                best_hamming[furthest_index] = count;
+                best_index[furthest_index] = c1;
+                int high_hamming = 0;
+                int high_index = 0;
+                for (int i=0; i<size; i++){
+                    if (best_hamming[i] > high_hamming){
+                        high_hamming = best_hamming[i];
+                        high_index = i;
+                    }
+                furthest_index = high_index;
+                }
+            }
+        }
+        #pragma omp critical
+        {
+            outFile << q_name_arr[c2];
+            for (int i=0; i<size; i++){
+                outFile << "," << name_arr[best_index[i]] << ":" << best_hamming[i];
+            }
+            outFile << std::endl;
+        }
+    }
+    outFile.close();
+    return 0;
+}