*/
#include "fastamap.h"
+#include "sequence.hpp"
/*******************************************************************************/
-void FastaMap::readFastaFile(ifstream& in) {
+
+void FastaMap::readFastaFile(string inFileName) {
try {
+ ifstream in;
+ m->openInputFile(inFileName, in);
string name, sequence, line;
sequence = "";
-
- getline(in, line);
- name = line.substr(1, line.length()); //rips off '>'
-
- //read through file
- while (getline(in, line)) {
- if (isalnum(line.at(0))){ //if it's a sequence line
- sequence += line;
- }
- else{
- //input sequence info into map
- it = data.find(sequence);
+ string temp;
+ map<string, string>::iterator itName;
+
+
+ while(!in.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ itName = seqmap.find(name);
+ if (itName == seqmap.end()) { seqmap[name] = sequence; }
+ else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+ map<string,group>::iterator it = data.find(sequence);
if (it == data.end()) { //it's unique.
data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
- data[sequence].groupnumber = 1;
+ // data[sequence].groupnumber = 1;
data[sequence].names = name;
}else { // its a duplicate.
data[sequence].names += "," + name;
- data[sequence].groupnumber++;
- }
- name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
- sequence = "";
+ // data[sequence].groupnumber++;
+ }
}
+ m->gobble(in);
}
-
- //store last sequence and name info.
- it = data.find(sequence);
- if (it == data.end()) { //it's unique.
- data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
- data[sequence].groupnumber = 1;
- data[sequence].names = name;
- }else { // its a duplicate.
- data[sequence].names += "," + name;
- data[sequence].groupnumber++;
- }
+ in.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FastaMap", "readFastaFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the FastaMap class function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
+}
+
+/*******************************************************************************/
+
+void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
+
+ ifstream oldNameFile;
+ m->openInputFile(oldNameFileName, oldNameFile);
+
+ map<string,string> oldNameMap;
+ map<string, string>::iterator itName;
+ string name, list;
+ while(!oldNameFile.eof()){
+ if (m->control_pressed) { break; }
+
+ oldNameFile >> name; m->gobble(oldNameFile);
+ oldNameFile >> list;
+ oldNameMap[name] = list;
+ m->gobble(oldNameFile);
}
+ oldNameFile.close();
+
+ ifstream inFASTA;
+ m->openInputFile(inFastaFile, inFASTA);
+ string sequence;
+ while(!inFASTA.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(inFASTA);
+ name = currSeq.getName();
+
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ itName = seqmap.find(name);
+ if (itName == seqmap.end()) { seqmap[name] = sequence; }
+ else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+ seqmap[name] = sequence;
+ map<string,group>::iterator it = data.find(sequence);
+ if (it == data.end()) { //it's unique.
+ data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
+ // data[sequence].groupnumber = 1;
+ data[sequence].names = oldNameMap[name];
+ }else { // its a duplicate.
+ data[sequence].names += "," + oldNameMap[name];
+ // data[sequence].groupnumber++;
+ }
+ }
+ m->gobble(inFASTA);
+ }
+
+
+ inFASTA.close();
}
+
/*******************************************************************************/
+
string FastaMap::getGroupName(string seq) { //pass a sequence name get its group
return data[seq].groupname;
}
+
/*******************************************************************************/
+
string FastaMap::getNames(string seq) { //pass a sequence get the string of names in the group separated by ','s.
return data[seq].names;
}
+
/*******************************************************************************/
-int FastaMap::getGroupNumber(string seq) { //pass a sequence get the number of identical sequences.
- return data[seq].groupnumber;
-}
-/*******************************************************************************/
-void FastaMap::push_back(string seq, string Name) {//sequencename, name
- data[seq].groupname = Name;
- data[seq].names = Name;
-}
-/*******************************************************************************/
-void FastaMap::set(string seq, string groupName, string Names) {
- data[seq].groupname = groupName;
- data[seq].names = Names;
-}
+
+string FastaMap::getSequence(string name) {
+
+ map<string,string>::iterator it = seqmap.find(name);
+ if (it == seqmap.end()) { return "not found"; }
+ else { return it->second; }
+
+}
+
/*******************************************************************************/
-void FastaMap::clear() { //clears out data
- data.clear();
+
+void FastaMap::push_back(string name, string seq) {
+
+ map<string,group>::iterator it = data.find(seq);
+ if (it == data.end()) { //it's unique.
+ data[seq].groupname = name; //group name will be the name of the first duplicate sequence found.
+ data[seq].names = name;
+ }else { // its a duplicate.
+ data[seq].names += "," + name;
+ }
+ seqmap[name] = seq;
}
+
/*******************************************************************************/
-int FastaMap::size(){ //returns datas size which is the number of unique sequences
+
+int FastaMap::sizeUnique(){ //returns datas size which is the number of unique sequences
return data.size();
}
+
/*******************************************************************************/
-void FastaMap::print(ostream& out){ //prints data
+
+void FastaMap::printNamesFile(string outFileName){ //prints data
try {
+ ofstream outFile;
+ m->openOutputFile(outFileName, outFile);
+
// two column file created with groupname and them list of identical sequence names
- for (it = data.begin(); it != data.end(); it++) {
- out << it->second.groupname << '\t' << it->second.names << endl;
+ for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
+ outFile << it->second.groupname << '\t' << it->second.names << endl;
}
+ outFile.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FastaMap", "printNamesFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the FastaMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/*******************************************************************************/
+
+void FastaMap::printCondensedFasta(string outFileName){ //prints data
+ try {
+ ofstream out;
+ m->openOutputFile(outFileName, out);
+ //creates a fasta file
+ for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
+ out << ">" << it->second.groupname << endl;
+ out << it->first << endl;
+ }
+ out.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FastaMap", "printCondensedFasta");
exit(1);
}
}
+
/*******************************************************************************/
+
projects / mothur.git / blobdiff