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/*
* fastamap.cpp
* mothur
*
* Created by Sarah Westcott on 1/16/09.
* Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
*
*/
#include "fastamap.h"
#include "sequence.hpp"
/*******************************************************************************/
void FastaMap::readFastaFile(string inFileName) {
try {
ifstream in;
m->openInputFile(inFileName, in);
string name, sequence, line;
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].names = name;
}else { // its a duplicate.
data[sequence].names += "," + name;
// data[sequence].groupnumber++;
}
}
m->gobble(in);
}
in.close();
}
catch(exception& e) {
m->errorOut(e, "FastaMap", "readFastaFile");
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;
}
/*******************************************************************************/
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::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::sizeUnique(){ //returns datas size which is the number of unique sequences
return data.size();
}
/*******************************************************************************/
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 (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) {
m->errorOut(e, "FastaMap", "printNamesFile");
exit(1);
}
}
/*******************************************************************************/
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);
}
}
/*******************************************************************************/
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