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//
// vsearchfileparser.cpp
// Mothur
//
// Created by Sarah Westcott on 10/13/15.
// Copyright (c) 2015 Schloss Lab. All rights reserved.
//
#include "vsearchfileparser.h"
/***********************************************************************/
VsearchFileParser::VsearchFileParser(){
try {
m = MothurOut::getInstance();
fastafile = "";
namefile = "";
countfile = "";
format = "count";
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "VsearchFileParser");
exit(1);
}
}
/***********************************************************************/
VsearchFileParser::VsearchFileParser(string f){
try {
m = MothurOut::getInstance();
fastafile = f;
namefile = "";
countfile = "";
format = "count";
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "VsearchFileParser");
exit(1);
}
}
/***********************************************************************/
VsearchFileParser::VsearchFileParser(string f, string nameOrCount, string forma) {
try {
m = MothurOut::getInstance();
fastafile = f;
namefile = "";
countfile = "";
format = forma;
if (format == "name") { namefile = nameOrCount; }
else if (format == "count") { countfile = nameOrCount; }
else { m->mothurOut("[ERROR]: " + format + " is not a valid file format for the VsearchFileParser, quitting.\n"); m->setControl_pressed(true); }
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "VsearchFileParser");
exit(1);
}
}
/***********************************************************************/
string VsearchFileParser::getVsearchFile() {
try {
Utils util;
if (fastafile == "") { m->mothurOut("[ERROR]: no fasta file given, cannot continue.\n"); m->setControl_pressed(true); }
//Run unique.seqs on the data if a name or count file is not given
if ((namefile == "") && (countfile == "")) { getNamesFile(fastafile); }
else if (namefile != "") { counts = util.readNames(namefile); }
if (countfile != "") { CountTable countTable; countTable.readTable(countfile, false, false); counts = countTable.getNameMap(); }
if (m->getControl_pressed()) { return 0; }
//Remove gap characters from each sequence if needed
//Append the number of sequences that each unique sequence represents to the end of the fasta file name
//Sorts by abundance
string vsearchFastafile = createVsearchFasta(fastafile);
return vsearchFastafile;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "getVsearchFile");
exit(1);
}
}
/**********************************************************************/
string VsearchFileParser::createVsearchFasta(string inputFile){
try {
Utils util;
string vsearchFasta = util.getSimpleName(fastafile) + ".sorted.fasta.temp";
vector<seqPriorityNode> seqs;
map<string, int>::iterator it;
ifstream in; util.openInputFile(inputFile, in);
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); return vsearchFasta; }
Sequence seq(in); gobble(in);
it = counts.find(seq.getName());
if (it == counts.end()) {
m->mothurOut("[ERROR]: " + seq.getName() + " is not in your name or countfile, quitting.\n"); m->setControl_pressed(true);
}else {
seqPriorityNode temp(it->second, seq.getUnaligned(), it->first);
seqs.push_back(temp);
}
}
in.close();
util.printVsearchFile(seqs, vsearchFasta, ";size=", ";");
return vsearchFasta;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "createVsearchFasta");
exit(1);
}
}
/*************************************************************************/
string VsearchFileParser::getNamesFile(string& inputFile){
try {
m->mothurOut("\nNo namesfile given, running unique.seqs command to generate one.\n\n");
//use unique.seqs to create new name and fastafile
string inputString = "fasta=" + inputFile + ", format=count";
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: unique.seqs(" + inputString + ")\n");
Command* uniqueCommand = new UniqueSeqsCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
m->mothurOut("/******************************************/\n");
countfile = filenames["count"][0];
fastafile = filenames["fasta"][0];
return countfile;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "getNamesFile");
exit(1);
}
}
/*************************************************************************/
//S 1 275 * * * * * GQY1XT001C44N8/ab=3677/ *
ListVector VsearchFileParser::createListFile(string inputFile, int numBins, string label, map<string, int>& ct){
try {
Utils util;
map<string, string>::iterator itName;
if (format == "name") { counts.clear(); util.readNames(namefile, nameMap); }
ifstream in; util.openInputFile(inputFile, in);
ListVector list(numBins); list.setLabel(label);
int clusterNumber;
string seqName, recordType, length, percentIdentity, strand, notUsed1, notUsed2, compressedAlignment, repSequence;
while(!in.eof()) {
if (m->getControl_pressed()) { break; }
in >> recordType >> clusterNumber >> length >> percentIdentity >> strand >> notUsed1 >> notUsed2 >> compressedAlignment >> seqName >> repSequence; gobble(in);
if (recordType != "S") {
seqName = removeAbundances(seqName);
if (format == "name") {
itName = nameMap.find(seqName);
if (itName == nameMap.end()) { m->mothurOut("[ERROR]: " + seqName + " is not in your name file. Parsing error???\n"); m->setControl_pressed(true); }
else{ seqName = itName->second; }
}
string bin = list.get(clusterNumber);
if (bin == "") { bin = seqName; }
else { bin += ',' + seqName; }
list.set(clusterNumber, bin);
}
}
in.close();
ct = counts;
return list;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "createListFile");
exit(1);
}
}
/*************************************************************************/
//GQY1XT001C44N8/ab=3677/ *
string VsearchFileParser::removeAbundances(string seqName){
try {
int pos = seqName.find_last_of(";", seqName.length()-2); //don't look at the last /
if (pos != string::npos) { seqName = seqName.substr(0, pos); }
return seqName;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "removeAbundances");
exit(1);
}
}
/*************************************************************************/
//GQY1XT001C44N8/ab=3677/ *
int VsearchFileParser::getNumBins(string logfile){
try {
int numBins = 0;
ifstream in; Utils util; util.openInputFile(logfile, in);
string line;
while(!in.eof()) {
if (m->getControl_pressed()) { break; }
line = util.getline(in); gobble(in);
int pos = line.find("Clusters:");
if (pos != string::npos) {
vector<string> pieces = util.splitWhiteSpace(line);
if (pieces.size() > 1) { util.mothurConvert(pieces[1], numBins); }
break;
}
}
in.close();
return numBins;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "getNumBins");
exit(1);
}
}
/***********************************************************************/
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