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//
// filefile.cpp
// Mothur
//
// Created by Sarah Westcott on 12/5/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#include "filefile.hpp"
#include "utils.hpp"
/**************************************************************************************************/
FileFile::FileFile(string f, string md) : filename(f), mode(md) {
try {
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
mpath = current->getProgramPath();
columnWithGroups = false;
fileOption = 0;
gz = false;
hasIndex = false;
read(f, mode);
}
catch(exception& e) {
m->errorOut(e, "FileFile", "FileFile");
exit(1);
}
}
/**************************************************************************************************
/*
file option 1
sfffile1 oligosfile1
sfffile2 oligosfile2
...
file option 2
fastqfile1 oligosfile1
fastqfile2 oligosfile2
...
file option 3
ffastqfile1 rfastqfile1
ffastqfile2 rfastqfile2
...
file option 4 - only vaild if mode is set to parsefastqpacbio
group1 pacBiofastqfile1
group2 pacBiofastqfile2
...
file option 5
group fastqfile fastqfile
group fastqfile fastqfile
group fastqfile fastqfile
...
file option 6
My.forward.fastq My.reverse.fastq none My.rindex.fastq //none is an option is no forward or reverse index file
...
file option 7 - for make.count command
group fastafile
file option 8 - for make.count command
group forwardFasta reverseFasta
*/
/**************************************************************************************************/
void FileFile::read(string f, string mode){
try {
filename = f;
bool allGZ = true; bool allPlainTxt = true;
ifstream in; util.openInputFile(filename, in);
while(!in.eof()) {
if (m->getControl_pressed()) { break; }
bool skip = false;
string line = util.getline(in); gobble(in);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + line +"\n"); }
if(line[0] == '#'){ } //ignore
else {
vector<string> pieces = util.splitWhiteSpace(line);
if (mode == "make.count") {
vector<string> thisGroupsFiles;
if ((pieces.size() == 2) || (pieces.size() == 3)) {
util.checkGroupName(pieces[0]);
bool skip = false;
//check to make fasta file opens
bool ableToOpen = util.checkLocations(pieces[1], current->getLocations());
if (ableToOpen) {
if (util.isBlank(pieces[1])) { m->mothurOut("[WARNING]: " + pieces[1] + " is blank, skipping.\n"); skip=true; }
}else { m->mothurOut("[WARNING]: can't find " + pieces[1] + ", ignoring.\n"); skip = true; }
if (pieces.size() == 3) {
//check to make fasta file opens
ableToOpen = util.checkLocations(pieces[2], current->getLocations());
if (ableToOpen) {
if (util.isBlank(pieces[2])) { m->mothurOut("[WARNING]: " + pieces[2] + " is blank, skipping.\n"); skip=true; }
}else { m->mothurOut("[WARNING]: can't find " + pieces[2] + ", ignoring.\n"); skip = true; }
}
if (!skip) {
groupNames.push_back(pieces[0]);
thisGroupsFiles.push_back(pieces[1]);
if (pieces.size() == 3) { thisGroupsFiles.push_back(pieces[2]); }
files.push_back(thisGroupsFiles);
}
}else {
m->mothurOut("[ERROR]: Found " + toString(pieces.size()) + " columns. mothur expects the file file for make.count to be in 2 or 3 column form. \n");
}
}else {
string group = ""; string forward, reverse, findex, rindex;
skip = validateFiles(pieces, forward, reverse, findex, rindex, group);
if (!skip) { //good pair
groupNames.push_back(group);
if (((findex != "") || (rindex != ""))) { hasIndex = true; }
if ((mode == "contigs") || (mode == "sra")) { setGZ(forward, reverse, findex, rindex, allGZ, allPlainTxt); }
vector<string> pair;
pair.push_back(forward); pair.push_back(reverse); pair.push_back(findex); pair.push_back(rindex);
files.push_back(pair);
}
}
}
}
in.close();
if ((mode == "contigs") || (mode == "sra")){ if (allGZ) { gz = true; } else { gz = false; } }
if (files.size() == 0) { m->setControl_pressed(true); return; }
if (mode == "make.count") {
fileOption = 6 + (int)files[0].size(); //either 1 or 2
}
}
catch(exception& e) {
m->errorOut(e, "FileFile", "read");
exit(1);
}
}
/**************************************************************************************************/
bool FileFile::validateFiles(vector<string> pieces, string& forward, string& reverse, string& findex, string& rindex, string& group){
try {
bool skip = false; //innocent until proven guilty
group = "";
if (pieces.size() == 2) {
if (mode == "parsefastqpacbio") {
group = pieces[0];
util.checkGroupName(group);
forward = pieces[1];
reverse = "";
}else {
forward = pieces[0];
reverse = pieces[1];
group = "";
}
findex = "";
rindex = "";
fileOption = 1;
}else if (pieces.size() == 3) {
group = pieces[0];
util.checkGroupName(group);
forward = pieces[1];
reverse = pieces[2];
if ((reverse == "none") || (reverse == "NONE")){ reverse = "NONE"; }
findex = "";
rindex = "";
fileOption = 2;
columnWithGroups = true;
}else if (pieces.size() == 4) {
forward = pieces[0];
reverse = pieces[1];
findex = pieces[2];
rindex = pieces[3];
if ((findex == "none") || (findex == "NONE")){ findex = "NONE"; }
if ((rindex == "none") || (rindex == "NONE")){ rindex = "NONE"; }
fileOption = 3;
}else {
m->mothurOut("[ERROR]: file lines can be 2, 3, or 4 columns. The forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file, or forward fastq file then reverse fastq then forward index and reverse index file. If you only have one index file add 'none' for the other one. \n"); m->setControl_pressed(true);
}
if (m->getDebug()) { m->mothurOut("[DEBUG]: group = " + group + ", forward = " + forward + ", reverse = " + reverse + ", forwardIndex = " + findex + ", reverseIndex = " + rindex + ".\n"); }
//check to make sure both are able to be opened
bool openForward = util.checkLocations(forward, current->getLocations());
if (openForward) {
if (util.isBlank(forward)) { m->mothurOut("[WARNING]: " + forward + " is blank, skipping.\n"); skip=true; }
}else { m->mothurOut("[WARNING]: can't find " + forward + ", ignoring pair.\n"); }
bool openReverse = true;
if ((reverse != "") && (reverse != "NONE")){
openReverse = util.checkLocations(reverse, current->getLocations());
if (openReverse) {
if (util.isBlank(reverse)) { m->mothurOut("[WARNING]: " + reverse + " is blank, skipping.\n"); skip=true; }
}else { m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n"); }
}
bool openFindex = true;
if ((findex != "") && (findex != "NONE")){
openFindex = util.checkLocations(findex, current->getLocations());
if (openFindex) {
if (util.isBlank(findex)) { m->mothurOut("[WARNING]: " + findex + " is blank, skipping.\n"); skip=true; }
}else { m->mothurOut("[WARNING]: can't find " + findex + ", ignoring pair.\n"); }
}
bool openRindex = true;
if ((rindex != "") && (rindex != "NONE")) {
openRindex = util.checkLocations(rindex, current->getLocations());
if (openRindex) {
if (util.isBlank(rindex)) { m->mothurOut("[WARNING]: " + rindex + " is blank, skipping.\n"); skip=true; }
}else { m->mothurOut("[WARNING]: can't find " + rindex + ", ignoring pair.\n"); }
}
if ((openForward) && (openReverse) && (openFindex) && (openRindex) && (!skip)) { //good pair
return false;
}else { return true; }
}
catch(exception& e) {
m->errorOut(e, "FileFile", "validateFiles");
exit(1);
}
}
/**************************************************************************************************/
void FileFile::setGZ(string forward, string reverse, string findex, string rindex, bool& allGZ, bool& allPlainTxt){
try {
#ifdef USE_BOOST
if (util.isGZ(forward)[1]) { allPlainTxt = false; }
else { allGZ = false; }
if (util.isGZ(reverse)[1]) { allPlainTxt = false; }
else { allGZ = false; }
if ((findex != "") && (findex != "NONE")) {
if (util.isGZ(findex)[1]) { allPlainTxt = false; }
else { allGZ = false; }
}
if ((rindex != "") && (rindex != "NONE")) {
if (util.isGZ(rindex)[1]) { allPlainTxt = false; }
else { allGZ = false; }
}
if (!allGZ && !allPlainTxt) { //mixed bag of files, uh oh...
m->mothurOut("[ERROR]: Your files must all be in compressed .gz form or all in plain text form. Please correct. \n"); m->setControl_pressed(true);
}
#else
allGZ=false;
#endif
}
catch(exception& e) {
m->errorOut(e, "FileFile", "setGZ");
exit(1);
}
}
/**************************************************************************************************/
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