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#ifndef SPLITGROUPSCOMMAND_H
#define SPLITGROUPSCOMMAND_H
/*
* splitgroupscommand.h
* Mothur
*
* Created by westcott on 9/20/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
/* split.groups - given a group file, split sequences and names files in to separate files *.group1.fasta and .group1.names. */
#include "command.hpp"
#include "groupmap.h"
#include "sequence.hpp"
#include "fastqread.h"
#include "getseqscommand.h"
//**********************************************************************************************************************
struct flowOutput {
string output;
string filename;
int total;
flowOutput(string f) { filename = f; output = ""; total = 0; }
flowOutput() { filename = ""; output = ""; total = 0; }
flowOutput(string f, string o, int t) : filename(f), output(o), total(t) {}
};
//**********************************************************************************************************************
struct fastqOutput {
vector<FastqRead> output;
string filename;
int total;
fastqOutput(string f) { filename = f; total = 0; }
fastqOutput() { filename = ""; total = 0; }
};
//**********************************************************************************************************************
struct splitGroupsStruct {
string groupfile, countfile, namefile, inputFileName, format;
int start, end;
bool isFastq;
vector<string> Groups;
map<string, fastqOutput> parsedFastqData;
map<string, flowOutput> parsedFlowData;
map<string, vector<string> > outputTypes;
vector<string> outputNames;
MothurOut* m;
Utils util;
splitGroupsStruct(string group, string count, string name, vector<string> g, int st, int en) : groupfile(group), countfile(count), namefile(name), start(st), end(en) {
m = MothurOut::getInstance(); format = "illumina1.8+"; isFastq = true;
for (int i = st; i < en; i++) { Groups.push_back(g[i]); }
}
void setFiles(string input, string outfileRoot, string ext) {
inputFileName = input;
int numFlows = 0;
if (ext != ".fastq") {
ifstream in; util.openInputFile(input, in);
in >> numFlows; in.close();
}
for (int i = 0; i < Groups.size(); i++) {
string newFileName = outfileRoot + Groups[i] + ext;
if (ext == ".fastq") {
fastqOutput thisGroupsInfo(newFileName);
parsedFastqData[Groups[i]] = thisGroupsInfo;
ofstream out; util.openOutputFile(newFileName, out); out.close(); //clear file for append
}else {
flowOutput thisGroupsInfo(newFileName);
parsedFlowData[Groups[i]] = thisGroupsInfo;
isFastq = false;
ofstream out; util.openOutputFile(newFileName, out); out << numFlows << endl; out.close(); //clear file for append
}
if (m->getControl_pressed()) { break; }
}
}
void setFormat(string form) { format = form; }
};
//**********************************************************************************************************************
struct splitGroups2Struct {
string groupfile, countfile, namefile, fastafile, listfile, outputDir;
int start, end;
vector<string> Groups;
map<string, vector<string> > group2Files; //GroupName -> files(fasta, list, count) or GroupName -> files(fasta, list, group, name)
map<string, vector<string> > outputTypes;
vector<string> outputNames;
MothurOut* m;
Utils util;
splitGroups2Struct(string group, string count, string name, vector<string> g, int st, int en) : groupfile(group), countfile(count), namefile(name), start(st), end(en) {
m = MothurOut::getInstance();
for (int i = st; i < en; i++) { Groups.push_back(g[i]); }
}
void setFiles(string fasta, string list, string outd) {
fastafile = fasta;
listfile = list;
outputDir = outd;
string fastaFileRoot = outputDir + util.getRootName(util.getSimpleName(fastafile));
string listFileRoot = outputDir + util.getRootName(util.getSimpleName(listfile));
string listExt = util.getExtension(listfile);
string fastaExt = util.getExtension(fastafile);
string countFileRoot, countExt, nameFileRoot, nameExt, groupFileRoot, groupExt;
if (countfile != "") {
countFileRoot = outputDir + util.getRootName(util.getSimpleName(countfile));
countExt = util.getExtension(countfile);
groupFileRoot = ""; groupExt = ""; nameFileRoot = ""; nameExt = "";
}else {
groupFileRoot = outputDir + util.getRootName(util.getSimpleName(groupfile));
groupExt = util.getExtension(groupfile);
if (namefile != "") {
nameFileRoot = outputDir + util.getRootName(util.getSimpleName(namefile));
nameExt = util.getExtension(namefile);
}else { nameFileRoot = ""; nameExt = ""; }
countFileRoot = ""; countExt = "";
}
for (int i = 0; i < Groups.size(); i++) {
if (m->getControl_pressed()) { break; }
string newListFileName = listFileRoot + Groups[i] + listExt;
string newFastaFileName = fastaFileRoot + Groups[i] + fastaExt;
string newCountFileName = countFileRoot + Groups[i] + countExt;
string newGroupFileName = groupFileRoot + Groups[i] + groupExt;
string newNameFileName = nameFileRoot + Groups[i] + nameExt;
vector<string> files;
if (fastafile != "") { files.push_back(newFastaFileName); }else { files.push_back(""); }
if (listfile != "") { files.push_back(newListFileName); }else { files.push_back(""); }
if (countfile != "") {
files.push_back(newCountFileName);
}else if (groupfile != "") {
files.push_back(newGroupFileName);
if (namefile != "") {
files.push_back(newNameFileName);
}//else{ files.push_back(""); }
}
group2Files[Groups[i]] = files;
}
}
};
//**********************************************************************************************************************
struct splitGroups3Struct {
string countfile, fastafile, outputDir;
int start, end, splitNum;
vector<string> Groups;
vector< string > fileRootExts; // fastafileRoot, fastaFileExtentsions, countfileRoot, countFileExtension,
map<string, vector<string> > outputTypes;
vector<string> outputNames;
MothurOut* m;
Utils util;
splitGroups3Struct(string count, string fasta, string outd, vector<string> g, int st, int en) : fastafile(fasta), countfile(count), outputDir(outd), start(st), end(en) {
m = MothurOut::getInstance();
for (int i = st; i < en; i++) { Groups.push_back(g[i]); }
splitNum = 10;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir = util.hasPath(fastafile); }
string fastaFileRoot = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
string fastaExt = util.getExtension(fastafile);
if (outputDir == "") { thisOutputDir = util.hasPath(countfile); }
string countFileRoot = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
string countExt = util.getExtension(countfile);
fileRootExts.push_back(fastaFileRoot); fileRootExts.push_back(fastaExt);
fileRootExts.push_back(countFileRoot); fileRootExts.push_back(countExt);
}
};
/***************************************************************************************/
class SplitGroupCommand : public Command {
public:
SplitGroupCommand(string);
SplitGroupCommand(vector<string>, string fasta, string count, string o); //used by splitbySample algos
~SplitGroupCommand() = default;
vector<string> setParameters();
string getCommandName() { return "split.groups"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
string getDescription() { return "split a name or fasta file by group"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
vector<linePair> lines;
string namefile, groupfile, countfile, groups, fastafile, flowfile, fastqfile, format, listfile;
vector<string> Groups;
bool abort;
int processors;
void splitCountOrGroup(bool);
void splitFastaCount();
void splitFastqOrFlow(string, string);
};
/***************************************************************************************/
#endif
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