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Changes make.contigs output from group to count
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#793 #792
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@mothur-westcott
mothur-westcott committed Sep 22, 2021
1 parent d1d3574 commit ca27345
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Showing 2 changed files with 16 additions and 20 deletions.
34 changes: 15 additions & 19 deletions source/commands/makecontigscommand.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

#include "makecontigscommand.h"
#include "contigsreport.hpp"
#include "counttable.h"

//**************************************************************************************************

Expand Down Expand Up @@ -126,7 +127,7 @@ vector<string> MakeContigsCommand::setParameters(){
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["report"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["count"] = tempOutNames;

vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
Expand All @@ -142,7 +143,7 @@ string MakeContigsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs a fasta file. \n";
helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a count file will be created.\n";
helpString += "If a forward index or reverse index file is provided barcodes be trimmed, and a group file will be created. The oligos parameter is required if an index file is given.\n";
helpString += "The make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, findex, rindex, qfile, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, maxee, allfiles and processors.\n";
helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
Expand Down Expand Up @@ -186,7 +187,7 @@ string MakeContigsCommand::getOutputPattern(string type) {

if (type == "fasta") { pattern = "[filename],[tag],contigs.fasta"; }
else if (type == "qfile") { pattern = "[filename],[tag],contigs.qual"; }
else if (type == "group") { pattern = "[filename],[tag],contigs.groups"; }
else if (type == "count") { pattern = "[filename],[tag],contigs.count_table"; }
else if (type == "report") { pattern = "[filename],[tag],contigs.report"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }

Expand Down Expand Up @@ -349,9 +350,6 @@ MakeContigsCommand::MakeContigsCommand(string option) : Command() {

temp = validParameter.valid(parameters, "checkorient"); if (temp == "not found") { temp = "T"; }
reorient = util.isTrue(temp);


if (allFiles && (oligosfile == "")) { m->mothurOut("[ERROR]: You can only use the allfiles option with an oligos file.\n"); abort = true; }
}

}
Expand Down Expand Up @@ -387,9 +385,9 @@ int MakeContigsCommand::execute(){
map<string, string> vars;
vars["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(inputFile));
vars["[tag]"] = "";
string outputGroupFileName = getOutputFileName("group",vars);
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
createGroupFile(outputGroupFileName, outFastaFile);
string outputCountFileName = getOutputFileName("count",vars);
outputNames.push_back(outputCountFileName); outputTypes["count"].push_back(outputCountFileName);
createCountFile(outputCountFileName, outFastaFile);
}

//add headers to mismatch file
Expand Down Expand Up @@ -437,18 +435,16 @@ int MakeContigsCommand::execute(){
}
}
/**************************************************************************************************/
int MakeContigsCommand::createGroupFile(string outputGroupFile, string resultFastafile) {
int MakeContigsCommand::createCountFile(string outputGroupFile, string resultFastafile) {
try {
ofstream outGroup; util.openOutputFile(outputGroupFile, outGroup);
for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
outGroup << itGroup->first << '\t' << itGroup->second << endl; //print group file
}
outGroup.close();


CountTable ct; ct.createTable(groupMap);
ct.printCompressedTable(outputGroupFile);

if(allFiles){
//run split.groups command
//use unique.seqs to create new name and fastafile
string inputString = "fasta=" + resultFastafile + ", group=" + outputGroupFile;
string inputString = "fasta=" + resultFastafile + ", count=" + outputGroupFile;
m->mothurOut("/******************************************/\n");
m->mothurOut("Generating allfiles... Running command: split.groups(" + inputString + ")\n");
current->setMothurCalling(true);
Expand All @@ -466,7 +462,7 @@ int MakeContigsCommand::createGroupFile(string outputGroupFile, string resultFas
return 0;
}
catch(exception& e) {
m->errorOut(e, "MakeContigsCommand", "createGroupFile");
m->errorOut(e, "MakeContigsCommand", "createCountFile");
exit(1);
}
}
Expand Down Expand Up @@ -2679,7 +2675,7 @@ bool MakeContigsCommand::getOligos(map<int, oligosPair>& pairedPrimers, map<int,
if (numSpacers != 0) { m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n"); }

vector<string> groupNames = oligos.getGroupNames();
if (groupNames.size() == 0) { allFiles = 0; allBlank = true; }
if (groupNames.size() == 0) { allFiles = false; allBlank = true; }

if (allBlank) {
m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile.\n");
Expand Down
2 changes: 1 addition & 1 deletion source/commands/makecontigscommand.h
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ class MakeContigsCommand : public Command {
unsigned long long createProcesses(vector<string>, vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, string, map<int, oligosPair>& pairedPrimers, map<int, oligosPair>& rpairedPrimers, map<int, oligosPair>&, map<int, oligosPair>& pairedBarcodes, map<int, oligosPair>& rpairedBarcodes,map<int, oligosPair>&, vector<string>& barcodeNames, vector<string>& primerNames);
unsigned long long createProcessesGroups(vector< vector<string> >, string compositeFastaFile, string compositeScrapFastaFile, string compositeQualFile, string compositeScrapQualFile, string compositeMisMatchFile, map<int, string>& file2Groups);

int createGroupFile(string outputGroupFile, string resultFastafile);
int createCountFile(string outputGroupFile, string resultFastafile);
vector< vector<string> > readFileNames(string, map<int, string>&);
bool getOligos(map<int, oligosPair>& pairedPrimers, map<int, oligosPair>& rpairedPrimers, map<int, oligosPair>&, map<int, oligosPair>& pairedBarcodes, map<int, oligosPair>& rpairedBarcodes, map<int, oligosPair>&, vector<string>& barcodeNames, vector<string>& primerNames);
int setLines(vector<string>, vector<string>, vector<linePair>& fastaFilePos, vector<linePair>& qfileFilePos, char delim); //the delim let you know whether this is fasta and qual, or fastq and index. linePair entries will always be in sets of two. One for the forward and one for hte reverse. (fastaFilePos[0] - ffasta, fastaFilePos[1] - rfasta) - processor1
Expand Down

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