*/
#include "seqsummarycommand.h"
-
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> SeqSummaryCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n";
- helpString += "The summary.seqs command parameters are fasta, name and processors, fasta is required, unless you have a valid current fasta file.\n";
+ helpString += "The summary.seqs command parameters are fasta, name, count and processors, fasta is required, unless you have a valid current fasta file.\n";
helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
+ helpString += "The count parameter allows you to enter a count file associated with your fasta file. \n";
helpString += "The summary.seqs command should be in the following format: \n";
helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
}
}
//**********************************************************************************************************************
-string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SeqSummaryCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
//initialize outputTypes
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
m->setProcessors(temp);
m->mothurConvert(temp, processors);
- if (namefile == "") {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
-
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
//set current fasta to fastafile
m->setFastaFile(fastafile);
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string summaryFile = getOutputFileName("summary",variables);
int numSeqs = 0;
vector<int> longHomoPolymer;
if (namefile != "") { nameMap = m->readNames(namefile); }
+ else if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile, false, false);
+ nameMap = ct.getNameMap();
+ }
if (m->control_pressed) { return 0; }
int size = startPosition.size();
//find means
- float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
+ unsigned long long meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
for (int i = 0; i < size; i++) {
meanStartPosition += startPosition[i];
meanAmbigBases += ambigBases[i];
meanLongHomoPolymer += longHomoPolymer[i];
}
- //this is an int divide so the remainder is lost
- meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
+
+ double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer;
+
+ meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size;
int ptile0_25 = int(size * 0.025);
int ptile25 = int(size * 0.250);
m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
- m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
+ m->mothurOut("Mean:\t" + toString(meanstartPosition) + "\t" + toString(meanendPosition) + "\t" + toString(meanseqLength) + "\t" + toString(meanambigBases) + "\t" + toString(meanlongHomoPolymer)); m->mothurOutEndLine();
- if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
+ if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
m->mothurOutEndLine();
}
#endif
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("summary");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
bool done = false;
int count = 0;
-
+
+
while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
-
+
+ if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n"); }
+
Sequence current(in); m->gobble(in);
-
+
if (current.getName() != "") {
+ if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
+
int num = 1;
- if (namefile != "") {
+ if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
- if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your name or count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
ambigBases.push_back(current.getAmbigBases());
longHomoPolymer.push_back(current.getLongHomoPolymer());
}
-
count++;
outSummary << current.getName() << '\t';
outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
if (in.eof()) { break; }
#endif
-
- //report progress
- //if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
- //report progress
- //if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+
in.close();
return count;
if (current.getName() != "") {
int num = 1;
- if (namefile != "") {
+ if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
- if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
+ if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your name or count file, please correct." << endl; m->control_pressed = true; }
else { num = it->second; }
}
//for each sequence this sequence represents
- for (int i = 0; i < num; i++) {
+ for (int j = 0; j < num; j++) {
startPosition.push_back(current.getStartPos());
endPosition.push_back(current.getEndPos());
seqLength.push_back(current.getNumBases());
vector<seqSumData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
-
+
+ bool hasNameMap = false;
+ if ((namefile !="") || (countfile != "")) { hasNameMap = true; }
+
//Create processor worker threads.
for( int i=0; i<processors-1; i++ ){
string extension = "";
if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
+ seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, hasNameMap, nameMap);
pDataArray.push_back(tempSum);
//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ if (pDataArray[i]->count != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) { startPosition.push_back(pDataArray[i]->startPosition[k]); }
for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) { endPosition.push_back(pDataArray[i]->endPosition[k]); }
for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); }
projects / mothur.git / blobdiff