CommandParameter prfastq("rfastq", "InputTypes", "", "", "none", "none", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(prfastq);
CommandParameter pfasta("ffasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastaGroup","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter prfasta("rfasta", "InputTypes", "", "", "none", "none", "none","fastaGroup",false,false,true); parameters.push_back(prfasta);
- CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(pfqual);
- CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(prqual);
+ CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",false,false,true); parameters.push_back(pfqual);
+ CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",false,false,true); parameters.push_back(prqual);
CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","fasta-qfile",false,false,true); parameters.push_back(pfile);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
- CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pthreshold("insert", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pdeltaq("deltaq", "Number", "", "6", "", "", "","",false,false); parameters.push_back(pdeltaq);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
- CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "","",false,false,true); parameters.push_back(pformat);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
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 new fasta. It will also provide new quality files if the fastq or file parameter is used.\n";
helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
- helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, format, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n";
+ helpString += "The make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, allfiles and processors.\n";
helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
- helpString += "The file parameter is 2 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column. Mothur will process each pair and create a combined fasta and qual file with all the sequences.\n";
+ helpString += "The file parameter is 2 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column. Mothur will process each pair and create a combined fasta and report file with all the sequences.\n";
helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process. If you provide one, you must provide the other.\n";
helpString += "The ffasta and rfasta parameters are used to provide a forward fasta and reverse fasta file to process. If you provide one, you must provide the other.\n";
helpString += "The fqfile and rqfile parameters are used to provide a forward quality and reverse quality files to process with the ffasta and rfasta parameters. If you provide one, you must provide the other.\n";
- helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa or illumina, default=sanger.\n";
+ helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.\n";
helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh and needleman. The default is needleman.\n";
helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
- helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
- helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+ //helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+ //helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
+ helpString += "The deltaq parameter allows you to specify the delta allowed between quality scores of a mismatched base. For example in the overlap, if deltaq=5 and in the alignment seqA, pos 200 has a quality score of 30 and the same position in seqB has a quality score of 20, you take the base from seqA (30-20 >= 5). If the quality score in seqB is 28 then the base in the consensus will be an N (30-28<5) The default is 6.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
- helpString += "The threshold parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=40.\n";
+ helpString += "The insert parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=25.\n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
helpString += "The make.contigs command should be in the following format: \n";
string pattern = "";
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 == "mismatch") { pattern = "[filename],[tag],contigs.mismatch"; }
+ else if (type == "report") { pattern = "[filename],[tag],contigs.report"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
- outputTypes["mismatch"] = tempOutNames;
+ outputTypes["report"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
- outputTypes["mismatch"] = tempOutNames;
+ outputTypes["report"] = tempOutNames;
outputTypes["group"] = tempOutNames;
m->mothurConvert(temp, gapExtend);
if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
- temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "40"; }
- m->mothurConvert(temp, threshold);
- if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
+ temp = validParameter.validFile(parameters, "insert", false); if (temp == "not found"){ temp = "25"; }
+ m->mothurConvert(temp, insert);
+ if ((insert < 0) || (insert > 40)) { m->mothurOut("[ERROR]: insert must be between 0 and 40.\n"); abort=true; }
+ temp = validParameter.validFile(parameters, "deltaq", false); if (temp == "not found"){ temp = "6"; }
+ m->mothurConvert(temp, deltaq);
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
- format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; }
+ format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "illumina1.8+"; }
- if ((format != "sanger") && (format != "illumina") && (format != "solexa")) {
- m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine();
+ if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
abort=true;
}
string compositeGroupFile = getOutputFileName("group",cvars);
cvars["[tag]"] = "trim";
string compositeFastaFile = getOutputFileName("fasta",cvars);
- string compositeQualFile = getOutputFileName("qfile",cvars);
cvars["[tag]"] = "scrap";
string compositeScrapFastaFile = getOutputFileName("fasta",cvars);
- string compositeScrapQualFile = getOutputFileName("qfile",cvars);
cvars["[tag]"] = "";
- string compositeMisMatchFile = getOutputFileName("mismatch",cvars);
+ string compositeMisMatchFile = getOutputFileName("report",cvars);
if (filesToProcess.size() > 1) { //clear files for append below
ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();
- m->openOutputFile(compositeQualFile, outCTQual); outCTQual.close();
- m->openOutputFile(compositeScrapQualFile, outCSQual); outCSQual.close();
outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);
- outputNames.push_back(compositeQualFile); outputTypes["qfile"].push_back(compositeQualFile);
- outputNames.push_back(compositeMisMatchFile); outputTypes["mismatch"].push_back(compositeMisMatchFile);
+ outputNames.push_back(compositeMisMatchFile); outputTypes["report"].push_back(compositeMisMatchFile);
outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);
- outputNames.push_back(compositeScrapQualFile); outputTypes["qfile"].push_back(compositeScrapQualFile);
}
for (int l = 0; l < filesToProcess.size(); l++) {
m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
vector<vector<string> > fastaFileNames;
- vector<vector<string> > qualFileNames;
createGroup = false;
string outputGroupFileName;
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
variables["[tag]"] = "";
if(oligosfile != ""){
- createGroup = getOligos(fastaFileNames, qualFileNames, variables["[filename]"]);
+ createGroup = getOligos(fastaFileNames, variables["[filename]"]);
if (createGroup) {
outputGroupFileName = getOutputFileName("group",variables);
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
variables["[tag]"] = "trim";
string outFastaFile = getOutputFileName("fasta",variables);
- string outQualFile = getOutputFileName("qfile",variables);
variables["[tag]"] = "scrap";
string outScrapFastaFile = getOutputFileName("fasta",variables);
- string outScrapQualFile = getOutputFileName("qfile",variables);
variables["[tag]"] = "";
- string outMisMatchFile = getOutputFileName("mismatch",variables);
+ string outMisMatchFile = getOutputFileName("report",variables);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
- if (filesToProcess[l][0][1] != "") {
- outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
- outputNames.push_back(outScrapQualFile); outputTypes["qfile"].push_back(outScrapQualFile);
- }
- outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
+ outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
m->mothurOut("Making contigs...\n");
- createProcesses(filesToProcess[l], outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames);
+ createProcesses(filesToProcess[l], outFastaFile, outScrapFastaFile, outMisMatchFile, fastaFileNames);
m->mothurOut("Done.\n");
//remove temp fasta and qual files
if(m->isBlank(fastaFileNames[i][j])){
m->mothurRemove(fastaFileNames[i][j]);
namesToRemove.insert(fastaFileNames[i][j]);
-
- if (filesToProcess[l][0][1] != "") {
- m->mothurRemove(qualFileNames[i][j]);
- namesToRemove.insert(qualFileNames[i][j]);
- }
}else{
it = uniqueFastaNames.find(fastaFileNames[i][j]);
if (it == uniqueFastaNames.end()) {
}
m->appendFiles(outMisMatchFile, compositeMisMatchFile);
m->appendFiles(outFastaFile, compositeFastaFile);
- m->appendFiles(outQualFile, compositeQualFile);
m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);
- m->appendFiles(outScrapQualFile, compositeScrapQualFile);
}
}
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
}
- string currentQual = "";
- itTypes = outputTypes.find("qfile");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
- }
-
string currentGroup = "";
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
}
}
//**********************************************************************************************************************
-int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
+int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames) {
try {
int num = 0;
vector<int> processIDS;
process++;
}else if (pid == 0){
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
- vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
if(allFiles){
ofstream temp;
if (tempFASTAFileNames[i][j] != "") {
tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
-
- if (files[processors-1][1] != "") {
- tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
- m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
- }
}
}
}
num = driver(files[process],
outputFasta + toString(getpid()) + ".temp",
- outputQual + toString(getpid()) + ".temp",
outputScrapFasta + toString(getpid()) + ".temp",
- outputScrapQual + toString(getpid()) + ".temp",
outputMisMatches + toString(getpid()) + ".temp",
- tempFASTAFileNames,
- tempPrimerQualFileNames);
+ tempFASTAFileNames, process);
//pass groupCounts to parent
ofstream out;
ofstream temp;
m->openOutputFile(outputFasta, temp); temp.close();
m->openOutputFile(outputScrapFasta, temp); temp.close();
- if (files[processors-1][1] != "") {
- m->openOutputFile(outputScrapQual, temp); temp.close();
- m->openOutputFile(outputQual, temp); temp.close();
- }
-
+
//do my part
- num = driver(files[processors-1], outputFasta, outputQual, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames);
+ num = driver(files[processors-1], outputFasta, outputScrapFasta, outputMisMatches, fastaFileNames, processors-1);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
string extension = "";
if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
- vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
-
+
if(allFiles){
ofstream temp;
if (tempFASTAFileNames[i][j] != "") {
tempFASTAFileNames[i][j] += extension;
m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
-
- if (files[processors-1][1] != "") {
- tempPrimerQualFileNames[i][j] += extension;
- m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
- }
}
}
}
}
- contigsData* tempcontig = new contigsData(files[h], (outputFasta + extension), (outputQual + extension), (outputScrapFasta + extension), (outputScrapQual + extension),(outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, barcodes, primers, tempFASTAFileNames, tempPrimerQualFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createGroup, allFiles, h);
+ contigsData* tempcontig = new contigsData(files[h], (outputFasta + extension), (outputScrapFasta + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, barcodes, primers, tempFASTAFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createGroup, allFiles, h);
pDataArray.push_back(tempcontig);
hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
}
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
- vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
if(allFiles){
ofstream temp;
if (tempFASTAFileNames[i][j] != "") {
tempFASTAFileNames[i][j] += extension;
m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
-
- if (files[processors-1][1] != "") {
- tempPrimerQualFileNames[i][j] += extension;
- m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
- }
}
}
}
ofstream temp;
m->openOutputFile(outputFasta, temp); temp.close();
m->openOutputFile(outputScrapFasta, temp); temp.close();
- if (files[processors-1][1] != "") {
- m->openOutputFile(outputScrapQual, temp); temp.close();
- m->openOutputFile(outputQual, temp); temp.close();
- }
//do my part
processIDS.push_back(processors-1);
- num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputQual+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputScrapQual+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames);
+ num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, processors-1);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
-
- if (files[processors-1][1] != "") {
- m->appendFiles((outputScrapQual + toString(processIDS[i]) + ".temp"), outputScrapQual);
- m->mothurRemove((outputScrapQual + toString(processIDS[i]) + ".temp"));
-
- m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
- m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
- }
m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
if (fastaFileNames[j][k] != "") {
m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
-
- if (files[processors-1][1] != "") {
- m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
- m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
- }
}
}
}
}
}
//**********************************************************************************************************************
-int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
+int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int process){
try {
Alignment* alignment;
if (m->debug) { m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
ifstream inFFasta, inRFasta, inFQual, inRQual;
- ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
+ ofstream outFasta, outMisMatch, outScrapFasta;
m->openInputFile(thisffastafile, inFFasta);
m->openInputFile(thisrfastafile, inRFasta);
if (thisfqualfile != "") {
m->openInputFile(thisfqualfile, inFQual);
m->openInputFile(thisrqualfile, inRQual);
- m->openOutputFile(outputScrapQual, outScrapQual);
- m->openOutputFile(outputQual, outQual);
}
m->openOutputFile(outputFasta, outFasta);
m->openOutputFile(outputScrapFasta, outScrapFasta);
m->openOutputFile(outputMisMatches, outMisMatch);
- outMisMatch << "Name\tLength\tMisMatches\n";
+ if (process == 0) { outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n"; }
TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
//traverse alignments merging into one contiguous seq
string contig = "";
- vector<int> contigScores;
int numMismatches = 0;
string seq1 = fSeq.getAligned();
string seq2 = rSeq.getAligned();
//bigger of the 2 starting positions is the location of the overlapping start
if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
overlapStart = seq2Start;
- for (int i = 0; i < overlapStart; i++) {
- contig += seq1[i];
- if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
- }
+ for (int i = 0; i < overlapStart; i++) { contig += seq1[i]; }
}else { //seq1 starts later so take from 0 to overlapStart from seq2
- for (int i = 0; i < overlapStart; i++) {
- contig += seq2[i];
- if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
- }
+ for (int i = 0; i < overlapStart; i++) { contig += seq2[i]; }
}
int seq1End = fSeq.getEndPos();
int overlapEnd = seq1End;
if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
+ int oStart = contig.length();
for (int i = overlapStart; i < overlapEnd; i++) {
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
- if (thisfqualfile != "") {
- contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
- }
- }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
if (thisfqualfile != "") {
- if (scores2[BBaseMap[i]] < threshold) { } //
- else {
- contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
- }
+ if (scores2[BBaseMap[i]] < insert) { } //
+ else { contig += seq2[i]; }
}else { contig += seq2[i]; } //with no quality info, then we keep it?
- }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below insert. In that case eliminate base
if (thisfqualfile != "") {
- if (scores1[ABaseMap[i]] < threshold) { } //
- else {
- contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- }
+ if (scores1[ABaseMap[i]] < insert) { } //
+ else { contig += seq1[i]; }
}else { contig += seq1[i]; } //with no quality info, then we keep it?
}else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
if (thisfqualfile != "") {
- char c = seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
- contig += c;
+ if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
+ char c = seq1[i];
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
+ contig += c;
+ }else { //if no, base becomes n
+ contig += 'N';
+ }
numMismatches++;
}else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
}else { //should never get here
m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
}
}
-
+ int oend = contig.length();
if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
- for (int i = overlapEnd; i < length; i++) {
- contig += seq2[i];
- if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
- }
+ for (int i = overlapEnd; i < length; i++) { contig += seq2[i]; }
}else { //seq2 ends before seq1 so take from overlap to length from seq1
- for (int i = overlapEnd; i < length; i++) {
- contig += seq1[i];
- if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
- }
-
+ for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
if(trashCode.length() == 0){
m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
output << ">" << fSeq.getName() << endl << contig << endl;
output.close();
-
- if (thisfqualfile != "") {
- m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
- output << ">" << fSeq.getName() << endl;
- for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
- output << endl;
- output.close();
- }
}
//output
outFasta << ">" << fSeq.getName() << endl << contig << endl;
- if (thisfqualfile != "") {
- outQual << ">" << fSeq.getName() << endl;
- for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
- outQual << endl;
- }
- outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+ int numNs = 0;
+ for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; } }
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << endl;
}else {
//output
outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
- if (thisfqualfile != "") {
- outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
- for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
- outScrapQual << endl;
- }
}
num++;
if (thisfqualfile != "") {
inFQual.close();
inRQual.close();
- outQual.close();
- outScrapQual.close();
}
delete alignment;
- if (m->control_pressed) { m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches); if (thisfqualfile != "") { m->mothurRemove(outputQual); m->mothurRemove(outputScrapQual); } }
+ if (m->control_pressed) { m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches); }
return num;
}
if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
- if (checkReads(fread, rread, ffastq, rfastq)) {
+ //if (checkReads(fread, rread, ffastq, rfastq)) {
if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close(); delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; }
//if the reads are okay write to output files
//report progress
if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
- }
+ //}
}
}
//report progress
if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
- if (checkReads(fread, rread, ffasta, rfasta)) {
+ // if (checkReads(fread, rread, ffasta, rfasta)) {
if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close(); delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); } return files; }
//if the reads are okay write to output files
//report progress
if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
- }
+ //}
}
}
//report progress
exit(1);
}
}
-//**********************************************************************************************************************
+/**********************************************************************************************************************
bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
try {
bool good = true;
m->errorOut(e, "MakeContigsCommand", "checkReads");
exit(1);
}
-}
+}*/
//***************************************************************************************************************
vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
try {
//BARCODE atgcatgc atgcatgc groupName
//PRIMER atgcatgc atgcatgc groupName
//PRIMER atgcatgc atgcatgc
-bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, string rootname){
+bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname){
try {
ifstream in;
m->openInputFile(oligosfile, in);
while(!in.eof()){
in >> type;
- cout << type << endl;
+
if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
if(type[0] == '#'){
barcodes[indexBarcode]=newPair; indexBarcode++;
barcodeNameVector.push_back(group);
- cout << group << endl;
}else if(type == "LINKER"){
linker.push_back(foligo);
m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i].assign(primerNameVector.size(), "");
}
- qualFileNames = fastaFileNames;
if(allFiles){
set<string> uniqueNames; //used to cleanup outputFileNames
fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
m->openOutputFile(fastaFileName, temp); temp.close();
-
- if ((fqualfile != "") || (ffastqfile != "") || (file != "")) {
- qualFileName = rootname + ".qual";
- if (uniqueNames.count(qualFileName) == 0) {
- outputNames.push_back(qualFileName);
- outputTypes["qfile"].push_back(qualFileName);
- }
-
- qualFileNames[itBar->first][itPrimer->first] = qualFileName;
- m->openOutputFile(qualFileName, temp); temp.close();
- }
}
}
}
vector<int> MakeContigsCommand::convertQual(string qual) {
try {
vector<int> qualScores;
+ bool negativeScores = false;
for (int i = 0; i < qual.length(); i++) {
temp = int(qual[i]);
if (format == "illumina") {
temp -= 64; //char '@'
+ }else if (format == "illumina1.8+") {
+ temp -= int('!'); //char '!'
}else if (format == "solexa") {
temp = int(convertTable[temp]); //convert to sanger
temp -= int('!'); //char '!'
}else {
temp -= int('!'); //char '!'
}
+
+ if (temp < -5) { negativeScores = true; }
qualScores.push_back(temp);
}
+ if (negativeScores) { m->mothurOut("[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding \n"); m->control_pressed = true; }
+
return qualScores;
}
catch(exception& e) {
vector<string> ScreenSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,true,true); parameters.push_back(pcontigsreport);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "report", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter psummary("summary", "InputTypes", "", "", "report", "none", "none","summary",false,false); parameters.push_back(psummary);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false); parameters.push_back(pqfile);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
+
CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false); parameters.push_back(ptax);
CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pstart);
CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pend);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pcriteria);
CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "","",true,false); parameters.push_back(poptimize);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ //report parameters
+ CommandParameter pminoverlap("minoverlap", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminoverlap);
+ CommandParameter postart("ostart", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(postart);
+ CommandParameter poend("oend", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(poend);
+ CommandParameter pmismatches("mismatches", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmismatches);
+ CommandParameter pmaxn("maxn", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxn);
+ CommandParameter pminscore("minscore", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminscore);
+ CommandParameter pmaxinsert("maxinsert", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxinsert);
+ CommandParameter pminsim("minsim", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminsim);
+
+
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
helpString += "The screen.seqs command reads a fastafile and screens sequences.\n";
- helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, count, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
+ helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, count, qfile, alignreport, contigsreport, summary, taxonomy, optimize, criteria and processors.\n";
helpString += "The fasta parameter is required.\n";
- helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
+ helpString += "The contigsreport parameter allows you to use the contigsreport file to determine if a sequence is good. Screening parameters include: minoverlap, ostart, oend and mismatches. \n";
+ helpString += "The alignreport parameter allows you to use the alignreport file to determine if a sequence is good. Screening parameters include: minsim, minscore and maxinsert. \n";
+ helpString += "The summary parameter allows you to use the summary file from summary.seqs to save time processing.\n";
+ helpString += "The taxonomy parameter allows you to remove bad seqs from taxonomy files.\n";
helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n";
helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
- helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
+ helpString += "The maxn parameter allows you to set and maximum number of N's allowed in a sequence. \n";
+ helpString += "The minoverlap parameter allows you to set and minimum overlap. The default is -1. \n";
+ helpString += "The ostart parameter is used to set an overlap position the \"good\" sequences must start by. The default is -1. \n";
+ helpString += "The oend parameter is used to set an overlap position the \"good\" sequences must end after. The default is -1.\n";
+ helpString += "The mismatches parameter allows you to set and maximum mismatches in the contigs.report. \n";
+ helpString += "The minsim parameter allows you to set the minimum similarity to template sequences during alignment. Found in column \'SimBtwnQuery&Template\' in align.report file.\n";
+ helpString += "The minscore parameter allows you to set the minimum search score during alignment. Found in column \'SearchScore\' in align.report file.\n";
+ helpString += "The maxinsert parameter allows you to set the maximum number of insertions during alignment. Found in column \'LongestInsert\' in align.report file.\n";
helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
else if (type == "accnos") { pattern = "[filename],bad.accnos"; }
else if (type == "qfile") { pattern = "[filename],good,[extension]"; }
else if (type == "alignreport") { pattern = "[filename],good.align.report"; }
+ else if (type == "contigsreport") { pattern = "[filename],good.contigs.report"; }
+ else if (type == "summary") { pattern = "[filename],good.summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
+ outputTypes["contigsreport"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["count"] = tempOutNames;
-
+ outputTypes["contigsreport"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["alignreport"] = inputDir + it->second; }
}
+
+ it = parameters.find("contigsreport");
+ //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["contigsreport"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("summary");
+ //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["summary"] = inputDir + it->second; }
+ }
it = parameters.find("qfile");
//user has given a template file
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
+ contigsreport = validParameter.validFile(parameters, "contigsreport", true);
+ if (contigsreport == "not open") { contigsreport = ""; abort = true; }
+ else if (contigsreport == "not found") { contigsreport = ""; }
+
+ summaryfile = validParameter.validFile(parameters, "summary", true);
+ if (summaryfile == "not open") { summaryfile = ""; abort = true; }
+ else if (summaryfile == "not found") { summaryfile = ""; }
+
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
}
m->setProcessors(temp);
m->mothurConvert(temp, processors);
+ temp = validParameter.validFile(parameters, "minoverlap", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, minOverlap);
+
+ temp = validParameter.validFile(parameters, "ostart", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, oStart);
+
+ temp = validParameter.validFile(parameters, "oend", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, oEnd);
+
+ temp = validParameter.validFile(parameters, "mismatches", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, mismatches);
+
+ temp = validParameter.validFile(parameters, "maxn", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, maxN);
+
+ temp = validParameter.validFile(parameters, "minscore", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, minScore);
+
+ temp = validParameter.validFile(parameters, "maxinsert", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, maxInsert);
+
+ temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, minSim);
+
temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
if (temp == "not found"){ temp = "none"; }
m->splitAtDash(temp, optimize);
+
+ if ((contigsreport != "") && ((summaryfile != "") || ( alignreport != ""))) {
+ m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true;
+ }
+
+ if ((alignreport != "") && ((summaryfile != "") || ( contigsreport != ""))) {
+ m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true;
+ }
+
+ if ((summaryfile != "") && ((alignreport != "") || ( contigsreport != ""))) {
+ m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true;
+ }
+ //check to make sure you have the files you need for certain screening
+ if ((contigsreport == "") && ((minOverlap != -1) || (oStart != -1) || (oEnd != -1) || (mismatches != -1))) {
+ m->mothurOut("[ERROR]: minoverlap, ostart, oend and mismatches can only be used with a contigs.report file, aborting.\n"); abort=true;
+ }
+
+ if ((alignreport == "") && ((minScore != -1) || (maxInsert != -1) || (minSim != -1))) {
+ m->mothurOut("[ERROR]: minscore, maxinsert and minsim can only be used with a align.report file, aborting.\n"); abort=true;
+ }
+
//check for invalid optimize options
set<string> validOptimizers;
- validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
+ validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength"); validOptimizers.insert("maxn");
+ if (contigsreport != "") { validOptimizers.insert("minoverlap"); validOptimizers.insert("ostart"); validOptimizers.insert("oend"); validOptimizers.insert("mismatches"); }
+ if (alignreport != "") { validOptimizers.insert("minscore"); validOptimizers.insert("maxinsert"); validOptimizers.insert("minsim"); }
+
for (int i = 0; i < optimize.size(); i++) {
if (validOptimizers.count(optimize[i]) == 0) {
- m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
+ m->mothurOut(optimize[i] + " is not a valid optimizer with your input files. Valid options are ");
+ string valid = "";
+ for (set<string>::iterator it = validOptimizers.begin(); it != validOptimizers.end(); it++) {
+ valid += (*it) + ", ";
+ }
+ if (valid.length() != 0) { valid = valid.substr(0, valid.length()-2); }
+ m->mothurOut(valid + ".");
+ m->mothurOutEndLine();
optimize.erase(optimize.begin()+i);
i--;
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- //if the user want to optimize we need to know the 90% mark
- vector<unsigned long long> positions;
- if (optimize.size() != 0) { //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
- //use the namefile to optimize correctly
- if (namefile != "") { nameMap = m->readNames(namefile); }
- else if (countfile != "") {
- CountTable ct;
- ct.readTable(countfile);
- nameMap = ct.getNameMap();
- }
- getSummary(positions);
- }
- else {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- positions = m->divideFile(fastafile, processors);
- for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
- #else
- if(processors == 1){ lines.push_back(linePair(0, 1000)); }
- else {
- int numFastaSeqs = 0;
- positions = m->setFilePosFasta(fastafile, numFastaSeqs);
- if (positions.size() < processors) { processors = positions.size(); }
-
- //figure out how many sequences you have to process
- int numSeqsPerProcessor = numFastaSeqs / processors;
- for (int i = 0; i < processors; i++) {
- int startIndex = i * numSeqsPerProcessor;
- if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
- lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
- }
- }
- #endif
- }
+ map<string, string> badSeqNames;
+ int start = time(NULL);
+ int numFastaSeqs = 0;
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string badAccnosFile = getOutputFileName("accnos",variables);
- variables["[extension]"] = m->getExtension(fastafile);
- string goodSeqFile = getOutputFileName("fasta", variables);
-
+ if ((contigsreport == "") && (summaryfile == "") && (alignreport == "")) { numFastaSeqs = screenFasta(badSeqNames); }
+ else { numFastaSeqs = screenReports(badSeqNames); }
- int numFastaSeqs = 0;
- set<string> badSeqNames;
- int start = time(NULL);
-
-#ifdef USE_MPI
- int pid, numSeqsPerProcessor;
- int tag = 2001;
- vector<unsigned long long> MPIPos;
-
- MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- MPI_File inMPI;
- MPI_File outMPIGood;
- MPI_File outMPIBadAccnos;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
-
- char outGoodFilename[1024];
- strcpy(outGoodFilename, goodSeqFile.c_str());
-
- char outBadAccnosFilename[1024];
- strcpy(outBadAccnosFilename, badAccnosFile.c_str());
-
- char inFileName[1024];
- strcpy(inFileName, fastafile.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
- MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
- MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
-
- if (pid == 0) { //you are the root process
-
- MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
-
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
- }
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numFastaSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
-
- //align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
-
- for (int i = 1; i < processors; i++) {
- //get bad lists
- int badSize;
- MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
- }
- }else{ //you are a child process
- MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPIPos.resize(numFastaSeqs+1);
- MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numFastaSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
-
- //align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
-
- //send bad list
- int badSize = badSeqNames.size();
- MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
- }
-
- //close files
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPIGood);
- MPI_File_close(&outMPIBadAccnos);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-
-#else
- if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
- else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
-#endif
-
- #ifdef USE_MPI
- MPI_Comm_rank(MPI_COMM_WORLD, &pid);
-
- if (pid == 0) { //only one process should fix files
-
- //read accnos file with all names in it, process 0 just has its names
- MPI_File inMPIAccnos;
- MPI_Offset size;
-
- char inFileName[1024];
- strcpy(inFileName, badAccnosFile.c_str());
-
- MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos); //comm, filename, mode, info, filepointer
- MPI_File_get_size(inMPIAccnos, &size);
-
- char* buffer = new char[size];
- MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
-
- string tempBuf = buffer;
- if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
- istringstream iss (tempBuf,istringstream::in);
-
- delete buffer;
- MPI_File_close(&inMPIAccnos);
-
- badSeqNames.clear();
- string tempName;
- while (!iss.eof()) {
- iss >> tempName; m->gobble(iss);
- badSeqNames.insert(tempName);
- }
- #endif
-
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should fix files
+ #endif
+
if(namefile != "" && groupfile != "") {
screenNameGroupFile(badSeqNames);
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}else if(namefile != "") {
screenNameGroupFile(badSeqNames);
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
else if (countfile != "") { screenCountFile(badSeqNames); }
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- if(alignreport != "") { screenAlignReport(badSeqNames); }
if(qualfile != "") { screenQual(badSeqNames); }
if(taxonomy != "") { screenTaxonomy(badSeqNames); }
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
#ifdef USE_MPI
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(goodSeqFile); m->mothurOutEndLine(); outputTypes["fasta"].push_back(goodSeqFile);
- m->mothurOut(badAccnosFile); m->mothurOutEndLine(); outputTypes["accnos"].push_back(badAccnosFile);
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
m->mothurOutEndLine();
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
- itTypes = outputTypes.find("count");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//***************************************************************************************************************/
+int ScreenSeqsCommand::runFastaScreening(map<string, string>& badSeqNames){
+ try{
+ int numFastaSeqs = 0;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string badAccnosFile = getOutputFileName("accnos",variables);
+ variables["[extension]"] = m->getExtension(fastafile);
+ string goodSeqFile = getOutputFileName("fasta", variables);
+ outputNames.push_back(goodSeqFile); outputTypes["fasta"].push_back(goodSeqFile);
+ outputNames.push_back(badAccnosFile); outputTypes["accnos"].push_back(badAccnosFile);
+
+#ifdef USE_MPI
+ int pid, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<unsigned long long> MPIPos;
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ MPI_File inMPI;
+ MPI_File outMPIGood;
+ MPI_File outMPIBadAccnos;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ char outGoodFilename[1024];
+ strcpy(outGoodFilename, goodSeqFile.c_str());
+
+ char outBadAccnosFilename[1024];
+ strcpy(outBadAccnosFilename, badAccnosFile.c_str());
+
+ char inFileName[1024];
+ strcpy(inFileName, fastafile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
+ MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
+
+ if (pid == 0) { //you are the root process
+
+ MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numFastaSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
+
+ for (int i = 1; i < processors; i++) {
+ //get bad lists
+ int badSize;
+ MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+ }
+ }else{ //you are a child process
+ MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numFastaSeqs+1);
+ MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numFastaSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
+
+ //send bad list
+ int badSize = badSeqNames.size();
+ MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ }
+
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPIGood);
+ MPI_File_close(&outMPIBadAccnos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+ if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+ else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+
+ if (m->control_pressed) { m->mothurRemove(goodSeqFile); return numFastaSeqs; }
+#endif
+
+#ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should fix files
+
+ //read accnos file with all names in it, process 0 just has its names
+ MPI_File inMPIAccnos;
+ MPI_Offset size;
+
+ char inFileName[1024];
+ strcpy(inFileName, badAccnosFile.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos); //comm, filename, mode, info, filepointer
+ MPI_File_get_size(inMPIAccnos, &size);
+
+ char* buffer = new char[size];
+ MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ delete buffer;
+ MPI_File_close(&inMPIAccnos);
+
+ badSeqNames.clear();
+ string tempName, trashCode;
+ while (!iss.eof()) {
+ iss >> tempName >> trashCode; m->gobble(iss);
+ badSeqNames[tempName] = trashCode;
+ }
+ }
+#endif
+
+
+ return numFastaSeqs;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "runFastaScreening");
+ exit(1);
+ }
+}
+//***************************************************************************************************************/
+int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
+ try{
+ int numFastaSeqs = 0;
+ bool summarizedFasta = false;
+
+ //did not provide a summary file, but set a parameter that requires summarizing the fasta file
+ //or did provide a summary file, but set maxn parameter so we must summarize the fasta file
+ vector<unsigned long long> positions;
+ if (((summaryfile == "") && ((m->inUsersGroups("maxambig", optimize)) ||(m->inUsersGroups("maxhomop", optimize)) ||(m->inUsersGroups("maxlength", optimize)) || (m->inUsersGroups("minlength", optimize)) || (m->inUsersGroups("start", optimize)) || (m->inUsersGroups("end", optimize)))) || ((summaryfile != "") && m->inUsersGroups("maxn", optimize))) {
+ //use the namefile to optimize correctly
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+ else if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile);
+ nameMap = ct.getNameMap();
+ }
+ getSummary(positions);
+ summarizedFasta = true;
+ } else {
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+ #else
+ if(processors == 1){ lines.push_back(linePair(0, 1000)); }
+ else {
+ int numFastaSeqs = 0;
+ positions = m->setFilePosFasta(fastafile, numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+ #endif
+ }
+
+ if ((summaryfile != "") && ((m->inUsersGroups("maxambig", optimize)) ||(m->inUsersGroups("maxhomop", optimize)) ||(m->inUsersGroups("maxlength", optimize)) || (m->inUsersGroups("minlength", optimize)) || (m->inUsersGroups("start", optimize)) || (m->inUsersGroups("end", optimize))) && !summarizedFasta) { //summarize based on summaryfile
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+ else if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile);
+ nameMap = ct.getNameMap();
+ }
+ getSummaryReport();
+ }else if ((contigsreport != "") && ((m->inUsersGroups("minoverlap", optimize)) || (m->inUsersGroups("ostart", optimize)) || (m->inUsersGroups("oend", optimize)) || (m->inUsersGroups("mismatches", optimize)))) { //optimize settings based on contigs file
+ optimizeContigs();
+ }else if ((alignreport != "") && ((m->inUsersGroups("minsim", optimize)) || (m->inUsersGroups("minscore", optimize)) || (m->inUsersGroups("maxinsert", optimize)))) { //optimize settings based on contigs file
+ optimizeAlign();
+ }
+
+
+ //provided summary file, and did not set maxn so no need to summarize fasta
+ if (summaryfile != "") { numFastaSeqs = screenSummary(badSeqNames); }
+ //add in any seqs that fail due to contigs report results
+ else if (contigsreport != "") { numFastaSeqs = screenContigs(badSeqNames); }
+ //add in any seqs that fail due to align report
+ else if (alignreport != "") { numFastaSeqs = screenAlignReport(badSeqNames); }
+
+ return numFastaSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenReports");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ScreenSeqsCommand::screenAlignReport(map<string, string>& badSeqNames){
+ try {
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(alignreport));
+ string outSummary = getOutputFileName("alignreport",variables);
+ outputNames.push_back(outSummary); outputTypes["alignreport"].push_back(outSummary);
+
+ string name, TemplateName, SearchMethod, AlignmentMethod;
+ //QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
+ //checking for minScore, maxInsert, minSim
+ int length, TemplateLength, QueryStart, QueryEnd, TemplateStart, TemplateEnd, PairwiseAlignmentLength, GapsInQuery, GapsInTemplate, LongestInsert;
+ float SearchScore, SimBtwnQueryTemplate;
+
+ ofstream out;
+ m->openOutputFile(outSummary, out);
+
+ //read summary file
+ ifstream in;
+ m->openInputFile(alignreport, in);
+ out << (m->getline(in)) << endl; //skip headers
+
+ int count = 0;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; m->gobble(in);
+
+ bool goodSeq = 1; // innocent until proven guilty
+ string trashCode = "";
+ if(maxInsert != -1 && maxInsert < LongestInsert) { goodSeq = 0; trashCode += "insert|"; }
+ if(minScore != -1 && minScore > SearchScore) { goodSeq = 0; trashCode += "score|"; }
+ if(minSim != -1 && minSim > SimBtwnQueryTemplate) { goodSeq = 0; trashCode += "sim|"; }
+
+ if(goodSeq == 1){
+ out << name << '\t' << length << '\t' << TemplateName << '\t' << TemplateLength << '\t' << SearchMethod << '\t' << SearchScore << '\t' << AlignmentMethod << '\t' << QueryStart << '\t' << QueryEnd << '\t' << TemplateStart << '\t' << TemplateEnd << '\t' << PairwiseAlignmentLength << '\t' << GapsInQuery << '\t' << GapsInTemplate << '\t' << LongestInsert << '\t' << SimBtwnQueryTemplate << endl;
+ }
+ else{ badSeqNames[name] = trashCode; }
+ count++;
+ }
+ in.close();
+ out.close();
+
+ int oldBadSeqsCount = badSeqNames.size();
+
+ int numFastaSeqs = runFastaScreening(badSeqNames);
+
+ if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns
+ m->renameFile(outSummary, outSummary+".temp");
+
+ ofstream out2;
+ m->openOutputFile(outSummary, out2);
+
+ //read summary file
+ ifstream in2;
+ m->openInputFile(outSummary+".temp", in2);
+ out2 << (m->getline(in2)) << endl; //skip headers
+
+ while (!in2.eof()) {
+
+ if (m->control_pressed) { in2.close(); out2.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in2 >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; m->gobble(in2);
+
+ if (badSeqNames.count(name) == 0) { //are you good?
+ out2 << name << '\t' << length << '\t' << TemplateName << '\t' << TemplateLength << '\t' << SearchMethod << '\t' << SearchScore << '\t' << AlignmentMethod << '\t' << QueryStart << '\t' << QueryEnd << '\t' << TemplateStart << '\t' << TemplateEnd << '\t' << PairwiseAlignmentLength << '\t' << GapsInQuery << '\t' << GapsInTemplate << '\t' << LongestInsert << '\t' << SimBtwnQueryTemplate << endl;
+ }
+ }
+ in2.close();
+ out2.close();
+ m->mothurRemove(outSummary+".temp");
+ }
+
+ if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->control_pressed = true; }
+
+
+ return count;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
+ exit(1);
+ }
+
+}
+//***************************************************************************************************************/
+int ScreenSeqsCommand::screenContigs(map<string, string>& badSeqNames){
+ try{
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(contigsreport));
+ string outSummary = getOutputFileName("contigsreport",variables);
+ outputNames.push_back(outSummary); outputTypes["contigsreport"].push_back(outSummary);
+
+ string name;
+ //Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
+ int length, OLength, thisOStart, thisOEnd, numMisMatches, numNs;
+
+ ofstream out;
+ m->openOutputFile(outSummary, out);
+
+ //read summary file
+ ifstream in;
+ m->openInputFile(contigsreport, in);
+ out << (m->getline(in)) << endl; //skip headers
+
+ int count = 0;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numNs; m->gobble(in);
+
+ bool goodSeq = 1; // innocent until proven guilty
+ string trashCode = "";
+ if(oStart != -1 && oStart < thisOStart) { goodSeq = 0; trashCode += "ostart|"; }
+ if(oEnd != -1 && oEnd > thisOEnd) { goodSeq = 0; trashCode += "oend|"; }
+ if(maxN != -1 && maxN < numNs) { goodSeq = 0; trashCode += "n|"; }
+ if(minOverlap != -1 && minOverlap > OLength) { goodSeq = 0; trashCode += "olength|"; }
+ if(mismatches != -1 && mismatches < numMisMatches) { goodSeq = 0; trashCode += "mismatches|"; }
+
+ if(goodSeq == 1){
+ out << name << '\t' << length << '\t' << OLength << '\t' << thisOStart << '\t' << thisOEnd << '\t' << numMisMatches << '\t' << numNs << endl;
+ }
+ else{ badSeqNames[name] = trashCode; }
+ count++;
+ }
+ in.close();
+ out.close();
+
+ int oldBadSeqsCount = badSeqNames.size();
+
+ int numFastaSeqs = runFastaScreening(badSeqNames);
+
+ if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns
+ m->renameFile(outSummary, outSummary+".temp");
+
+ ofstream out2;
+ m->openOutputFile(outSummary, out2);
+
+ //read summary file
+ ifstream in2;
+ m->openInputFile(outSummary+".temp", in2);
+ out2 << (m->getline(in2)) << endl; //skip headers
+
+ while (!in2.eof()) {
+
+ if (m->control_pressed) { in2.close(); out2.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in2 >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numNs; m->gobble(in2);
+
+ if (badSeqNames.count(name) == 0) { //are you good?
+ out2 << name << '\t' << length << '\t' << OLength << '\t' << thisOStart << '\t' << thisOEnd << '\t' << numMisMatches << '\t' << numNs << endl;
+ }
+ }
+ in2.close();
+ out2.close();
+ m->mothurRemove(outSummary+".temp");
+ }
+
+ if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->control_pressed = true; }
+
+
+ return count;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenContigs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************/
+int ScreenSeqsCommand::screenSummary(map<string, string>& badSeqNames){
+ try{
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(summaryfile));
+ string outSummary = getOutputFileName("summary",variables);
+ outputNames.push_back(outSummary); outputTypes["summary"].push_back(outSummary);
+
+ string name;
+ int start, end, length, ambigs, polymer, numReps;
+
+ ofstream out;
+ m->openOutputFile(outSummary, out);
+
+ //read summary file
+ ifstream in;
+ m->openInputFile(summaryfile, in);
+ out << (m->getline(in)) << endl; //skip headers
+
+ int count = 0;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> start >> end >> length >> ambigs >> polymer >> numReps; m->gobble(in);
+
+ bool goodSeq = 1; // innocent until proven guilty
+ string trashCode = "";
+ if(startPos != -1 && startPos < start) { goodSeq = 0; trashCode += "start|"; }
+ if(endPos != -1 && endPos > end) { goodSeq = 0; trashCode += "end|"; }
+ if(maxAmbig != -1 && maxAmbig < ambigs) { goodSeq = 0; trashCode += "ambig|"; }
+ if(maxHomoP != -1 && maxHomoP < polymer) { goodSeq = 0; trashCode += "homop|"; }
+ if(minLength != -1 && minLength > length) { goodSeq = 0; trashCode += "<length|"; }
+ if(maxLength != -1 && maxLength < length) { goodSeq = 0; trashCode += ">length|"; }
+
+ if(goodSeq == 1){
+ out << name << '\t' << start << '\t' << end << '\t' << length << '\t' << ambigs << '\t' << polymer << '\t' << numReps << endl;
+ }
+ else{ badSeqNames[name] = trashCode; }
+ count++;
+ }
+ in.close();
+ out.close();
+
+ int oldBadSeqsCount = badSeqNames.size();
+
+ int numFastaSeqs = runFastaScreening(badSeqNames);
+
+ if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns
+ m->renameFile(outSummary, outSummary+".temp");
+
+ ofstream out2;
+ m->openOutputFile(outSummary, out2);
+
+ //read summary file
+ ifstream in2;
+ m->openInputFile(outSummary+".temp", in2);
+ out2 << (m->getline(in2)) << endl; //skip headers
+
+ while (!in2.eof()) {
+
+ if (m->control_pressed) { in2.close(); out2.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in2 >> name >> start >> end >> length >> ambigs >> polymer >> numReps; m->gobble(in2);
+
+ if (badSeqNames.count(name) == 0) { //are you good?
+ out2 << name << '\t' << start << '\t' << end << '\t' << length << '\t' << ambigs << '\t' << polymer << '\t' << numReps << endl;
+ }
+ }
+ in2.close();
+ out2.close();
+ m->mothurRemove(outSummary+".temp");
+ }
+
+ if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your summary file, quitting.\n"); m->control_pressed = true; }
+
+
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenSummary");
+ exit(1);
+ }
+}
+//***************************************************************************************************************/
+int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
+ try{
+
+
+ //if the user want to optimize we need to know the 90% mark
+ vector<unsigned long long> positions;
+ if (optimize.size() != 0) { //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
+ //use the namefile to optimize correctly
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+ else if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile);
+ nameMap = ct.getNameMap();
+ }
+ getSummary(positions);
+ }else {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if(processors == 1){ lines.push_back(linePair(0, 1000)); }
+ else {
+ int numFastaSeqs = 0;
+ positions = m->setFilePosFasta(fastafile, numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+#endif
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ int numFastaSeqs = runFastaScreening(badSeqNames);
+
+ return numFastaSeqs;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenFasta");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int ScreenSeqsCommand::screenNameGroupFile(map<string, string> badSeqNames){
+ try {
+ ifstream inputNames;
+ m->openInputFile(namefile, inputNames);
+ map<string, string> badSeqGroups;
+ string seqName, seqList, group;
+ map<string, string>::iterator it;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string goodNameFile = getOutputFileName("name", variables);
+ outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
+
+ ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
+
+ while(!inputNames.eof()){
+ if (m->control_pressed) { goodNameOut.close(); inputNames.close(); m->mothurRemove(goodNameFile); return 0; }
+
+ inputNames >> seqName; m->gobble(inputNames); inputNames >> seqList;
+ it = badSeqNames.find(seqName);
+
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
+
+ if(namefile != ""){
+ int start = 0;
+ for(int i=0;i<seqList.length();i++){
+ if(seqList[i] == ','){
+ badSeqGroups[seqList.substr(start,i-start)] = it->second;
+ start = i+1;
+ }
+ }
+ badSeqGroups[seqList.substr(start,seqList.length()-start)] = it->second;
+ }
+ }
+ else{
+ goodNameOut << seqName << '\t' << seqList << endl;
+ }
+ m->gobble(inputNames);
+ }
+ inputNames.close();
+ goodNameOut.close();
+
+ //we were unable to remove some of the bad sequences
+ if (badSeqNames.size() != 0) {
+ for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
+ m->mothurOut("Your namefile does not include the sequence " + it->first + " please correct.");
+ m->mothurOutEndLine();
+ }
+ }
+
+ if(groupfile != ""){
+
+ ifstream inputGroups;
+ m->openInputFile(groupfile, inputGroups);
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string goodGroupFile = getOutputFileName("group", variables);
+
+ outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
+
+ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
+
+ while(!inputGroups.eof()){
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile); m->mothurRemove(goodGroupFile); return 0; }
+
+ inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
+
+ it = badSeqGroups.find(seqName);
+
+ if(it != badSeqGroups.end()){
+ badSeqGroups.erase(it);
+ }
+ else{
+ goodGroupOut << seqName << '\t' << group << endl;
+ }
+ m->gobble(inputGroups);
+ }
+ inputGroups.close();
+ goodGroupOut.close();
+
+ //we were unable to remove some of the bad sequences
+ if (badSeqGroups.size() != 0) {
+ for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
+ m->mothurOut("Your groupfile does not include the sequence " + it->first + " please correct.");
+ m->mothurOutEndLine();
+ }
+ }
+ }
+
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ScreenSeqsCommand::getSummaryReport(){
+ try {
+
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) {
+#endif
+
+
+ //read summary file
+ ifstream in;
+ m->openInputFile(summaryfile, in);
+ m->getline(in);
+
+ string name;
+ int start, end, length, ambigs, polymer, numReps;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> start >> end >> length >> ambigs >> polymer >> numReps; m->gobble(in);
+
+ int num = 1;
+ if ((namefile != "") || (countfile !="")) {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(name);
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ startPosition.push_back(start);
+ endPosition.push_back(end);
+ seqLength.push_back(length);
+ ambigBases.push_back(ambigs);
+ longHomoPolymer.push_back(polymer);
+ }
+
+ }
+ in.close();
+
+ sort(startPosition.begin(), startPosition.end());
+ sort(endPosition.begin(), endPosition.end());
+ sort(seqLength.begin(), seqLength.end());
+ sort(ambigBases.begin(), ambigBases.end());
+ sort(longHomoPolymer.begin(), longHomoPolymer.end());
+
+ //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
+ int criteriaPercentile = int(startPosition.size() * (criteria / (float) 100));
+
+ for (int i = 0; i < optimize.size(); i++) {
+ if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
+ else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
+ }
+
+#ifdef USE_MPI
+ }
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ if (pid == 0) {
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ }
+ }else {
+ MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+#endif
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getSummaryReport");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ScreenSeqsCommand::optimizeContigs(){
+ try {
+ vector<int> olengths;
+ vector<int> oStarts;
+ vector<int> oEnds;
+ vector<int> numMismatches;
+ vector<int> numNs;
+
+ vector<unsigned long long> positions;
+ vector<linePair> contigsLines;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFilePerLine(contigsreport, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { contigsLines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if(processors == 1){ contigsLines.push_back(linePair(0, 1000)); }
+ else {
+ int numContigsSeqs = 0;
+ positions = m->setFilePosEachLine(contigsreport, numContigsSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numContigsSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numContigsSeqs - i * numSeqsPerProcessor; }
+ contigsLines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+#endif
+
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) {
+ driverContigsSummary(olengths, oStarts, oEnds, numMismatches, numNs, contigsLines[0]);
+#else
+ createProcessesContigsSummary(olengths, oStarts, oEnds, numMismatches, numNs, contigsLines);
+
+ if (m->control_pressed) { return 0; }
+#endif
+ sort(olengths.begin(), olengths.end());
+ sort(oStarts.begin(), oStarts.end());
+ sort(oEnds.begin(), oEnds.end());
+ sort(numMismatches.begin(), numMismatches.end());
+ sort(numNs.begin(), numNs.end());
+
+ //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
+ int criteriaPercentile = int(oStarts.size() * (criteria / (float) 100));
+
+ for (int i = 0; i < optimize.size(); i++) {
+ if (optimize[i] == "ostart") { oStart = oStarts[criteriaPercentile]; m->mothurOut("Optimizing ostart to " + toString(oStart) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "oend") { int endcriteriaPercentile = int(oEnds.size() * ((100 - criteria) / (float) 100)); oEnd = oEnds[endcriteriaPercentile]; m->mothurOut("Optimizing oend to " + toString(oEnd) + "."); m->mothurOutEndLine();}
+ else if (optimize[i] == "mismatches") { mismatches = numMismatches[criteriaPercentile]; m->mothurOut("Optimizing mismatches to " + toString(mismatches) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxn") { maxN = numNs[criteriaPercentile]; m->mothurOut("Optimizing maxn to " + toString(maxN) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "minoverlap") { int mincriteriaPercentile = int(olengths.size() * ((100 - criteria) / (float) 100)); minOverlap = olengths[mincriteriaPercentile]; m->mothurOut("Optimizing minoverlap to " + toString(minOverlap) + "."); m->mothurOutEndLine(); }
+
+ }
+
+#ifdef USE_MPI
+ }
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ if (pid == 0) {
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&minOverlap, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&oStart, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&oEnd, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&mismatches, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&maxN, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ }
+ }else {
+ MPI_Recv(&minOverlap, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&oStart, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&oEnd, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&mismatches, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&maxN, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+#endif
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "optimizeContigs");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int ScreenSeqsCommand::driverContigsSummary(vector<int>& oLength, vector<int>& ostartPosition, vector<int>& oendPosition, vector<int>& omismatches, vector<int>& numNs, linePair filePos) {
+ try {
+
+ string name;
+ //Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
+ int length, OLength, thisOStart, thisOEnd, numMisMatches, numns;
+
+ ifstream in;
+ m->openInputFile(contigsreport, in);
+
+ in.seekg(filePos.start);
+ if (filePos.start == 0) { //read headers
+ m->getline(in); m->gobble(in);
+ }
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numns; m->gobble(in);
+
+ int num = 1;
+ if ((namefile != "") || (countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(name);
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ ostartPosition.push_back(thisOStart);
+ oendPosition.push_back(thisOEnd);
+ oLength.push_back(OLength);
+ omismatches.push_back(numMisMatches);
+ numNs.push_back(numns);
+ }
+
+ count++;
+
+ //if((count) % 100 == 0){ m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); }
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+ }
+
+ in.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driverContigsSummary");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+int ScreenSeqsCommand::createProcessesContigsSummary(vector<int>& oLength, vector<int>& ostartPosition, vector<int>& oendPosition, vector<int>& omismatches, vector<int>& numNs, vector<linePair> contigsLines) {
+ try {
+
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driverContigsSummary(oLength, ostartPosition, oendPosition, omismatches, numNs, contigsLines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = contigsreport + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << num << endl;
+ out << ostartPosition.size() << endl;
+ for (int k = 0; k < ostartPosition.size(); k++) { out << ostartPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < oendPosition.size(); k++) { out << oendPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < oLength.size(); k++) { out << oLength[k] << '\t'; } out << endl;
+ for (int k = 0; k < omismatches.size(); k++) { out << omismatches[k] << '\t'; } out << endl;
+ for (int k = 0; k < numNs.size(); k++) { out << numNs[k] << '\t'; } out << endl;
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ num = driverContigsSummary(oLength, ostartPosition, oendPosition, omismatches, numNs, contigsLines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = contigsreport + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ int temp, tempNum;
+ in >> tempNum; m->gobble(in); num += tempNum;
+ in >> tempNum; m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; ostartPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; oendPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; oLength.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; omismatches.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; numNs.push_back(temp); } m->gobble(in);
+
+ in.close();
+ m->mothurRemove(tempFilename);
+ }
+
+
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to allow both threads to add info to vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ /*
+ vector<contigsSumData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+
+ // Allocate memory for thread data.
+ contigsSumData* tempSum = new contigsSumData(contigsreport, m, contigsLines[i].start, contigsLines[i].end, namefile, countfile, nameMap);
+ pDataArray.push_back(tempSum);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i] = CreateThread(NULL, 0, MyContigsSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+ */
+ contigsLines[processors-1].start = 0;
+ //do your part
+ num = driverContigsSummary(oLength, ostartPosition, oendPosition, omismatches, numNs, contigsLines[processors-1]);
+ /*
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //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]->ostartPosition.size(); k++) { ostartPosition.push_back(pDataArray[i]->ostartPosition[k]); }
+ for (int k = 0; k < pDataArray[i]->oendPosition.size(); k++) { oendPosition.push_back(pDataArray[i]->oendPosition[k]); }
+ for (int k = 0; k < pDataArray[i]->oLength.size(); k++) { oLength.push_back(pDataArray[i]->oLength[k]); }
+ for (int k = 0; k < pDataArray[i]->omismatches.size(); k++) { omismatches.push_back(pDataArray[i]->omismatches[k]); }
+ for (int k = 0; k < pDataArray[i]->numNs.size(); k++) { numNs.push_back(pDataArray[i]->numNs[k]); }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+ */
+#endif
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "createProcessesContigsSummary");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ScreenSeqsCommand::optimizeAlign(){
+ try {
+
+ vector<float> sims;
+ vector<float> scores;
+ vector<int> inserts;
+
+ vector<unsigned long long> positions;
+ vector<linePair> alignLines;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFilePerLine(alignreport, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { alignLines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if(processors == 1){ alignLines.push_back(linePair(0, 1000)); }
+ else {
+ int numAlignSeqs = 0;
+ positions = m->setFilePosEachLine(alignreport, numAlignSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numAlignSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numAlignSeqs - i * numSeqsPerProcessor; }
+ alignLines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+#endif
+
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) {
+ driverAlignSummary(sims, scores, inserts, alignLines[0]);
+#else
+ createProcessesAlignSummary(sims, scores, inserts, alignLines);
+
+ if (m->control_pressed) { return 0; }
+#endif
+ sort(sims.begin(), sims.end());
+ sort(scores.begin(), scores.end());
+ sort(inserts.begin(), inserts.end());
+
+ //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
+ int criteriaPercentile = int(sims.size() * (criteria / (float) 100));
+
+ for (int i = 0; i < optimize.size(); i++) {
+ if (optimize[i] == "minsim") { int mincriteriaPercentile = int(sims.size() * ((100 - criteria) / (float) 100)); minSim = sims[mincriteriaPercentile]; m->mothurOut("Optimizing minsim to " + toString(minSim) + "."); m->mothurOutEndLine();}
+ else if (optimize[i] == "minscore") { int mincriteriaPercentile = int(scores.size() * ((100 - criteria) / (float) 100)); minScore = scores[mincriteriaPercentile]; m->mothurOut("Optimizing minscore to " + toString(minScore) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxinsert") { maxInsert = inserts[criteriaPercentile]; m->mothurOut("Optimizing maxinsert to " + toString(maxInsert) + "."); m->mothurOutEndLine(); }
+ }
+
+#ifdef USE_MPI
+ }
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ if (pid == 0) {
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&minSim, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&minScore, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&maxInsert, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ }
+ }else {
+ MPI_Recv(&minSim, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&minScore, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&maxInsert, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
}
-
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
- m->mothurOutEndLine();
-
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+#endif
return 0;
}
catch(exception& e) {
- m->errorOut(e, "ScreenSeqsCommand", "execute");
+ m->errorOut(e, "ScreenSeqsCommand", "optimizeContigs");
exit(1);
}
}
-
-//***************************************************************************************************************
-
-int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
+/**************************************************************************************/
+int ScreenSeqsCommand::driverAlignSummary(vector<float>& sims, vector<float>& scores, vector<int>& inserts, linePair filePos) {
try {
- ifstream inputNames;
- m->openInputFile(namefile, inputNames);
- set<string> badSeqGroups;
- string seqName, seqList, group;
- set<string>::iterator it;
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
- variables["[extension]"] = m->getExtension(namefile);
- string goodNameFile = getOutputFileName("name", variables);
- outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
- ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
+ string name, TemplateName, SearchMethod, AlignmentMethod;
+ //QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
+ //checking for minScore, maxInsert, minSim
+ int length, TemplateLength, QueryStart, QueryEnd, TemplateStart, TemplateEnd, PairwiseAlignmentLength, GapsInQuery, GapsInTemplate, LongestInsert;
+ float SearchScore, SimBtwnQueryTemplate;
+
+ ifstream in;
+ m->openInputFile(alignreport, in);
+
+ in.seekg(filePos.start);
+ if (filePos.start == 0) { //read headers
+ m->getline(in); m->gobble(in);
+ }
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ in >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; m->gobble(in);
+
+ int num = 1;
+ if ((namefile != "") || (countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(name);
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ sims.push_back(SimBtwnQueryTemplate);
+ scores.push_back(SearchScore);
+ inserts.push_back(LongestInsert);
+ }
+
+ count++;
+
+ //if((count) % 100 == 0){ m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); }
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+ }
- while(!inputNames.eof()){
- if (m->control_pressed) { goodNameOut.close(); inputNames.close(); m->mothurRemove(goodNameFile); return 0; }
+ in.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driverAlignSummary");
+ exit(1);
+ }
+}
- inputNames >> seqName; m->gobble(inputNames); inputNames >> seqList;
- it = badSeqNames.find(seqName);
+/**************************************************************************************************/
+int ScreenSeqsCommand::createProcessesAlignSummary(vector<float>& sims, vector<float>& scores, vector<int>& inserts, vector<linePair> alignLines) {
+ try {
+
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driverAlignSummary(sims, scores, inserts, alignLines[process]);
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = alignreport + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
- if(namefile != ""){
- int start = 0;
- for(int i=0;i<seqList.length();i++){
- if(seqList[i] == ','){
- badSeqGroups.insert(seqList.substr(start,i-start));
- start = i+1;
- }
- }
- badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
- }
- }
- else{
- goodNameOut << seqName << '\t' << seqList << endl;
- }
- m->gobble(inputNames);
- }
- inputNames.close();
- goodNameOut.close();
-
- //we were unable to remove some of the bad sequences
- if (badSeqNames.size() != 0) {
- for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
- m->mothurOutEndLine();
- }
- }
-
- if(groupfile != ""){
-
- ifstream inputGroups;
- m->openInputFile(groupfile, inputGroups);
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
- variables["[extension]"] = m->getExtension(groupfile);
- string goodGroupFile = getOutputFileName("group", variables);
-
- outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
-
- ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
-
- while(!inputGroups.eof()){
- if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile); m->mothurRemove(goodGroupFile); return 0; }
-
- inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
+ out << num << endl;
+ out << sims.size() << endl;
+ for (int k = 0; k < sims.size(); k++) { out << sims[k] << '\t'; } out << endl;
+ for (int k = 0; k < scores.size(); k++) { out << scores[k] << '\t'; } out << endl;
+ for (int k = 0; k < inserts.size(); k++) { out << inserts[k] << '\t'; } out << endl;
- it = badSeqGroups.find(seqName);
+ out.close();
- if(it != badSeqGroups.end()){
- badSeqGroups.erase(it);
- }
- else{
- goodGroupOut << seqName << '\t' << group << endl;
- }
- m->gobble(inputGroups);
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
}
- inputGroups.close();
- goodGroupOut.close();
+ }
+
+ num = driverAlignSummary(sims, scores, inserts, alignLines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = alignreport + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
- //we were unable to remove some of the bad sequences
- if (badSeqGroups.size() != 0) {
- for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
- m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
- m->mothurOutEndLine();
- }
- }
+ int temp, tempNum;
+ float temp2;
+ in >> tempNum; m->gobble(in); num += tempNum;
+ in >> tempNum; m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp2; sims.push_back(temp2); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp2; scores.push_back(temp2); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; inserts.push_back(temp); } m->gobble(in);
+
+ in.close();
+ m->mothurRemove(tempFilename);
}
- return 0;
-
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to allow both threads to add info to vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ /*
+ vector<alignsData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+
+ // Allocate memory for thread data.
+ alignsData* tempSum = new alignsData(alignreport, m, alignLines[i].start, alignLines[i].end, namefile, countfile, nameMap);
+ pDataArray.push_back(tempSum);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i] = CreateThread(NULL, 0, MyAlignsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }*/
+ alignLines[processors-1].start = 0;
+ //do your part
+ num = driverAlignSummary(sims, scores, inserts, alignLines[processors-1]);
+ /*
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //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]->sims.size(); k++) { sims.push_back(pDataArray[i]->sims[k]); }
+ for (int k = 0; k < pDataArray[i]->scores.size(); k++) { scores.push_back(pDataArray[i]->scores[k]); }
+ for (int k = 0; k < pDataArray[i]->inserts.size(); k++) { inserts.push_back(pDataArray[i]->inserts[k]); }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+ */
+#endif
+ return num;
}
catch(exception& e) {
- m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
+ m->errorOut(e, "ScreenSeqsCommand", "createProcessesAlignSummary");
exit(1);
}
}
vector<int> seqLength;
vector<int> ambigBases;
vector<int> longHomoPolymer;
+ vector<int> numNs;
vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if (pid == 0) {
- driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]);
#else
int numSeqs = 0;
//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
- numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]);
}else{
- numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
+ numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile);
}
if (m->control_pressed) { return 0; }
- //#else
- // numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
- // if (m->control_pressed) { return 0; }
- //#endif
#endif
sort(startPosition.begin(), startPosition.end());
sort(endPosition.begin(), endPosition.end());
sort(seqLength.begin(), seqLength.end());
sort(ambigBases.begin(), ambigBases.end());
sort(longHomoPolymer.begin(), longHomoPolymer.end());
+ sort(numNs.begin(), numNs.end());
//numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
int criteriaPercentile = int(startPosition.size() * (criteria / (float) 100));
else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxn") { maxN = numNs[criteriaPercentile]; m->mothurOut("Optimizing maxn to " + toString(maxN) + "."); m->mothurOutEndLine(); }
}
#ifdef USE_MPI
MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&maxN, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
}
}else {
MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Recv(&maxN, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
}
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#endif
}
}
/**************************************************************************************/
-int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair filePos) {
+int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, vector<int>& numNs, string filename, linePair filePos) {
try {
ifstream in;
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());
}
//for each sequence this sequence represents
+ int numns = current.getNumNs();
for (int i = 0; i < num; i++) {
startPosition.push_back(current.getStartPos());
endPosition.push_back(current.getEndPos());
seqLength.push_back(current.getNumBases());
ambigBases.push_back(current.getAmbigBases());
longHomoPolymer.push_back(current.getLongHomoPolymer());
+ numNs.push_back(numns);
}
count++;
}
}
/**************************************************************************************************/
-int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
+int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, vector<int>& numNs, string filename) {
try {
int process = 1;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[process]);
//pass numSeqs to parent
ofstream out;
for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl;
for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl;
for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } out << endl;
+ for (int k = 0; k < numNs.size(); k++) { out << numNs[k] << '\t'; } out << endl;
out.close();
}
}
- num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in);
for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in);
for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; numNs.push_back(temp); } m->gobble(in);
in.close();
m->mothurRemove(tempFilename);
for( int i=0; i<processors-1; i++ ){
// Allocate memory for thread data.
- sumData* tempSum = new sumData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+ sumData* tempSum = new sumData(filename, m, lines[i].start, lines[i].end, namefile, countfile, nameMap);
pDataArray.push_back(tempSum);
//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
}
//do your part
- num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[processors-1]);
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[processors-1]);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); }
for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) { ambigBases.push_back(pDataArray[i]->ambigBases[k]); }
for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) { longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]); }
+ for (int k = 0; k < pDataArray[i]->numNs.size(); k++) { numNs.push_back(pDataArray[i]->numNs[k]); }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
//***************************************************************************************************************
-int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenGroupFile(map<string, string> badSeqNames){
try {
ifstream inputGroups;
m->openInputFile(groupfile, inputGroups);
string seqName, group;
- set<string>::iterator it;
+ map<string, string>::iterator it;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[extension]"] = m->getExtension(groupfile);
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
+ m->mothurOut("Your groupfile does not include the sequence " + it->first + " please correct.");
m->mothurOutEndLine();
}
}
}
}
//***************************************************************************************************************
-int ScreenSeqsCommand::screenCountFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
try {
ifstream in;
m->openInputFile(countfile, in);
- set<string>::iterator it;
+ map<string, string>::iterator it;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
variables["[extension]"] = m->getExtension(countfile);
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your count file does not include the sequence " + *it + " please correct.");
+ m->mothurOut("Your count file does not include the sequence " + it->first + " please correct.");
m->mothurOutEndLine();
}
}
}
//***************************************************************************************************************
-int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
- try {
- ifstream inputAlignReport;
- m->openInputFile(alignreport, inputAlignReport);
- string seqName, group;
- set<string>::iterator it;
-
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(alignreport));
- string goodAlignReportFile = getOutputFileName("alignreport", variables);
-
- outputNames.push_back(goodAlignReportFile); outputTypes["alignreport"].push_back(goodAlignReportFile);
- ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
-
- while (!inputAlignReport.eof()) { // need to copy header
- char c = inputAlignReport.get();
- goodAlignReportOut << c;
- if (c == 10 || c == 13){ break; }
- }
-
- while(!inputAlignReport.eof()){
- if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; }
-
- inputAlignReport >> seqName;
- it = badSeqNames.find(seqName);
- string line;
- while (!inputAlignReport.eof()) { // need to copy header
- char c = inputAlignReport.get();
- line += c;
- if (c == 10 || c == 13){ break; }
- }
-
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
- }
- else{
- goodAlignReportOut << seqName << '\t' << line;
- }
- m->gobble(inputAlignReport);
- }
-
- if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; }
-
- //we were unable to remove some of the bad sequences
- if (badSeqNames.size() != 0) {
- for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
- m->mothurOutEndLine();
- }
- }
-
- inputAlignReport.close();
- goodAlignReportOut.close();
-
- if (m->control_pressed) { m->mothurRemove(goodAlignReportFile); return 0; }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
- exit(1);
- }
-
-}
-//***************************************************************************************************************
-
-int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
+int ScreenSeqsCommand::screenTaxonomy(map<string, string> badSeqNames){
try {
ifstream input;
m->openInputFile(taxonomy, input);
string seqName, tax;
- set<string>::iterator it;
+ map<string, string>::iterator it;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxonomy));
variables["[extension]"] = m->getExtension(taxonomy);
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your taxonomy file does not include the sequence " + *it + " please correct.");
+ m->mothurOut("Your taxonomy file does not include the sequence " + it->first + " please correct.");
m->mothurOutEndLine();
}
}
}
//***************************************************************************************************************
-int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
+int ScreenSeqsCommand::screenQual(map<string, string> badSeqNames){
try {
ifstream in;
m->openInputFile(qualfile, in);
- set<string>::iterator it;
+ map<string, string>::iterator it;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile));
variables["[extension]"] = m->getExtension(qualfile);
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
+ m->mothurOut("Your qual file does not include the sequence " + it->first + " please correct.");
m->mothurOutEndLine();
}
}
}
//**********************************************************************************************************************
-int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
+int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, map<string, string>& badSeqNames){
try {
ofstream goodFile;
m->openOutputFile(goodFName, goodFile);
bool done = false;
int count = 0;
-
+
while (!done) {
if (m->control_pressed) { return 0; }
Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
bool goodSeq = 1; // innocent until proven guilty
- if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
- if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; }
- if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
- if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
- if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; }
- if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; }
+ string trashCode = "";
+ //have the report files found you bad
+ map<string, string>::iterator it = badSeqNames.find(currSeq.getName());
+ if (it != badSeqNames.end()) { goodSeq = 0; trashCode = it->second; }
+
+ if (summaryfile == "") { //summaryfile includes these so no need to check again
+ if(startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; trashCode += "start|"; }
+ if(endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|";}
+ if(maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|";}
+ if(maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|";}
+ if(minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|";}
+ if(maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; trashCode += ">length|";}
+ }
+
+ if (contigsreport == "") { //contigs report includes this so no need to check again
+ if(maxN != -1 && maxN < currSeq.getNumNs()) { goodSeq = 0; trashCode += "n|"; }
+ }
if(goodSeq == 1){
currSeq.printSequence(goodFile);
+ }else{
+ badAccnosFile << currSeq.getName() << '\t' << trashCode.substr(0, trashCode.length()-1) << endl;
+ badSeqNames[currSeq.getName()] = trashCode;
}
- else{
- badAccnosFile << currSeq.getName() << endl;
- badSeqNames.insert(currSeq.getName());
- }
- count++;
+ count++;
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, set<string>& badSeqNames){
+int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, map<string, string>& badSeqNames){
try {
string outputString = "";
MPI_Status statusGood;
//process seq
if (currSeq.getName() != "") {
bool goodSeq = 1; // innocent until proven guilty
- if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
- if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; }
- if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
- if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
- if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; }
- if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; }
+ string trashCode = "";
+ //have the report files found you bad
+ map<string, string>::iterator it = badSeqNames.find(currSeq.getName());
+ if (it != badSeqNames.end()) { goodSeq = 0; trashCode = it->second; }
+
+ if (summaryfile == "") { //summaryfile includes these so no need to check again
+ if(startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; trashCode += "start|"; }
+ if(endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|";}
+ if(maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|";}
+ if(maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|";}
+ if(minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|";}
+ if(maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; trashCode += ">length|";}
+ }
+
+ if (contigsreport == "") { //contigs report includes this so no need to check again
+ if(maxN != -1 && maxN < currSeq.getNumNs()) { goodSeq = 0; trashCode += "n|"; }
+ }
+
if(goodSeq == 1){
outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
}
else{
- badSeqNames.insert(currSeq.getName());
+ badSeqNames[currSeq.getName()] = trashCode;
//write to bad accnos file
- outputString = currSeq.getName() + "\n";
+ outputString = currSeq.getName() + "\t" + trashCode.substr(0, trashCode.length()-1) + "\n";
length = outputString.length();
char* buf3 = new char[length];
#endif
/**************************************************************************************************/
-int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
+int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, map<string, string>& badSeqNames) {
try {
vector<int> processIDS;
if (ableToOpen == 0) {
badSeqNames.clear();
- string tempName;
+ string tempName, trashCode;
while (!inBad.eof()) {
- inBad >> tempName; m->gobble(inBad);
- badSeqNames.insert(tempName);
+ inBad >> tempName >> trashCode; m->gobble(inBad);
+ badSeqNames[tempName] = trashCode;
}
inBad.close();
}
if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
+ sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, maxN, badSeqNames, filename, summaryfile, contigsreport, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
pDataArray.push_back(tempSum);
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
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 (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it); }
+ for (map<string, string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames[it->first] = it->second; }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
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