CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
try {
string helpString = "";
helpString += "The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n";
- helpString += "The consensus.seqs command parameters are fasta, list, name and label.\n";
+ helpString += "The consensus.seqs command parameters are fasta, list, name, cutoff and label.\n";
helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
helpString += "The list parameter allows you to enter a your list file. \n";
helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The cutoff parameter allows you set a percentage of sequences that support the base. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.\n";
helpString += "The consensus.seqs command should be in the following format: \n";
helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
+ string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, cutoff);
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
int seqLength = 0;
for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
string seq = fastaMap[it->second];
seqs.push_back(seq);
//get counts
for (int j = 0; j < seqLength; j++) {
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
int numDots = 0;
}
char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts); }
+ if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
consSeq += conBase;
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete list; delete input; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts); }
+ if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
consSeq += conBase;
}
//***************************************************************************************************************
-char ConsensusSeqsCommand::getBase(vector<int> counts){ //A,T,G,C,Gap
+char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
try{
/* A = adenine
* C = cytosine
char conBase = 'N';
+ //zero out counts that don't make the cutoff
+ float percentage = (100.0 - cutoff) / 100.0;
+ int zeroCutoff = percentage * size;
+
+ for (int i = 0; i < counts.size(); i++) {
+ if (counts[i] < zeroCutoff) { counts[i] = 0; }
+ }
+
//any
if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
//any no gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
//only gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
+ //cutoff removed all counts
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
return conBase;
projects / mothur.git / blobdiff