//**********************************************************************************************************************
vector<string> TrimFlowsCommand::setParameters(){
try {
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
- CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
- CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
- CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
- CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow-file",false,true,true); parameters.push_back(pflow);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
+ CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter porder("order", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder);
+ CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
helpString += "The trim.flows command reads a flowgram file and creates .....\n";
+ helpString += "The order parameter options are A, B or I. Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
return helpString;
}
}
//**********************************************************************************************************************
-string TrimFlowsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string TrimFlowsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "flow") { outputFileName = "flow"; }
- else if (type == "fasta") { outputFileName = "flow.fasta"; }
- else if (type == "file") { outputFileName = "flow.files"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimFlowsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "flow") { pattern = "[filename],[tag],flow"; }
+ else if (type == "fasta") { pattern = "[filename],flow.fasta"; }
+ else if (type == "file") { pattern = "[filename],flow.files"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
m->setProcessors(temp);
m->mothurConvert(temp, processors);
- flowOrder = validParameter.validFile(parameters, "order", false);
- if (flowOrder == "not found"){ flowOrder = "TACG"; }
- else if(flowOrder.length() != 4){
- m->mothurOut("The value of the order option must be four bases long\n");
- }
-
+ temp = validParameter.validFile(parameters, "order", false); if (temp == "not found"){ temp = "A"; }
+ if (temp.length() > 1) { m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true;
+ }
+ else {
+ if (toupper(temp[0]) == 'A') { flowOrder = "TACG"; }
+ else if(toupper(temp[0]) == 'B'){
+ flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC"; }
+ else if(toupper(temp[0]) == 'I'){
+ flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC"; }
+ else {
+ m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true;
+ }
+ }
+
if(oligoFileName == "") { allFiles = 0; }
else { allFiles = 1; }
numLinkers = 0;
numSpacers = 0;
}
-
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string fastaFileName = getOutputFileName("fasta",variables);
+ if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
+
+ variables["[tag]"] = "trim";
+ string trimFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
- string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap." + getOutputFileNameTag("flow");;
+ variables["[tag]"] = "scrap";
+ string scrapFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
- string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
- if(fasta){
- outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
- }
+
vector<unsigned long long> flowFilePos;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(allFiles){
set<string> namesAlreadyProcessed;
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
+ flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
for(int i=0;i<barcodePrimerComboFileNames.size();i++){
for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
- FILE * pFile;
- unsigned long long size;
-
- //get num bytes in file
- pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
- if (pFile==NULL) perror ("Error opening file");
- else{
- fseek (pFile, 0, SEEK_END);
- size=ftell(pFile);
- fclose (pFile);
- }
-
- if(size < 10){
- m->mothurRemove(barcodePrimerComboFileNames[i][j]);
- }
- else{
- output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
- outputNames.push_back(barcodePrimerComboFileNames[i][j]);
- outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
- }
- namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
+ if (barcodePrimerComboFileNames[i][j] != "") {
+ FILE * pFile;
+ unsigned long long size;
+
+ //get num bytes in file
+ pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell(pFile);
+ fclose (pFile);
+ }
+
+ if(size < 10){
+ m->mothurRemove(barcodePrimerComboFileNames[i][j]);
+ }
+ else{
+ output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
+ outputNames.push_back(barcodePrimerComboFileNames[i][j]);
+ outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
+ }
+ namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
+ }
}
}
}
output.close();
}
else{
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
+ flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
output << m->getFullPathName(trimFlowFileName) << endl;
output.close();
}
- outputTypes["flow.files"].push_back(flowFilesFileName);
+ outputTypes["file"].push_back(flowFilesFileName);
outputNames.push_back(flowFilesFileName);
-
-// set fasta file as new current fastafile
-// string current = "";
-// itTypes = outputTypes.find("fasta");
-// if (itTypes != outputTypes.end()) {
-// if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
-// }
-
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
if(line->start == 0){
flowFile >> numFlows; m->gobble(flowFile);
- scrapFlowFile << maxFlows << endl;
+ scrapFlowFile << numFlows << endl;
trimFlowFile << maxFlows << endl;
if(allFiles){
for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
- ofstream temp;
- m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
- temp << maxFlows << endl;
- temp.close();
+ if (thisBarcodePrimerComboFileNames[i][j] != "") {
+ ofstream temp;
+ m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
+ temp << maxFlows << endl;
+ temp.close();
+ }
}
}
}
string trashCode = "";
flowData.getNext(flowFile);
- //cout << "driver good bit " << flowFile.good() << endl;
flowData.capFlows(maxFlows);
Sequence currSeq = flowData.getSequence();
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
if(!flowData.hasMinFlows(minFlows)){ //screen to see if sequence is of a minimum number of flows
success = 0;
trashCode += 'l';
}
-
+ if(!flowData.hasGoodHomoP()){ //screen to see if sequence meets the maximum homopolymer limit
+ success = 0;
+ trashCode += 'h';
+ }
+
int primerIndex = 0;
int barcodeIndex = 0;
}
+ if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
+
if(barcodes.size() != 0){
success = trimOligos.stripBarcode(currSeq, barcodeIndex);
if(success > bdiffs) { trashCode += 'b'; }
}
if(trashCode.length() == 0){
-
- flowData.printFlows(trimFlowFile);
-
- if(fasta) { currSeq.printSequence(fastaFile); }
-
- if(allFiles){
- ofstream output;
- m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
- output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
-
- flowData.printFlows(output);
- output.close();
- }
+ string thisGroup = "";
+ if(barcodes.size() != 0){
+ thisGroup = barcodeNameVector[barcodeIndex];
+ if (primers.size() != 0) {
+ if (primerNameVector[primerIndex] != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + primerNameVector[primerIndex];
+ }else {
+ thisGroup = primerNameVector[primerIndex];
+ }
+ }
+ }
+ }
+
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ flowData.printFlows(trimFlowFile);
+
+ if(fasta) { currSeq.printSequence(fastaFile); }
+
+ if(allFiles){
+ ofstream output;
+ m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
+ output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
+
+ flowData.printFlows(output);
+ output.close();
+ }
+ }
}
else{
flowData.printFlows(scrapFlowFile, trashCode);
while(!oligosFile.eof()){
- oligosFile >> type; m->gobble(oligosFile); //get the first column value of the row - is it a comment or a feature we are interested in?
-
+ oligosFile >> type; //get the first column value of the row - is it a comment or a feature we are interested in?
+
+ if (m->debug) { m->mothurOut("[DEBUG]: type = " + type + ".\n"); }
+
if(type[0] == '#'){ //igore the line because there's a comment
- while (!oligosFile.eof()) { char c = oligosFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ while (!oligosFile.eof()) { char c = oligosFile.get(); if (c == 10 || c == 13){ break; } }
+ m->gobble(oligosFile);// get rest of line if there's any crap there
}
else{ //there's a feature we're interested in
-
+ m->gobble(oligosFile);
for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); } //make type case insensitive
oligosFile >> oligo; //get the DNA sequence for the feature
oligo[i] = toupper(oligo[i]);
if(oligo[i] == 'U') { oligo[i] = 'T'; }
}
-
+
+ if (m->debug) { m->mothurOut("[DEBUG]: oligos = " + oligo + ".\n"); }
+
if(type == "FORWARD"){ //if the feature is a forward primer...
group = "";
while (!oligosFile.eof()) { // get rest of line in case there is a primer name = will have the name of the primer
char c = oligosFile.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
else if(type == "REVERSE"){
string oligoRC = reverseOligo(oligo);
revPrimer.push_back(oligoRC);
+ if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
}
else if(type == "BARCODE"){
oligosFile >> group;
//check for repeat barcodes
map<string, int>::iterator itBar = barcodes.find(oligo);
if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
-
+
+ if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ".\n"); }
+
barcodes[oligo]=indexBarcode; indexBarcode++;
barcodeNameVector.push_back(group);
}else if(type == "LINKER"){
primers[""] = 0;
primerNameVector.push_back("");
}
-
-
+
outFlowFileNames.resize(barcodeNameVector.size());
for(int i=0;i<outFlowFileNames.size();i++){
outFlowFileNames[i].assign(primerNameVector.size(), "");
string primerName = primerNameVector[itPrimer->second];
string barcodeName = barcodeNameVector[itBar->second];
-
- string comboGroupName = "";
- string fileName = "";
-
- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->second];
- fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
- }
- else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->second];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
- }
- fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
- }
-
- outFlowFileNames[itBar->second][itPrimer->second] = fileName;
-
- ofstream temp;
- m->openOutputFile(fileName, temp);
- temp.close();
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fileName = "";
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
+ }
+
+ outFlowFileNames[itBar->second][itPrimer->second] = fileName;
+
+ ofstream temp;
+ m->openOutputFile(fileName, temp);
+ temp.close();
+ }
}
}
}
if(allFiles){
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
- tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
- ofstream temp;
- m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
- temp.close();
-
+ if (tempBarcodePrimerComboFileNames[i][j] != "") {
+ tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
+ ofstream temp;
+ m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
+ temp.close();
+ }
}
}
}
if(allFiles){
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
- tempBarcodePrimerComboFileNames[i][j] += extension;
- ofstream temp;
- m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
- temp.close();
-
+ if (tempBarcodePrimerComboFileNames[i][j] != "") {
+ tempBarcodePrimerComboFileNames[i][j] += extension;
+ ofstream temp;
+ m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
+ temp.close();
+ }
}
}
}
if(allFiles){
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
- tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
- ofstream temp;
- m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
- temp.close();
+ if (tempBarcodePrimerComboFileNames[i][j] != "") {
+ tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
+ ofstream temp;
+ m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
+ temp.close();
+ }
}
}
if(allFiles){
for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
- m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
- m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+ if (barcodePrimerComboFileNames[j][k] != "") {
+ m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
+ m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+ }
}
}
}
projects / mothur.git / blobdiff