X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shhhercommand.cpp;h=4a6e5ff2375ce40560db1aa706edbdacefac0e0d;hp=19ffc899d60ac778ac4eedbeb2034a62b5e04bd7;hb=615301e57c25e241356a9c2380648d117709458d;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d diff --git a/shhhercommand.cpp b/shhhercommand.cpp index 19ffc89..4a6e5ff 100644 --- a/shhhercommand.cpp +++ b/shhhercommand.cpp @@ -12,18 +12,17 @@ //********************************************************************************************************************** vector ShhherCommand::setParameters(){ try { - CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow); - CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile); - CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup); - CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter); - CommandParameter plarge("large", "Number", "", "-1", "", "", "",false,false); parameters.push_back(plarge); - CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma); - CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta); - CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder); - 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", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pflow); + CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pfile); + CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(plookup); + CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pcutoff); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pmaxiter); + CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge); + CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma); + CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta); + CommandParameter porder("order", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -39,6 +38,11 @@ string ShhherCommand::getHelpString(){ try { string helpString = ""; helpString += "The shhh.flows command reads a file containing flowgrams and creates a file of corrected sequences.\n"; + helpString += "The shhh.flows command parameters are flow, file, lookup, cutoff, processors, large, maxiter, sigma, mindelta and order.\n"; + helpString += "The flow parameter is used to input your flow file.\n"; + helpString += "The file parameter is used to input the *flow.files file created by trim.flows.\n"; + helpString += "The lookup parameter is used specify the lookup file you would like to use. http://www.mothur.org/wiki/Lookup_files.\n"; + helpString += "The order parameter options are A, B or I. Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"; return helpString; } catch(exception& e) { @@ -47,28 +51,23 @@ string ShhherCommand::getHelpString(){ } } //********************************************************************************************************************** -string ShhherCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; - - //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 == "fasta") { outputFileName = "shhh.fasta"; } - else if (type == "name") { outputFileName = "shhh.names"; } - else if (type == "group") { outputFileName = "shhh.groups"; } - else if (type == "counts") { outputFileName = "shhh.counts"; } - else if (type == "qfile") { outputFileName = "shhh.qual"; } - 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, "ShhherCommand", "getOutputFileNameTag"); - exit(1); - } +string ShhherCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],shhh.fasta"; } + else if (type == "name") { pattern = "[filename],shhh.names"; } + else if (type == "group") { pattern = "[filename],shhh.groups"; } + else if (type == "counts") { pattern = "[filename],shhh.counts"; } + else if (type == "qfile") { pattern = "[filename],shhh.qual"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** @@ -267,7 +266,17 @@ ShhherCommand::ShhherCommand(string option) { string temp; temp = validParameter.validFile(parameters, "lookup", true); if (temp == "not found") { - lookupFileName = "LookUp_Titanium.pat"; + string path = m->argv; + string tempPath = path; + for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); } + path = path.substr(0, (tempPath.find_last_of('m'))); + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + path += "lookupFiles/"; +#else + path += "lookupFiles\\"; +#endif + lookupFileName = m->getFullPathName(path) + "LookUp_Titanium.pat"; int ableToOpen; ifstream in; @@ -277,7 +286,7 @@ ShhherCommand::ShhherCommand(string option) { //if you can't open it, try input location if (ableToOpen == 1) { if (inputDir != "") { //default path is set - string tryPath = inputDir + lookupFileName; + string tryPath = inputDir + m->getSimpleName(lookupFileName); m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine(); ifstream in2; ableToOpen = m->openInputFile(tryPath, in2, "noerror"); @@ -325,7 +334,7 @@ ShhherCommand::ShhherCommand(string option) { for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); } exepath = exepath.substr(0, (tempPath.find_last_of('m'))); - string tryPath = m->getFullPathName(exepath) + lookupFileName; + string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName); m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine(); ifstream in2; int ableToOpen = m->openInputFile(tryPath, in2, "noerror"); @@ -362,11 +371,20 @@ ShhherCommand::ShhherCommand(string option) { temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found") { temp = "60"; } m->mothurConvert(temp, sigma); - 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; + } + } + } #ifdef USE_MPI @@ -801,8 +819,9 @@ string ShhherCommand::createNamesFile(){ for(int i=0;igetRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name"); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName)); + string nameFileName = getOutputFileName("name",variables); ofstream nameFile; m->openOutputFile(nameFileName, nameFile); @@ -851,7 +870,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){ } } if(i % 100 == 0){ - m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); + m->mothurOutJustToScreen(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); } } @@ -860,7 +879,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){ if (m->control_pressed) { return fDistFileName; } - m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); + m->mothurOutJustToScreen(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); ofstream distFile(fDistFileName.c_str()); distFile << outStream.str(); @@ -1651,7 +1670,9 @@ void ShhherCommand::writeQualities(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile"); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName)); + string qualityFileName = getOutputFileName("qfile",variables); ofstream qualityFile; m->openOutputFile(qualityFileName, qualityFile); @@ -1758,7 +1779,9 @@ void ShhherCommand::writeSequences(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string fastaFileName = getOutputFileName("fasta",variables); ofstream fastaFile; m->openOutputFile(fastaFileName, fastaFile); @@ -1777,7 +1800,7 @@ void ShhherCommand::writeSequences(vector otuCounts){ for(int j=0;j otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string nameFileName = getOutputFileName("name",variables); ofstream nameFile; m->openOutputFile(nameFileName, nameFile); @@ -1848,7 +1873,9 @@ void ShhherCommand::writeGroups(){ int pos = fileRoot.find_first_of('.'); string fileGroup = fileRoot; if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); } - string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group"); + map variables; + variables["[filename]"] = thisOutputDir + fileRoot; + string groupFileName = getOutputFileName("group",variables); ofstream groupFile; m->openOutputFile(groupFileName, groupFile); @@ -1872,7 +1899,9 @@ void ShhherCommand::writeClusters(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) +getOutputFileNameTag("counts"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string otuCountsFileName = getOutputFileName("counts",variables); ofstream otuCountsFile; m->openOutputFile(otuCountsFileName, otuCountsFile); @@ -1889,7 +1918,7 @@ void ShhherCommand::writeClusters(vector otuCounts){ otuCountsFile << "ideal\t"; for(int j=8;j otuCounts){ string newSeq = ""; for(int k=0;k rightsize); +} /**************************************************************************************************/ int ShhherCommand::createProcesses(vector filenames){ @@ -1975,9 +2038,31 @@ int ShhherCommand::createProcesses(vector filenames){ //sanity check if (filenames.size() < processors) { processors = filenames.size(); } - + + //sort file names by size to divide load better + sort(filenames.begin(), filenames.end(), compareFileSizes); + + vector < vector > dividedFiles; //dividedFiles[1] = vector of filenames for process 1... + dividedFiles.resize(processors); + + //for each file, figure out which process will complete it + //want to divide the load intelligently so the big files are spread between processes + for (int i = 0; i < filenames.size(); i++) { + int processToAssign = (i+1) % processors; + if (processToAssign == 0) { processToAssign = processors; } + + dividedFiles[(processToAssign-1)].push_back(filenames[i]); + } + + //now lets reverse the order of ever other process, so we balance big files running with little ones + for (int i = 0; i < processors; i++) { + int remainder = ((i+1) % processors); + if (remainder) { reverse(dividedFiles[i].begin(), dividedFiles[i].end()); } + } + + //divide the groups between the processors - vector lines; + /*vector lines; vector numFilesToComplete; int numFilesPerProcessor = filenames.size() / processors; for (int i = 0; i < processors; i++) { @@ -1986,7 +2071,7 @@ int ShhherCommand::createProcesses(vector filenames){ if(i == (processors - 1)){ endIndex = filenames.size(); } lines.push_back(linePair(startIndex, endIndex)); numFilesToComplete.push_back((endIndex-startIndex)); - } + }*/ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) @@ -1998,7 +2083,7 @@ int ShhherCommand::createProcesses(vector filenames){ 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 = driver(filenames, compositeFASTAFileName + toString(getpid()) + ".temp", compositeNamesFileName + toString(getpid()) + ".temp", lines[process].start, lines[process].end); + num = driver(dividedFiles[process], compositeFASTAFileName + toString(getpid()) + ".temp", compositeNamesFileName + toString(getpid()) + ".temp"); //pass numSeqs to parent ofstream out; @@ -2016,7 +2101,7 @@ int ShhherCommand::createProcesses(vector filenames){ } //do my part - driver(filenames, compositeFASTAFileName, compositeNamesFileName, lines[0].start, lines[0].end); + driver(dividedFiles[0], compositeFASTAFileName, compositeNamesFileName); //force parent to wait until all the processes are done for (int i=0;i filenames){ if (!in.eof()) { int tempNum = 0; in >> tempNum; - if (tempNum != numFilesToComplete[i+1]) { - m->mothurOut("[ERROR]: main process expected " + toString(processIDS[i]) + " to complete " + toString(numFilesToComplete[i+1]) + " files, and it only reported completing " + toString(tempNum) + ". This will cause file mismatches. The flow files may be too large to process with multiple processors. \n"); + if (tempNum != dividedFiles[i+1].size()) { + m->mothurOut("[ERROR]: main process expected " + toString(processIDS[i]) + " to complete " + toString(dividedFiles[i+1].size()) + " files, and it only reported completing " + toString(tempNum) + ". This will cause file mismatches. The flow files may be too large to process with multiple processors. \n"); } } in.close(); m->mothurRemove(tempFile); @@ -2146,12 +2231,12 @@ vector ShhherCommand::parseFlowFiles(string filename){ } /**************************************************************************************************/ -int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName, int start, int end){ +int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName){ try { int numCompleted = 0; - for(int i=start;icontrol_pressed) { break; } @@ -2163,6 +2248,8 @@ int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFil double begClock = clock(); unsigned long long begTime; + string fileNameForOutput = filenames[i]; + for (int g = 0; g < theseFlowFileNames.size(); g++) { string flowFileName = theseFlowFileNames[g]; @@ -2196,7 +2283,7 @@ int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFil begTime = time(NULL); - flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI); + flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI); m->mothurOutEndLine(); m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n'); @@ -2323,15 +2410,17 @@ int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFil if ((large) && (g == 0)) { flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; } string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir = m->hasPath(flowFileName); } - string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile"); - string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta"); - string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name"); - string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("counts"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string qualityFileName = getOutputFileName("qfile",variables); + string fastaFileName = getOutputFileName("fasta",variables); + string nameFileName = getOutputFileName("name",variables); + string otuCountsFileName = getOutputFileName("counts",variables); string fileRoot = m->getRootName(m->getSimpleName(flowFileName)); int pos = fileRoot.find_first_of('.'); string fileGroup = fileRoot; if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); } - string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group"); + string groupFileName = getOutputFileName("group",variables); writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; } @@ -2342,15 +2431,16 @@ int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFil if (large) { if (g > 0) { - m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("qfile"))); + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])); + m->appendFiles(qualityFileName, getOutputFileName("qfile",variables)); m->mothurRemove(qualityFileName); - m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("fasta"))); + m->appendFiles(fastaFileName, getOutputFileName("fasta",variables)); m->mothurRemove(fastaFileName); - m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("name"))); + m->appendFiles(nameFileName, getOutputFileName("name",variables)); m->mothurRemove(nameFileName); - m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("counts"))); + m->appendFiles(otuCountsFileName, getOutputFileName("counts",variables)); m->mothurRemove(otuCountsFileName); - m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("group"))); + m->appendFiles(groupFileName, getOutputFileName("group",variables)); m->mothurRemove(groupFileName); } m->mothurRemove(theseFlowFileNames[g]); @@ -2358,7 +2448,7 @@ int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFil } numCompleted++; - m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n'); + m->mothurOut("Total time to process " + fileNameForOutput + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n'); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -2467,9 +2557,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int } } if(i % 100 == 0){ - m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime)); - m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)); - m->mothurOutEndLine(); + m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - begTime)); + m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n"); } } @@ -2479,9 +2568,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int if (m->control_pressed) {} else { - m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime)); - m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)); - m->mothurOutEndLine(); + m->mothurOutJustToScreen(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime)); + m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n"); } return 0; @@ -2649,7 +2737,8 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil RAbundVector* rabund = new RAbundVector(list->getRAbundVector()); - Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); + float adjust = -1.0; + Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest", adjust); string tag = cluster->getTag(); double clusterCutoff = cutoff; @@ -3298,7 +3387,7 @@ void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTU for(int j=0;j