X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;fp=deconvolutecommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=3d0c0d51acaac8844b71a3efa40c7925674ad4c5;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp deleted file mode 100644 index 3d0c0d5..0000000 --- a/deconvolutecommand.cpp +++ /dev/null @@ -1,283 +0,0 @@ -/* - * deconvolute.cpp - * Mothur - * - * Created by Sarah Westcott on 1/21/09. - * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. - * - */ - -#include "deconvolutecommand.h" -#include "sequence.hpp" - -//********************************************************************************************************************** -vector DeconvoluteCommand::setParameters(){ - try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter 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); } - return myArray; - } - catch(exception& e) { - m->errorOut(e, "DeconvoluteCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string DeconvoluteCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The unique.seqs command reads a fastafile and creates a namesfile.\n"; - helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n"; - helpString += "If the sequence is unique the second column will just contain its name. \n"; - helpString += "The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.\n"; - helpString += "The unique.seqs command should be in the following format: \n"; - helpString += "unique.seqs(fasta=yourFastaFile) \n"; - return helpString; - } - catch(exception& e) { - m->errorOut(e, "DeconvoluteCommand", "getHelpString"); - exit(1); - } -} -//********************************************************************************************************************** -DeconvoluteCommand::DeconvoluteCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["name"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand"); - exit(1); - } -} -/**************************************************************************************/ -DeconvoluteCommand::DeconvoluteCommand(string option) { - try { - abort = false; calledHelp = false; - - //allow user to run help - if(option == "help") { help(); abort = true; calledHelp = true; } - else if(option == "citation") { citation(); abort = true; calledHelp = true;} - - else { - vector myArray = setParameters(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - map::iterator it; - - //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["name"] = 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 = ""; } - else { - string path; - it = parameters.find("fasta"); - //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["fasta"] = inputDir + it->second; } - } - - it = parameters.find("name"); - //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["name"] = inputDir + it->second; } - } - } - - - //check for required parameters - inFastaName = validParameter.validFile(parameters, "fasta", true); - if (inFastaName == "not open") { abort = true; } - else if (inFastaName == "not found") { - inFastaName = m->getFastaFile(); - if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " 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(inFastaName); } - - //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 = ""; - outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it - } - - oldNameMapFName = validParameter.validFile(parameters, "name", true); - if (oldNameMapFName == "not open") { oldNameMapFName = ""; abort = true; } - else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; } - else { m->setNameFile(oldNameMapFName); } - - if (oldNameMapFName == "") { - vector files; files.push_back(inFastaName); - parser.getNameFile(files); - } - - } - - } - catch(exception& e) { - m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand"); - exit(1); - } -} -/**************************************************************************************/ -int DeconvoluteCommand::execute() { - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - //prepare filenames and open files - string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names"; - string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName); - - map nameMap; - map::iterator itNames; - if (oldNameMapFName != "") { - m->readNames(oldNameMapFName, nameMap); - if (oldNameMapFName == outNameFile){ outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique.names"; } - } - - if (m->control_pressed) { return 0; } - - ifstream in; - m->openInputFile(inFastaName, in); - - ofstream outFasta; - m->openOutputFile(outFastaFile, outFasta); - - map sequenceStrings; //sequenceString -> list of names. "atgc...." -> seq1,seq2,seq3. - map::iterator itStrings; - set nameInFastaFile; //for sanity checking - set::iterator itname; - vector nameFileOrder; - int count = 0; - while (!in.eof()) { - - if (m->control_pressed) { in.close(); outFasta.close(); m->mothurRemove(outFastaFile); return 0; } - - Sequence seq(in); - - if (seq.getName() != "") { - - //sanity checks - itname = nameInFastaFile.find(seq.getName()); - if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName()); } - else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct."); m->mothurOutEndLine(); } - - itStrings = sequenceStrings.find(seq.getAligned()); - - if (itStrings == sequenceStrings.end()) { //this is a new unique sequence - //output to unique fasta file - seq.printSequence(outFasta); - - if (oldNameMapFName != "") { - itNames = nameMap.find(seq.getName()); - - if (itNames == nameMap.end()) { //namefile and fastafile do not match - m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine(); - }else { - sequenceStrings[seq.getAligned()] = itNames->second; - nameFileOrder.push_back(seq.getAligned()); - } - }else { sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(seq.getAligned()); } - }else { //this is a dup - if (oldNameMapFName != "") { - itNames = nameMap.find(seq.getName()); - - if (itNames == nameMap.end()) { //namefile and fastafile do not match - m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine(); - }else { - sequenceStrings[seq.getAligned()] += "," + itNames->second; - } - }else { sequenceStrings[seq.getAligned()] += "," + seq.getName(); } - } - - count++; - } - - m->gobble(in); - - if(count % 1000 == 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); } - } - - if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); } - - in.close(); - outFasta.close(); - - if (m->control_pressed) { m->mothurRemove(outFastaFile); return 0; } - - //print new names file - ofstream outNames; - m->openOutputFile(outNameFile, outNames); - - for (int i = 0; i < nameFileOrder.size(); i++) { - //for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) { - if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); m->mothurRemove(outNameFile); return 0; } - - itStrings = sequenceStrings.find(nameFileOrder[i]); - - if (itStrings != sequenceStrings.end()) { - //get rep name - int pos = (itStrings->second).find_first_of(','); - - if (pos == string::npos) { // only reps itself - outNames << itStrings->second << '\t' << itStrings->second << endl; - }else { - outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl; - } - }else{ m->mothurOut("[ERROR]: mismatch in namefile print."); m->mothurOutEndLine(); m->control_pressed = true; } - } - outNames.close(); - - if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); m->mothurRemove(outNameFile); return 0; } - - m->mothurOutEndLine(); - m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(outFastaFile); m->mothurOutEndLine(); - m->mothurOut(outNameFile); m->mothurOutEndLine(); - outputNames.push_back(outFastaFile); outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile); outputTypes["name"].push_back(outNameFile); - m->mothurOutEndLine(); - - //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); } - } - - itTypes = outputTypes.find("name"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } - } - - return 0; - } - catch(exception& e) { - m->errorOut(e, "DeconvoluteCommand", "execute"); - exit(1); - } -} -/**************************************************************************************/