--- /dev/null
+/*
+ * degapseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 6/21/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "degapseqscommand.h"
+#include "sequence.hpp"
+
+//***************************************************************************************************************
+
+DegapSeqsCommand::DegapSeqsCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::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; }
+ }
+
+ //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 = ""; }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", false);
+ if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fastafile, fastaFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = openInputFile(fastaFileNames[i], in);
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+
+ //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 += hasPath(fastafile); //if user entered a file with a path then preserve it
+ }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void DegapSeqsCommand::help(){
+ try {
+ m->mothurOut("The degap.seqs command reads a fastafile and removes all gap characters.\n");
+ m->mothurOut("The degap.seqs command parameter is fasta.\n");
+ m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
+ m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
+ m->mothurOut("The degap.seqs command should be in the following format: \n");
+ m->mothurOut("degap.seqs(fasta=yourFastaFile) \n");
+ m->mothurOut("Example: degap.seqs(fasta=abrecovery.align) \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "help");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+DegapSeqsCommand::~DegapSeqsCommand(){ /* do nothing */ }
+
+//***************************************************************************************************************
+
+
+int DegapSeqsCommand::execute(){
+ try{
+
+ if (abort == true) { return 0; }
+
+ for (int s = 0; s < fastaFileNames.size(); s++) {
+
+ m->mothurOut("Degapping sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[s], inFASTA);
+
+ ofstream outFASTA;
+ string degapFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ng.fasta";
+ openOutputFile(degapFile, outFASTA);
+
+ while(!inFASTA.eof()){
+ if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+
+ Sequence currSeq(inFASTA); gobble(inFASTA);
+ if (currSeq.getName() != "") {
+ outFASTA << ">" << currSeq.getName() << endl;
+ outFASTA << currSeq.getUnaligned() << endl;
+ }
+ }
+ inFASTA.close();
+ outFASTA.close();
+
+ outputNames.push_back(degapFile);
+
+ if (m->control_pressed) { remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
projects / mothur.git / blobdiff