5 * Created by Sarah Westcott on 1/21/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "deconvolutecommand.h"
12 /**************************************************************************************/
13 DeconvoluteCommand::DeconvoluteCommand(string option) {
17 //allow user to run help
18 if(option == "help") { help(); abort = true; }
21 //valid paramters for this command
22 string Array[] = {"fasta", "name"};
23 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
25 OptionParser parser(option);
26 map<string,string> parameters = parser.getParameters();
28 ValidParameters validParameter;
30 //check to make sure all parameters are valid for command
31 for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
32 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
35 //check for required parameters
36 inFastaName = validParameter.validFile(parameters, "fasta", true);
37 if (inFastaName == "not open") { abort = true; }
38 else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true; }
40 oldNameMapFName = validParameter.validFile(parameters, "name", true);
41 if (oldNameMapFName == "not open") { abort = true; }
42 else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; }
47 errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
51 //**********************************************************************************************************************
53 void DeconvoluteCommand::help(){
55 mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
56 mothurOut("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");
57 mothurOut("If the sequence is unique the second column will just contain its name. \n");
58 mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
59 mothurOut("The unique.seqs command should be in the following format: \n");
60 mothurOut("unique.seqs(fasta=yourFastaFile) \n");
63 errorOut(e, "DeconvoluteCommand", "help");
68 /**************************************************************************************/
69 int DeconvoluteCommand::execute() {
72 if (abort == true) { return 0; }
74 //prepare filenames and open files
75 string outNameFile = (getRootName(inFastaName) + "names");
76 string outFastaFile = (getRootName(inFastaName) + "unique" + getExtension(inFastaName));
80 if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); }
81 else { fastamap.readFastaFile(inFastaName, oldNameMapFName); }
83 fastamap.printCondensedFasta(outFastaFile);
84 fastamap.printNamesFile(outNameFile);
89 errorOut(e, "DeconvoluteCommand", "execute");
93 /**************************************************************************************/