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"};
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 filename = validParameter.validFile(parameters, "fasta", true);
37 if (filename == "not open") { abort = true; }
38 else if (filename == "not found") { filename = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true; }
44 cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
48 cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
52 //**********************************************************************************************************************
54 void DeconvoluteCommand::help(){
56 cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
57 cout << "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";
58 cout << "If the sequence is unique the second column will just contain its name. " << "\n";
59 cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
60 cout << "The unique.seqs command should be in the following format: " << "\n";
61 cout << "unique.seqs(fasta=yourFastaFile) " << "\n";
64 cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
68 cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
73 /**************************************************************************************/
74 int DeconvoluteCommand::execute() {
77 if (abort == true) { return 0; }
79 //prepare filenames and open files
80 outputFileName = (getRootName(filename) + "names");
81 outFastafile = (getRootName(filename) + "unique.fasta");
83 openInputFile(filename, in);
84 openOutputFile(outputFileName, out);
85 openOutputFile(outFastafile, outFasta);
87 //constructor reads in file and store internally
88 fastamap = new FastaMap();
90 //two columns separated by tabs sequence name and then sequence
91 fastamap->readFastaFile(in);
93 //print out new names file
94 //file contains 2 columns separated by tabs. the first column is the groupname(name of first sequence found.
95 //the second column is the list of names of identical sequences separated by ','.
96 fastamap->printNamesFile(out);
97 fastamap->printCondensedFasta(outFasta);
104 catch(exception& e) {
105 cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
109 cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
113 /**************************************************************************************/