#include "listseqscommand.h"
#include "sequence.hpp"
+#include "listvector.hpp"
//**********************************************************************************************************************
else {
//valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport" };
+ string Array[] = {"fasta","name", "group", "alignreport","list","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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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 = ""; }
+
+ //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("alignreport");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["alignreport"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+ }
+
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
if (alignfile == "not open") { abort = true; }
else if (alignfile == "not found") { alignfile = ""; }
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide a file."); mothurOutEndLine(); abort = true; }
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+
+ if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide a file."); mothurOutEndLine(); abort = true; }
+
+ int okay = 1;
+ if (outputDir != "") { okay++; }
- if (parameters.size() > 1) { mothurOut("You may only enter one file."); mothurOutEndLine(); abort = true; }
+ if (parameters.size() > okay) { mothurOut("You may only enter one file."); mothurOutEndLine(); abort = true; }
}
}
void ListSeqsCommand::help(){
try {
- mothurOut("The list.seqs command reads a fasta, name, group or alignreport file and outputs a .accnos file containing sequence names.\n");
+ mothurOut("The list.seqs command reads a fasta, name, group, list or alignreport file and outputs a .accnos file containing sequence names.\n");
mothurOut("The list.seqs command parameters are fasta, name, group and alignreport. You must provide one of these parameters.\n");
mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
else if (namefile != "") { inputFileName = namefile; readName(); }
else if (groupfile != "") { inputFileName = groupfile; readGroup(); }
else if (alignfile != "") { inputFileName = alignfile; readAlign(); }
+ else if (listfile != "") { inputFileName = listfile; readList(); }
//sort in alphabetical order
sort(names.begin(), names.end());
- string outputFileName = getRootName(inputFileName) + "accnos";
+ if (outputDir == "") { outputDir += hasPath(inputFileName); }
+
+ string outputFileName = outputDir + getRootName(getSimpleName(inputFileName)) + "accnos";
+
ofstream out;
openOutputFile(outputFileName, out);
exit(1);
}
}
+//**********************************************************************************************************************
+void ListSeqsCommand::readList(){
+ try {
+ ifstream in;
+ openInputFile(listfile, in);
+
+ if(!in.eof()){
+ //read in list vector
+ ListVector list(in);
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+ string binnames = list.get(i);
+
+ while (binnames.find_first_of(',') != -1) {
+ string name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+ names.push_back(name);
+ }
+
+ names.push_back(binnames);
+ }
+ }
+ in.close();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "ListSeqsCommand", "readList");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
void ListSeqsCommand::readName(){
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