#include "getseqscommand.h"
#include "sequence.hpp"
+#include "listvector.hpp"
//**********************************************************************************************************************
else {
//valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport", "accnos" };
+ string Array[] = {"fasta","name", "group", "alignreport", "accnos", "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++) {
+ for (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("accnos");
+ //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["accnos"] = 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
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "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 one of the following: fasta, name, group, alignreport."); mothurOutEndLine(); abort = true; }
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
- if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport."); mothurOutEndLine(); abort = true; }
+ int okay = 2;
+ if (outputDir != "") { okay++; }
+
+ if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
}
}
void GetSeqsCommand::help(){
try {
- mothurOut("The get.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n");
+ mothurOut("The get.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
mothurOut("It outputs a file containing only the sequences in the .accnos file.\n");
- mothurOut("The get.seqs command parameters are accnos, fasta, name, group and alignreport. You must provide accnos and one of the other parameters.\n");
+ mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list and alignreport. You must provide accnos and one of the other parameters.\n");
mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
else if (namefile != "") { readName(); }
else if (groupfile != "") { readGroup(); }
else if (alignfile != "") { readAlign(); }
+ else if (listfile != "") { readList(); }
return 0;
}
//**********************************************************************************************************************
void GetSeqsCommand::readFasta(){
try {
- string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
+ if (outputDir == "") { outputDir += hasPath(fastafile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
ofstream out;
openOutputFile(outputFileName, out);
exit(1);
}
}
+//**********************************************************************************************************************
+void GetSeqsCommand::readList(){
+ try {
+ if (outputDir == "") { outputDir += hasPath(listfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" + getExtension(listfile);
+ ofstream out;
+ openOutputFile(outputFileName, out);
+
+ ifstream in;
+ openInputFile(listfile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ //read in list vector
+ ListVector list(in);
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+
+ string newNames = "";
+ 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());
+
+ //if that name is in the .accnos file, add it
+ if (names.count(name) == 1) { newNames += name + ","; }
+ }
+
+ //get last name
+ if (names.count(binnames) == 1) { newNames += binnames; }
+ //if there are names in this bin add to new list
+ if (newNames != "") { newList.push_back(newNames); }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) {
+ mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+ remove(outputFileName.c_str());
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "GetSeqsCommand", "readList");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
void GetSeqsCommand::readName(){
try {
-
- string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
+ if (outputDir == "") { outputDir += hasPath(namefile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
ofstream out;
openOutputFile(outputFileName, out);
//**********************************************************************************************************************
void GetSeqsCommand::readGroup(){
try {
-
- string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+ if (outputDir == "") { outputDir += hasPath(groupfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
ofstream out;
openOutputFile(outputFileName, out);
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
void GetSeqsCommand::readAlign(){
try {
- string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+ if (outputDir == "") { outputDir += hasPath(alignfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
ofstream out;
openOutputFile(outputFileName, out);
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