#include "secondarystructurecommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "name","map", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","map"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-AlignCheckCommand::AlignCheckCommand(string option){
+AlignCheckCommand::AlignCheckCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
haderror = 0;
-
+
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string Array[] = {"fasta","map", "outputdir","inputdir"};
+ string Array[] = {"fasta","name","map", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
+
//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 = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->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("map");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["map"] = inputDir + it->second; }
}
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->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; }
+ }
}
//check for required parameters
mapfile = validParameter.validFile(parameters, "map", true);
if (mapfile == "not open") { abort = true; }
- else if (mapfile == "not found") { mapfile = ""; mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; }
+ else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
//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
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
}
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
+ m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
exit(1);
}
}
void AlignCheckCommand::help(){
try {
- mothurOut("The align.check command reads a fasta file and map file.\n");
- mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
- mothurOut("The align.check command parameters are fasta and map, both are required.\n");
- mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
- mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ m->mothurOut("The align.check command reads a fasta file and map file.\n");
+ m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
+ m->mothurOut("The align.check command parameters are fasta and map, both are required.\n");
+ m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
+ m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "help");
+ m->errorOut(e, "AlignCheckCommand", "help");
exit(1);
}
}
int AlignCheckCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get secondary structure info.
readMap();
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+
+ if (m->control_pressed) { return 0; }
+
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
- openOutputFile(outfile, out);
+ string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+ m->openOutputFile(outfile, out);
+
out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
- out << "loop" << '\t' << "tilde" << '\t' << "total" << endl;
+ out << "loop" << '\t' << "tilde" << '\t' << "total" << '\t' << "numseqs" << endl;
while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
- Sequence seq(in); gobble(in);
+ Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
statData data = getStats(seq.getAligned());
if (haderror == 1) { break; }
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(seq.getName());
+
+ if (it == nameMap.end()) { cout << "[ERROR]: " << seq.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
- out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
+ out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
}
}
in.close();
out.close();
+ if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "execute");
+ m->errorOut(e, "AlignCheckCommand", "execute");
exit(1);
}
}
structMap.resize(1, 0);
ifstream in;
- openInputFile(mapfile, in);
+ m->openInputFile(mapfile, in);
while(!in.eof()){
int position;
in >> position;
structMap.push_back(position);
- gobble(in);
+ m->gobble(in);
}
in.close();
for(int i=0;i<seqLength;i++){
if(structMap[i] != 0){
if(structMap[structMap[i]] != i){
- mothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); mothurOutEndLine();
+ m->mothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine();
}
}
}
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "readMap");
+ m->errorOut(e, "AlignCheckCommand", "readMap");
exit(1);
}
}
int length = sequence.length();
- if (length != seqLength) { mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); mothurOutEndLine(); haderror = 1; return data; }
+ if (length != seqLength) { m->mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); m->mothurOutEndLine(); haderror = 1; return data; }
for(int i=1;i<length;i++){
if(structMap[i] != 0){
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "getStats");
+ m->errorOut(e, "AlignCheckCommand", "getStats");
exit(1);
}
}
-
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff