//**********************************************************************************************************************
-AlignCheckCommand::AlignCheckCommand(string option){
+AlignCheckCommand::AlignCheckCommand(string option) {
try {
abort = false;
-
+ haderror = 0;
+
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string Array[] = {"fasta","map"};
+ string Array[] = {"fasta","map", "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 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("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("map");
+ //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["map"] = 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; }
+ //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
+ }
+
}
}
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);
}
}
openInputFile(fastafile, in);
ofstream out;
- string outfile = getRootName(fastafile) + "align.check";
+ string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
openOutputFile(outfile, out);
out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
if (seq.getName() != "") {
statData data = getStats(seq.getAligned());
+ if (haderror == 1) { break; }
+
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;
}
in.close();
out.close();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outfile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "execute");
+ m->errorOut(e, "AlignCheckCommand", "execute");
exit(1);
}
}
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);
}
}
statData data;
sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
- int seqLength = sequence.length();
- for(int i=1;i<seqLength;i++){
+ int length = sequence.length();
+
+ 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){
if(sequence[i] == 'A'){
if(sequence[structMap[i]] == 'T') { data.tilde++; }
}
catch(exception& e) {
- errorOut(e, "AlignCheckCommand", "getStats");
+ m->errorOut(e, "AlignCheckCommand", "getStats");
exit(1);
}
}
projects / mothur.git / blobdiff