#include "secondarystructurecommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","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;
+ //initialize outputTypes
+ 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;
-
+ 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; }
}
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("map");
+ //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["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 += 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 remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n");
- //mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
- //mothurOut("The remove.seqs command parameters are accnos, fasta, name, group and alignreport. You must provide accnos and one of the other parameters.\n");
- //mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
- //mothurOut("Example remove.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");
+ 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);
}
}
//get secondary structure info.
readMap();
-
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ ofstream 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;
+
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
+
+ Sequence seq(in); m->gobble(in);
+ 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();
+
+ 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();
-
+
seqLength = structMap.size();
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", "readFasta");
+ m->errorOut(e, "AlignCheckCommand", "readMap");
exit(1);
}
}
+/**************************************************************************************************/
+
+statData AlignCheckCommand::getStats(string sequence){
+ try {
+
+ statData data;
+ sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
+
+ 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++; }
+ else if(sequence[structMap[i]] == 'A') { data.pound++; }
+ else if(sequence[structMap[i]] == 'G') { data.equal++; }
+ else if(sequence[structMap[i]] == 'C') { data.pound++; }
+ else if(sequence[structMap[i]] == '-') { data.pound++; }
+ data.total++;
+ }
+ else if(sequence[i] == 'T'){
+ if(sequence[structMap[i]] == 'T') { data.plus++; }
+ else if(sequence[structMap[i]] == 'A') { data.tilde++; }
+ else if(sequence[structMap[i]] == 'G') { data.dash++; }
+ else if(sequence[structMap[i]] == 'C') { data.pound++; }
+ else if(sequence[structMap[i]] == '-') { data.pound++; }
+ data.total++;
+ }
+ else if(sequence[i] == 'G'){
+ if(sequence[structMap[i]] == 'T') { data.dash++; }
+ else if(sequence[structMap[i]] == 'A') { data.equal++; }
+ else if(sequence[structMap[i]] == 'G') { data.pound++; }
+ else if(sequence[structMap[i]] == 'C') { data.tilde++; }
+ else if(sequence[structMap[i]] == '-') { data.pound++; }
+ data.total++;
+ }
+ else if(sequence[i] == 'C'){
+ if(sequence[structMap[i]] == 'T') { data.pound++; }
+ else if(sequence[structMap[i]] == 'A') { data.pound++; }
+ else if(sequence[structMap[i]] == 'G') { data.tilde++; }
+ else if(sequence[structMap[i]] == 'C') { data.pound++; }
+ else if(sequence[structMap[i]] == '-') { data.pound++; }
+ data.total++;
+ }
+ else if(sequence[i] == '-'){
+ if(sequence[structMap[i]] == 'T') { data.pound++; data.total++; }
+ else if(sequence[structMap[i]] == 'A') { data.pound++; data.total++; }
+ else if(sequence[structMap[i]] == 'G') { data.pound++; data.total++; }
+ else if(sequence[structMap[i]] == 'C') { data.pound++; data.total++; }
+ else if(sequence[structMap[i]] == '-') { /*donothing*/ }
+ }
+ }
+ else if(isalnum(sequence[i])){
+ data.loop++;
+ data.total++;
+ }
+ }
+ return data;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getStats");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
projects / mothur.git / blobdiff