#include "sequence.hpp"
//**********************************************************************************************************************
-vector<string> ChopSeqsCommand::getValidParameters(){
+vector<string> ChopSeqsCommand::setParameters(){
try {
- string AlignArray[] = {"fasta","short","numbases","countgaps","keep","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnumbases);
+ CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcountgaps);
+ CommandParameter pshort("short", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshort);
+ CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "",false,false); parameters.push_back(pkeep);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ChopSeqsCommand::ChopSeqsCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
+ m->errorOut(e, "ChopSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ChopSeqsCommand::getRequiredParameters(){
+string ChopSeqsCommand::getHelpString(){
try {
- string Array[] = {"fasta","numbases"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
+ helpString += "The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
+ helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
+ helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
+ helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
+ helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
+ helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
+ helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
+ helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "ChopSeqsCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> ChopSeqsCommand::getRequiredFiles(){
+ChopSeqsCommand::ChopSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
exit(1);
}
}
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","numbases","countgaps","keep","short","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") { //if there is a current fasta file, use it
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
//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 = m->hasPath(fastafile); }
string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
- convert(temp, numbases);
+ m->mothurConvert(temp, numbases);
temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
countGaps = m->isTrue(temp);
}
//**********************************************************************************************************************
-void ChopSeqsCommand::help(){
- try {
- m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n");
- m->mothurOut("The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta and numbases are required required.\n");
- m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n");
- m->mothurOut("The numbases parameter allows you to specify the number of bases you want to keep.\n");
- m->mothurOut("The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n");
- m->mothurOut("The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n");
- m->mothurOut("The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n");
- m->mothurOut("For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n");
- m->mothurOut("Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int ChopSeqsCommand::execute(){
try {
Sequence seq(in);
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0; }
if (seq.getName() != "") {
string newSeqString = getChopped(seq);
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
- else { remove(outputFileNameAccnos.c_str()); }
+ else { m->mothurRemove(outputFileNameAccnos); }
m->mothurOutEndLine();
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+ if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
numBasesCounted++;
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ else { temp = temp.substr(0, stopSpot+1); }
}else {
if (!Short) { temp = ""; } //sequence too short
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+ if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
numBasesCounted++;
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
+ temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ else { temp = temp.substr(0, stopSpot+1); }
}else {
if (!Short) { temp = ""; } //sequence too short
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
+ temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(stopSpot+1); }
+ else { temp = temp.substr(stopSpot); }
}else {
if (!Short) { temp = ""; } //sequence too short
}
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