#include "sequence.hpp"
//**********************************************************************************************************************
-
+vector<string> ChopSeqsCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta","short","numbases","countgaps","keep","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ 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");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChopSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","numbases"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChopSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//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","numbases","countgaps","keep","outputdir","inputdir"};
+ string Array[] = {"fasta","numbases","countgaps","keep","short","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["fasta"] = tempOutNames;
+ outputTypes["accnos"] = 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 = ""; }
convert(temp, numbases);
temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
- countGaps = m->isTrue(temp);
+ countGaps = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "short", false); if (temp == "not found") { temp = "f"; }
+ Short = m->isTrue(temp);
keep = validParameter.validFile(parameters, "keep", false); if (keep == "not found") { keep = "front"; }
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");
}
int ChopSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
Sequence seq(in);
- if (m->control_pressed) { 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(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0; }
if (seq.getName() != "") {
string newSeqString = getChopped(seq);
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
- if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); }
+ if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
else { remove(outputFileNameAccnos.c_str()); }
m->mothurOutEndLine();
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(0, stopSpot); }
- }else { temp = ""; } //sequence too short
-
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
}else { //you are keeping the back
int tempLength = temp.length();
if (tempLength > numbases) { //you have enough bases to remove some
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot+1); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
}
- else { temp = ""; } //sequence too short
}
}else{
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(0, stopSpot); }
- }else { temp = ""; } //sequence too short
-
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
}else { //you are keeping the back
int tempLength = tempUnaligned.length();
if (tempLength > numbases) { //you have enough bases to remove some
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot+1); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
}
- else { temp = ""; } //sequence too short
}
}