X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.cpp;h=4e06201cd352104b5ee9c9d1c41764d16473003e;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=8775d95abab9a4577aaad0f29feec2d15bc39694;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 8775d95..4e06201 100644
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -43,7 +43,7 @@ string ChopSeqsCommand::getHelpString(){
 		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\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -73,6 +73,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -114,13 +115,13 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 				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);  
@@ -164,7 +165,7 @@ int ChopSeqsCommand::execute(){
 			
 			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);
@@ -187,7 +188,7 @@ int ChopSeqsCommand::execute(){
 		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();
 		
@@ -232,7 +233,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					
 					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++; 
 						
@@ -240,7 +241,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					}
 					
 					if (stopSpot == 0) { temp = ""; }
-					else {  temp = temp.substr(0, stopSpot);  }
+					else {  temp = temp.substr(0, stopSpot+1);  }
 							
 				}else { 
 					if (!Short) { temp = ""; } //sequence too short
@@ -254,7 +255,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					
 					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++; 
 
@@ -282,7 +283,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					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; }
 						}
@@ -293,7 +294,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					}
 					
 					if (stopSpot == 0) { temp = ""; }
-					else {  temp = temp.substr(0, stopSpot);  }
+					else {  temp = temp.substr(0, stopSpot+1);  }
 							
 				}else { 
 					if (!Short) { temp = ""; } //sequence too short
@@ -308,7 +309,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					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; }
 						}
@@ -319,7 +320,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					}
 				
 					if (stopSpot == 0) { temp = ""; }
-					else {  temp = temp.substr(stopSpot+1);  }
+					else {  temp = temp.substr(stopSpot);  }
 				}else { 
 					if (!Short) { temp = ""; } //sequence too short
 				}