X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.cpp;h=9020d2b4763515e1b6e1ead544247e676b043f41;hb=62568a297aaf939ab753334f17abde82ec8e8531;hp=adf0910589c7d65161027bedae6cc74236e2ef5f;hpb=b8f3e71c8a0310e25261464d27e6fcfe891483b0;p=mothur.git

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index adf0910..9020d2b 100644
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -21,7 +21,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"fasta","end","outputdir","inputdir"};
+			string Array[] =  {"fasta","end","fromend","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -57,13 +57,14 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 			if (fastafile == "not open") { abort = true; }
 			else if (fastafile == "not found") {  m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }  	
 			
-			string temp = validParameter.validFile(parameters, "end", false);	
-			if (temp == "not found") {  m->mothurOut("You must provide an end for the chops.seqs command."); m->mothurOutEndLine(); abort = true; } 
-			else {	
-				convert(temp, end);   
-				if (end < 0) { m->mothurOut("End must be positive."); m->mothurOutEndLine(); abort = true;  }
-			}
-			
+			string temp = validParameter.validFile(parameters, "end", false);	if (temp == "not found") { temp = "0"; } 
+			convert(temp, end);   
+		
+			temp = validParameter.validFile(parameters, "fromend", false);		if (temp == "not found") { temp = "0"; } 
+			convert(temp, fromend);   
+				
+			if ((end == 0) && (fromend == 0))  { m->mothurOut("You must provide either end or fromend for the chops.seqs command."); m->mothurOutEndLine(); abort = true;  }
+			if ((end != 0) && (fromend != 0))  { m->mothurOut("You must provide either end or fromend for the chops.seqs command, not both."); m->mothurOutEndLine(); abort = true;  }
 		}
 
 	}
@@ -77,8 +78,10 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 void ChopSeqsCommand::help(){
 	try {
 		m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta with sequences trimmed to the end position.\n");
-		m->mothurOut("The chop.seqs command parameters are fasta and end, both are required.\n");
+		m->mothurOut("The chop.seqs command parameters are fasta, end and fromend, fasta is required.\n");
 		m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, end=yourEnd).\n");
+		m->mothurOut("The end parameter allows you to specify an end base position for your sequences, default = 0.\n");
+		m->mothurOut("The fromend parameter allows you to remove the last X bases from the end of the sequence, default = 0.\n");
 		m->mothurOut("Example chop.seqs(fasta=amazon.fasta, end=200).\n");
 		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 	}
@@ -96,38 +99,53 @@ int ChopSeqsCommand::execute(){
 		if (abort == true) { return 0; }
 		
 		string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
+		string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos";
 		
 		ofstream out;
 		openOutputFile(outputFileName, out);
 		
+		ofstream outAcc;
+		openOutputFile(outputFileNameAccnos, outAcc);
+		
 		ifstream in;
 		openInputFile(fastafile, in);
 		
-		while (!in.eof()) {
+		bool wroteAccnos = false;
 		
-			Sequence seq(in, "no align");
+		while (!in.eof()) {
+			
+			Sequence seq(in);
 			
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0;  }
+			if (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
 			
 			if (seq.getName() != "") {
-				string temp = seq.getUnaligned();
-				
-				//output sequence name
-				out << ">" << seq.getName() << endl;
-				
-				//if needed trim sequence
-				if (temp.length() > end) {  temp = temp.substr(0, end);		}
+				string newSeqString = "";
+				if (seq.getIsAligned()) { //sequence is aligned
+					newSeqString = getChoppedAligned(seq);
+				}else{
+					newSeqString = getChoppedUnaligned(seq);
+				}
 				
-				//output trimmed sequence	
-				out << temp << endl;
+				//output trimmed sequence
+				if (newSeqString != "") {
+					out << ">" << seq.getName() << endl << newSeqString << endl;
+				}else{
+					outAcc << seq.getName() << endl;
+					wroteAccnos = true;
+				}
 			}
 		}
 		in.close();
 		out.close();
+		outAcc.close();
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 		m->mothurOut(outputFileName); m->mothurOutEndLine();	
+		
+		if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine();  }
+		else {  remove(outputFileNameAccnos.c_str());  }
+		
 		m->mothurOutEndLine();
 		
 		return 0;		
@@ -138,7 +156,74 @@ int ChopSeqsCommand::execute(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ChopSeqsCommand::getChoppedUnaligned(Sequence seq) {
+	try {
+		string temp = seq.getUnaligned();
+				
+		//if needed trim sequence
+		if (end != 0) {
+			if (temp.length() > end) {  temp = temp.substr(0, end);		}
+			else { temp = "";  }
+		}else { //you are using fromend
+			if (temp.length() > fromend) { temp = temp.substr(0, (temp.length()-fromend));  }
+			else {  temp = ""; } //sequence too short
+		}
+
+		return temp;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string ChopSeqsCommand::getChoppedAligned(Sequence seq) {
+	try {
+		string temp = seq.getAligned();
+		string tempUnaligned = seq.getUnaligned();
+				
+		//if needed trim sequence
+		if (end != 0) {
+			if (tempUnaligned.length() > end) { //you have enough bases to remove some
+				
+				int stopSpot = 0;
+				int numBases = 0;
+				
+				for (int i = 0; i < temp.length(); i++) {
+					if(isalpha(temp[i])) { numBases++; }
 
+					if (numBases >= end) { stopSpot = i; break; }
+				}
+				
+				temp = temp.substr(0, stopSpot);		
+			}else { temp = ""; } //sequence too short
+			
+		}else { //you are using fromend
+		
+			if (tempUnaligned.length() > fromend) { 
+				
+				int stopSpot = 0;
+				int numBases = 0;
+				
+				for (int i = (temp.length()-1); i >= 0; i--) {
+					if(isalpha(temp[i])) { numBases++; }
+
+					if (numBases >= fromend) { stopSpot = i; break; }
+				}
+				
+				temp = temp.substr(0, stopSpot);
+			}
+			else {  temp = ""; } //sequence too short
+		}
+
+		return temp;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************