#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 {
+ //initialize outputTypes
+ 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;
else {
//valid paramters for this command
- string Array[] = {"fasta","numbases","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; }
}
- //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 = ""; }
-
+ //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 = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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; }
}
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { m->mothurOut("You must provide a 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 = m->hasPath(fastafile); }
+
string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
convert(temp, numbases);
+
+ temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
+ 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"; }
void ChopSeqsCommand::help(){
try {
m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences.\n");
- m->mothurOut("The chop.seqs command parameters are fasta, numbases, and keep. fasta and numbases are required required.\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");
}
if (abort == true) { return 0; }
- string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
- string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
+ string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
ofstream out;
- openOutputFile(outputFileName, out);
+ m->openOutputFile(outputFileName, out);
ofstream outAcc;
- openOutputFile(outputFileNameAccnos, outAcc);
+ m->openOutputFile(outputFileNameAccnos, outAcc);
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
bool wroteAccnos = false;
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();
try {
string temp = seq.getAligned();
string tempUnaligned = seq.getUnaligned();
-
- //if needed trim sequence
- if (keep == "front") {//you want to keep the beginning
- int tempLength = tempUnaligned.length();
+
+ if (countGaps) {
+ //if needed trim sequence
+ if (keep == "front") {//you want to keep the beginning
+ int tempLength = temp.length();
- if (tempLength > numbases) { //you have enough bases to remove some
-
- int stopSpot = 0;
- int numBasesCounted = 0;
+ if (tempLength > numbases) { //you have enough bases to remove some
- for (int i = 0; i < temp.length(); i++) {
- //eliminate N's
- if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
- tempLength--;
- if (tempLength < numbases) { stopSpot = 0; break; }
- }
+ int stopSpot = 0;
+ int numBasesCounted = 0;
- if(isalpha(temp[i])) { numBasesCounted++; }
+ for (int i = 0; i < temp.length(); i++) {
+ //eliminate N's
+ if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+
+ numBasesCounted++;
+
+ if (numBasesCounted >= numbases) { stopSpot = i; break; }
+ }
- if (numBasesCounted >= numbases) { stopSpot = i; break; }
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(0, stopSpot); }
+
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
}
-
- if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ }else { //you are keeping the back
+ int tempLength = temp.length();
+ if (tempLength > numbases) { //you have enough bases to remove some
+
+ int stopSpot = 0;
+ int numBasesCounted = 0;
+
+ for (int i = (temp.length()-1); i >= 0; i--) {
+ //eliminate N's
+ if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
- }else { temp = ""; } //sequence too short
-
- }else { //you are keeping the back
- int tempLength = tempUnaligned.length();
- if (tempLength > numbases) { //you have enough bases to remove some
+ numBasesCounted++;
+
+ if (numBasesCounted >= numbases) { stopSpot = i; break; }
+ }
- int stopSpot = 0;
- int numBasesCounted = 0;
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(stopSpot+1); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
+ }
+
+ }else{
- for (int i = (temp.length()-1); i >= 0; i--) {
- //eliminate N's
- if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
- tempLength--;
- if (tempLength < numbases) { stopSpot = 0; break; }
+ //if needed trim sequence
+ if (keep == "front") {//you want to keep the beginning
+ int tempLength = tempUnaligned.length();
+
+ if (tempLength > numbases) { //you have enough bases to remove some
+
+ int stopSpot = 0;
+ int numBasesCounted = 0;
+
+ for (int i = 0; i < temp.length(); i++) {
+ //eliminate N's
+ if (toupper(temp[i]) == 'N') {
+ temp[i] == '.';
+ tempLength--;
+ if (tempLength < numbases) { stopSpot = 0; break; }
+ }
+
+ if(isalpha(temp[i])) { numBasesCounted++; }
+
+ if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
- if(isalpha(temp[i])) { numBasesCounted++; }
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(0, stopSpot); }
+
+ }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
+
+ int stopSpot = 0;
+ int numBasesCounted = 0;
+
+ for (int i = (temp.length()-1); i >= 0; i--) {
+ //eliminate N's
+ if (toupper(temp[i]) == 'N') {
+ temp[i] == '.';
+ tempLength--;
+ if (tempLength < numbases) { stopSpot = 0; break; }
+ }
+
+ if(isalpha(temp[i])) { numBasesCounted++; }
- if (numBasesCounted >= numbases) { stopSpot = i; break; }
+ if (numBasesCounted >= numbases) { stopSpot = i; break; }
+ }
+
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(stopSpot+1); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
}
-
- if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(stopSpot+1); }
}
- else { temp = ""; } //sequence too short
}
-
+
return temp;
}
catch(exception& e) {
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