#include "sequence.hpp"
//**********************************************************************************************************************
+vector<string> ChopSeqsCommand::setParameters(){
+ try {
+ 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", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChopSeqsCommand::getHelpString(){
+ try {
+ 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", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChopSeqsCommand::ChopSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
+ 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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","end","fromend","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
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; }
}
//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"; }
+ m->mothurConvert(temp, numbases);
- string temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "0"; }
- convert(temp, end);
+ 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);
- temp = validParameter.validFile(parameters, "fromend", false); if (temp == "not found") { temp = "0"; }
- convert(temp, fromend);
+ keep = validParameter.validFile(parameters, "keep", false); if (keep == "not found") { keep = "front"; }
- 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; }
+ if (numbases == 0) { m->mothurOut("You must provide the number of bases you want to keep for the chops.seqs command."); m->mothurOutEndLine(); abort = true; }
}
}
}
//**********************************************************************************************************************
-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, 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");
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int ChopSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- 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(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0; }
if (seq.getName() != "") {
- string newSeqString = "";
- if (seq.getIsAligned()) { //sequence is aligned
- newSeqString = getChoppedAligned(seq);
- }else{
- newSeqString = getChoppedUnaligned(seq);
- }
+ string newSeqString = getChopped(seq);
//output trimmed sequence
if (newSeqString != "") {
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(); }
- else { remove(outputFileNameAccnos.c_str()); }
+ if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
+ else { m->mothurRemove(outputFileNameAccnos); }
m->mothurOutEndLine();
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ if (wroteAccnos) { //set accnos file as new current accnosfile
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+ }
+
+
return 0;
}
}
}
//**********************************************************************************************************************
-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) {
+string ChopSeqsCommand::getChopped(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 (countGaps) {
+ //if needed trim sequence
+ if (keep == "front") {//you want to keep the beginning
+ int tempLength = temp.length();
- if (numBases >= end) { stopSpot = i; break; }
- }
+ if (tempLength > numbases) { //you have enough bases to remove some
- temp = temp.substr(0, stopSpot);
- }else { temp = ""; } //sequence too short
-
- }else { //you are using fromend
-
- if (tempUnaligned.length() > fromend) {
+ int stopSpot = 0;
+ int numBasesCounted = 0;
+
+ 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 (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(0, stopSpot+1); }
+
+ }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
+
+ 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] == '.'; }
+
+ numBasesCounted++;
+
+ if (numBasesCounted >= numbases) { stopSpot = i; break; }
+ }
- int stopSpot = 0;
- int numBases = 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--) {
- if(isalpha(temp[i])) { numBases++; }
+ //if needed trim sequence
+ if (keep == "front") {//you want to keep the beginning
+ int tempLength = tempUnaligned.length();
- if (numBases >= fromend) { stopSpot = i; break; }
- }
+ 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 (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(0, stopSpot+1); }
+
+ }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; }
+ }
- temp = temp.substr(0, stopSpot);
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(stopSpot); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
}
- else { temp = ""; } //sequence too short
}
-
+
return temp;
}
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+ m->errorOut(e, "ChopSeqsCommand", "getChopped");
exit(1);
}
}
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