--- /dev/null
+/*
+ * chopseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "chopseqscommand.h"
+#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; calledHelp = false;
+
+ //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();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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 = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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") { //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);
+
+ 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"; }
+
+ 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; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ChopSeqsCommand::execute(){
+ try {
+
+ 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";
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ofstream outAcc;
+ m->openOutputFile(outputFileNameAccnos, outAcc);
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ bool wroteAccnos = false;
+
+ while (!in.eof()) {
+
+ Sequence seq(in);
+
+ 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);
+
+ //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(); 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 { 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;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChopSeqsCommand::getChopped(Sequence seq) {
+ try {
+ string temp = seq.getAligned();
+ string tempUnaligned = seq.getUnaligned();
+
+ 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;
+
+ 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; }
+ }
+
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(stopSpot+1); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
+ }
+
+ }else{
+
+ //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 (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; }
+ }
+
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(stopSpot); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
+ }
+ }
+
+ return temp;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getChopped");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff