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|
/*
* chopseqscommand.cpp
* Mothur
*
* Created by westcott on 5/10/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "chopseqscommand.h"
#include "sequence.hpp"
#include "removeseqscommand.h"
//**********************************************************************************************************************
vector<string> ChopSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,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, name, group, count, 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 += "If you provide a name, group or count file any sequences removed from the fasta file will also be removed from those files.\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 += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \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);
}
}
//**********************************************************************************************************************
string ChopSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],chop.fasta"; }
else if (type == "name") { pattern = "[filename],chop.names"; }
else if (type == "group") { pattern = "[filename],chop.groups"; }
else if (type == "count") { pattern = "[filename],chop.count_table"; }
else if (type == "accnos") { pattern = "[filename],chop.accnos"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["count"] = 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;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["count"] = 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; }
}
it = parameters.find("name");
//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["name"] = inputDir + it->second; }
}
it = parameters.find("group");
//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["group"] = inputDir + it->second; }
}
it = parameters.find("count");
//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["count"] = 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); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count."); 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 = ""; }
string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, numbases);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
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; }
map<string, string> variables;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
string outputFileName = getOutputFileName("fasta", variables);
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
string outputFileNameAccnos = getOutputFileName("accnos", variables);
vector<unsigned long long> positions;
vector<linePair> lines;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
int numSeqs = 0;
positions = m->setFilePosFasta(fastafile, numSeqs);
if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
}
#endif
bool wroteAccnos = false;
if(processors == 1) { wroteAccnos = driver(lines[0], fastafile, outputFileName, outputFileNameAccnos); }
else { wroteAccnos = createProcesses(lines, fastafile, outputFileName, outputFileNameAccnos); }
if (m->control_pressed) { return 0; }
if (wroteAccnos) {
outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos);
//use remove.seqs to create new name, group and count file
if ((countfile != "") || (namefile != "") || (groupfile != "")) {
string inputString = "accnos=" + outputFileNameAccnos;
if (countfile != "") { inputString += ", count=" + countfile; }
else{
if (namefile != "") { inputString += ", name=" + namefile; }
if (groupfile != "") { inputString += ", group=" + groupfile; }
}
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: remove.seqs(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
Command* removeCommand = new RemoveSeqsCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
if (groupfile != "") {
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
string outGroup = getOutputFileName("group", variables);
m->renameFile(filenames["group"][0], outGroup);
outputNames.push_back(outGroup); outputTypes["group"].push_back(outGroup);
}
if (namefile != "") {
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
string outName = getOutputFileName("name", variables);
m->renameFile(filenames["name"][0], outName);
outputNames.push_back(outName); outputTypes["name"].push_back(outName);
}
if (countfile != "") {
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
string outCount = getOutputFileName("count", variables);
m->renameFile(filenames["count"][0], outCount);
outputNames.push_back(outCount); outputTypes["count"].push_back(outCount);
}
}
}
else { m->mothurRemove(outputFileNameAccnos); }
//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); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
bool ChopSeqsCommand::createProcesses(vector<linePair> lines, string filename, string outFasta, string outAccnos) {
try {
int process = 1;
bool wroteAccnos = false;
vector<int> processIDS;
vector<string> nonBlankAccnosFiles;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
wroteAccnos = driver(lines[process], filename, outFasta + toString(getpid()) + ".temp", outAccnos + toString(getpid()) + ".temp");
//pass numSeqs to parent
ofstream out;
string tempFile = fastafile + toString(getpid()) + ".bool.temp";
m->openOutputFile(tempFile, out);
out << wroteAccnos << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
}
}
//do your part
wroteAccnos = driver(lines[0], filename, outFasta, outAccnos);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
//parent reads in and combine Filter info
for (int i = 0; i < processIDS.size(); i++) {
string tempFilename = fastafile + toString(processIDS[i]) + ".bool.temp";
ifstream in;
m->openInputFile(tempFilename, in);
bool temp;
in >> temp; m->gobble(in);
if (temp) { wroteAccnos = temp; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp"); }
else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp")); }
in.close();
m->mothurRemove(tempFilename);
}
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the seqSumData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
//Taking advantage of shared memory to allow both threads to add info to vectors.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<chopData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
//Create processor worker threads.
for( int i=0; i<processors-1; i++ ){
string extension = "";
if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
chopData* tempChop = new chopData(filename, (outFasta+extension), (outAccnos+extension), m, lines[i].start, lines[i].end, keep, countGaps, numbases, Short);
pDataArray.push_back(tempChop);
//MyChopThreadFunction is in header. It must be global or static to work with the threads.
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
hThreadArray[i] = CreateThread(NULL, 0, MyChopThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
//do your part
wroteAccnos = driver(lines[processors-1], filename, (outFasta + toString(processors-1) + ".temp"), (outAccnos + toString(processors-1) + ".temp"));
processIDS.push_back(processors-1);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
if (pDataArray[i]->wroteAccnos) { wroteAccnos = pDataArray[i]->wroteAccnos; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp"); }
else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp")); }
//check to make sure the process finished
if (pDataArray[i]->count != pDataArray[i]->end) {
m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
}
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
for (int i = 0; i < processIDS.size(); i++) {
m->appendFiles((outFasta + toString(processIDS[i]) + ".temp"), outFasta);
m->mothurRemove((outFasta + toString(processIDS[i]) + ".temp"));
}
if (nonBlankAccnosFiles.size() != 0) {
m->renameFile(nonBlankAccnosFiles[0], outAccnos);
for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
m->appendFiles(nonBlankAccnosFiles[h], outAccnos);
m->mothurRemove(nonBlankAccnosFiles[h]);
}
}else { //recreate the accnosfile if needed
ofstream out;
m->openOutputFile(outAccnos, out);
out.close();
}
return wroteAccnos;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "createProcesses");
exit(1);
}
}
/**************************************************************************************/
bool ChopSeqsCommand::driver(linePair filePos, string filename, string outFasta, string outAccnos) {
try {
ofstream out;
m->openOutputFile(outFasta, out);
ofstream outAcc;
m->openOutputFile(outAccnos, outAcc);
ifstream in;
m->openInputFile(filename, in);
in.seekg(filePos.start);
bool done = false;
bool wroteAccnos = false;
int count = 0;
while (!done) {
if (m->control_pressed) { in.close(); out.close(); return 1; }
Sequence seq(in); m->gobble(in);
if (m->control_pressed) { in.close(); out.close(); outAcc.close(); m->mothurRemove(outFasta); m->mothurRemove(outAccnos); 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;
}
count++;
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos.end)) { break; }
#else
if (in.eof()) { break; }
#endif
//report progress
if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
//report progress
if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
in.close();
out.close();
outAcc.close();
return wroteAccnos;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "driver");
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);
}
}
//**********************************************************************************************************************
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