else {
//valid paramters for this command
- string Array[] = {"fasta","end","outputdir","inputdir"};
+ string Array[] = {"fasta","numbases","countgaps","keep","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 = ""; }
-
//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; }
- 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; }
- }
+ //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);
+
+ 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; }
}
}
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 should be in the following format: chop.seqs(fasta=yourFasta, end=yourEnd).\n");
- m->mothurOut("Example chop.seqs(fasta=amazon.fasta, end=200).\n");
+ 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, 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("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");
}
catch(exception& e) {
if (abort == true) { return 0; }
- string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
+ 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;
+ m->openOutputFile(outputFileNameAccnos, outAcc);
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
- while (!in.eof()) {
+ bool wroteAccnos = false;
- Sequence seq(in, "no align");
+ while (!in.eof()) {
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ Sequence seq(in);
+
+ 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 = getChopped(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;
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); }
+
+ }else { 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 { 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); }
+
+ }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
+
+ 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+1); }
+ }
+ else { temp = ""; } //sequence too short
+ }
+ }
+
+ return temp;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getChopped");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff