else {
//valid paramters for this command
- string Array[] = {"fasta","end","fromend","outputdir","inputdir"};
+ string Array[] = {"fasta","numbases","keep","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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") { temp = "0"; }
- convert(temp, end);
+ string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, numbases);
- 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("The chop.seqs command parameters are fasta, numbases, 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("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 (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); 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 != "") {
}
}
//**********************************************************************************************************************
-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
+ 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 numBases = 0;
+ int numBasesCounted = 0;
for (int i = 0; i < temp.length(); i++) {
- if(isalpha(temp[i])) { numBases++; }
-
- if (numBases >= end) { stopSpot = i; break; }
+ //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(0, stopSpot); }
+
}else { temp = ""; } //sequence too short
- }else { //you are using fromend
-
- if (tempUnaligned.length() > fromend) {
+ }else { //you are keeping the back
+ int tempLength = tempUnaligned.length();
+ if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
- int numBases = 0;
+ int numBasesCounted = 0;
for (int i = (temp.length()-1); i >= 0; i--) {
- if(isalpha(temp[i])) { numBases++; }
+ //eliminate N's
+ if (toupper(temp[i]) == 'N') {
+ temp[i] == '.';
+ tempLength--;
+ if (tempLength < numbases) { stopSpot = 0; break; }
+ }
+
+ if(isalpha(temp[i])) { numBasesCounted++; }
- if (numBases >= fromend) { stopSpot = i; break; }
+ if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
-
- temp = temp.substr(0, stopSpot);
+
+ if (stopSpot == 0) { temp = ""; }
+ else { temp = temp.substr(stopSpot+1); }
}
else { temp = ""; } //sequence too short
}
return temp;
}
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+ m->errorOut(e, "ChopSeqsCommand", "getChopped");
exit(1);
}
}