else {
//valid paramters for this command
- string Array[] = {"fasta","end","outputdir","inputdir"};
+ string Array[] = {"fasta","end","fromend","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") { 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; }
- }
-
+ string temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, end);
+
+ temp = validParameter.validFile(parameters, "fromend", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, fromend);
+
+ 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; }
}
}
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 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");
}
if (abort == true) { return 0; }
string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
+ string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos";
ofstream out;
openOutputFile(outputFileName, out);
+ ofstream outAcc;
+ openOutputFile(outputFileNameAccnos, outAcc);
+
ifstream in;
openInputFile(fastafile, in);
- while (!in.eof()) {
+ bool wroteAccnos = false;
- Sequence seq(in, "no align");
+ while (!in.eof()) {
+
+ Sequence seq(in);
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ 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 = "";
+ if (seq.getIsAligned()) { //sequence is aligned
+ newSeqString = getChoppedAligned(seq);
+ }else{
+ newSeqString = getChoppedUnaligned(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::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) {
+ 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 (numBases >= end) { stopSpot = i; break; }
+ }
+
+ temp = temp.substr(0, stopSpot);
+ }else { temp = ""; } //sequence too short
+
+ }else { //you are using fromend
+
+ if (tempUnaligned.length() > fromend) {
+
+ int stopSpot = 0;
+ int numBases = 0;
+
+ for (int i = (temp.length()-1); i >= 0; i--) {
+ if(isalpha(temp[i])) { numBases++; }
+
+ if (numBases >= fromend) { stopSpot = i; break; }
+ }
+
+ temp = temp.substr(0, stopSpot);
+ }
+ else { temp = ""; } //sequence too short
+ }
+
+ return temp;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff