//check for required parameters
fastaFile = validParameter.validFile(parameters, "fasta", true);
- if (fastaFile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
+ if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
else if (fastaFile == "not open") { abort = true; }
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
allFiles = isTrue(temp);
-
+
if(allFiles && oligoFile == ""){
- cout << "You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request." << endl;
+ mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); mothurOutEndLine();
+ }
+ if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
+ mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
+ qAverage=0;
+ qThreshold=0;
}
-
if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
- cout << "You didn't set any options... quiting command." << endl;
+ mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
abort = true;
}
-
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TrimSeqsCommand class function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void TrimSeqsCommand::help(){
try {
- cout << "The trim.seqs command reads a fastaFile and creates ....." << "\n";
- cout << "The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength." << "\n";
- cout << "The fasta parameter is required." << "\n";
- cout << "The flip parameter .... The default is 0." << "\n";
- cout << "The oligos parameter .... The default is ""." << "\n";
- cout << "The maxambig parameter .... The default is -1." << "\n";
- cout << "The maxhomop parameter .... The default is 0." << "\n";
- cout << "The minlength parameter .... The default is 0." << "\n";
- cout << "The maxlength parameter .... The default is 0." << "\n";
- cout << "The trim.seqs command should be in the following format: " << "\n";
- cout << "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, " << "\n";
- cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) " << "\n";
- cout << "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...)." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+ mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
+ mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength.\n");
+ mothurOut("The fasta parameter is required.\n");
+ mothurOut("The flip parameter .... The default is 0.\n");
+ mothurOut("The oligos parameter .... The default is "".\n");
+ mothurOut("The maxambig parameter .... The default is -1.\n");
+ mothurOut("The maxhomop parameter .... The default is 0.\n");
+ mothurOut("The minlength parameter .... The default is 0.\n");
+ mothurOut("The maxlength parameter .... The default is 0.\n");
+ mothurOut("The trim.seqs command should be in the following format: \n");
+ mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
+ mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
+ mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TrimSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TrimSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
try{
if (abort == true) { return 0; }
-
- vector<ofstream*> groupFileNames;
- vector<ofstream*> fastaFileNames;
- if(oligoFile != "") { getOligos(fastaFileNames, groupFileNames); }
ifstream inFASTA;
openInputFile(fastaFile, inFASTA);
-
+
ofstream outFASTA;
string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
openOutputFile(trimSeqFile, outFASTA);
ofstream outGroups;
- string groupFile = getRootName(fastaFile) + "groups";
- openOutputFile(groupFile, outGroups);
+ vector<ofstream*> fastaFileNames;
+ if(oligoFile != ""){
+ string groupFile = getRootName(fastaFile) + "groups";
+ openOutputFile(groupFile, outGroups);
+ getOligos(fastaFileNames);
+ }
ofstream scrapFASTA;
string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
if(!success) { trashCode += 'q'; }
+ qFile.close();
}
if(barcodes.size() != 0){
success = stripBarcode(currSeq, group);
outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
if(allFiles){
- *groupFileNames[group] << currSeq.getName() << '\t' << groupVector[group] << endl;
currSeq.printSequence(*fastaFileNames[group]);
}
}
scrapFASTA.close();
outGroups.close();
- for(int i=0;i<groupFileNames.size();i++){
- groupFileNames[i]->close();
- delete groupFileNames[i];
-
+ for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i]->close();
delete fastaFileNames[i];
+ }
+
+ for(int i=0;i<fastaFileNames.size();i++){
+ string seqName;
+ openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
+ ofstream outGroups;
+ openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
+
+ while(!inFASTA.eof()){
+ if(inFASTA.get() == '>'){
+ inFASTA >> seqName;
+ outGroups << seqName << '\t' << groupVector[i] << endl;
+ }
+ while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ }
+ outGroups.close();
+ inFASTA.close();
}
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the TrimSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TrimSeqsCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec, vector<ofstream*>& outGroupsVec){
+void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
ifstream inOligos;
openInputFile(oligoFile, inOligos);
string type, oligo, group;
int index=0;
-
+
while(!inOligos.eof()){
inOligos >> type;
-
+
if(type[0] == '#'){
while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
}
if(allFiles){
outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
- outGroupsVec.push_back(new ofstream((getRootName(fastaFile) + group + ".groups").c_str(), ios::ate));
}
}
}
}
+ inOligos.close();
+
numFPrimers = forPrimer.size();
numRPrimers = revPrimer.size();
}
string name;
qFile >> name;
- if(name.substr(1) != seq.getName()) { cout << "sequence name mismatch btwn fasta and qual file" << endl; }
+ if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); }
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
int score;
string name;
qFile >> name;
- if(name.substr(1) != seq.getName()) { cout << "sequence name mismatch btwn fasta and qual file" << endl; }
+ if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); }
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
float score;
projects / mothur.git / blobdiff