//**********************************************************************************************************************
-RemoveSeqsCommand::RemoveSeqsCommand(string option){
+RemoveSeqsCommand::RemoveSeqsCommand(string option) {
try {
abort = false;
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { abort = true; }
- else if (accnosfile == "not found") { accnosfile = ""; mothurOut("You must provide an accnos file."); mothurOutEndLine(); abort = true; }
+ else if (accnosfile == "not found") { accnosfile = ""; m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
dups = isTrue(temp);
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); mothurOutEndLine(); abort = true; }
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); m->mothurOutEndLine(); abort = true; }
- int okay = 2;
- if (outputDir != "") { okay++; }
- if (usedDups != "") { okay++; }
+ //int okay = 2;
+ //if (outputDir != "") { okay++; }
+ //if (usedDups != "") { okay++; }
- if ((usedDups != "") && (namefile == "")) { mothurOut("You may only use dups with the name option."); mothurOutEndLine(); abort = true; }
+ if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
- if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); mothurOutEndLine(); abort = true; }
+ //if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true; }
}
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
+ m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
exit(1);
}
}
void RemoveSeqsCommand::help(){
try {
- mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
- mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
- mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, alignreport and dups. You must provide accnos and one of the file parameters.\n");
- mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new .accnos file containing all the sequences removed. \n");
- mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
- mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ m->mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
+ m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
+ m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, alignreport and dups. You must provide accnos and one of the file parameters.\n");
+ m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new .accnos file containing all the sequences removed. \n");
+ m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
+ m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "help");
+ m->errorOut(e, "RemoveSeqsCommand", "help");
exit(1);
}
}
//get names you want to keep
readAccnos();
+ if (m->control_pressed) { return 0; }
+
//read through the correct file and output lines you want to keep
if (fastafile != "") { readFasta(); }
- else if (namefile != "") { readName(); }
- else if (groupfile != "") { readGroup(); }
- else if (alignfile != "") { readAlign(); }
- else if (listfile != "") { readList(); }
+ if (namefile != "") { readName(); }
+ if (groupfile != "") { readGroup(); }
+ if (alignfile != "") { readAlign(); }
+ if (listfile != "") { readList(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if (outputNames.size() != 0) {
+ 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) {
- errorOut(e, "RemoveSeqsCommand", "execute");
+ m->errorOut(e, "RemoveSeqsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::readFasta(){
+int RemoveSeqsCommand::readFasta(){
try {
if (outputDir == "") { outputDir += hasPath(fastafile); }
- string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
+ string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
ofstream out;
openOutputFile(outputFileName, out);
bool wroteSomething = false;
while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
Sequence currSeq(in);
name = currSeq.getName();
wroteSomething = true;
currSeq.printSequence(out);
- }else { names.erase(name); }
+ }//else { names.erase(name); }
}
gobble(in);
}
out.close();
if (wroteSomething == false) {
- mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+ m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
remove(outputFileName.c_str());
- }
-
+ }else { outputNames.push_back(outputFileName); }
+
+ return 0;
+
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "readFasta");
+ m->errorOut(e, "RemoveSeqsCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::readList(){
+int RemoveSeqsCommand::readList(){
try {
if (outputDir == "") { outputDir += hasPath(listfile); }
- string outputFileName = getRootName(listfile) + "pick" + getExtension(listfile);
+ string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" + getExtension(listfile);
ofstream out;
openOutputFile(outputFileName, out);
//for each bin
for (int i = 0; i < list.getNumBins(); i++) {
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
//parse out names that are in accnos file
string binnames = list.get(i);
}
//get last name
- if (names.count(binnames) == 0) { newNames += binnames; }
+ if (names.count(binnames) == 0) { newNames += binnames + ","; }
//if there are names in this bin add to new list
- if (newNames != "") { newList.push_back(newNames); }
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
}
//print new listvector
out.close();
if (wroteSomething == false) {
- mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+ m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
remove(outputFileName.c_str());
- }
+ }else { outputNames.push_back(outputFileName); }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "readList");
+ m->errorOut(e, "RemoveSeqsCommand", "readList");
exit(1);
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::readName(){
+int RemoveSeqsCommand::readName(){
try {
if (outputDir == "") { outputDir += hasPath(namefile); }
- string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
- string outputFileName2 = getRootName(namefile) + "dups.accnos";
+ string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
+ string outputFileName2 = outputDir + getRootName(getSimpleName(namefile)) + "dups.accnos";
ofstream out2;
if (dups) { openOutputFile(outputFileName2, out2); }
bool wroteSomething = false;
while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); if (dups) { out2.close(); remove(outputFileName2.c_str()); } return 0; }
in >> firstCol;
in >> secondCol;
if (dups) { out2.close(); }
if (wroteDups == false) {
remove(outputFileName2.c_str());
- }
+ }else { outputNames.push_back(outputFileName2); }
if (wroteSomething == false) {
- mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+ m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
remove(outputFileName.c_str());
- }
+ }else { outputNames.push_back(outputFileName); }
+ return 0;
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "readName");
+ m->errorOut(e, "RemoveSeqsCommand", "readName");
exit(1);
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::readGroup(){
+int RemoveSeqsCommand::readGroup(){
try {
if (outputDir == "") { outputDir += hasPath(groupfile); }
- string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+ string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
ofstream out;
openOutputFile(outputFileName, out);
bool wroteSomething = false;
while(!in.eof()){
-
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
in >> name; //read from first column
in >> group; //read from second column
if (names.count(name) == 0) {
wroteSomething = true;
out << name << '\t' << group << endl;
- }else { names.erase(name); }
+ }//else { names.erase(name); }
gobble(in);
}
out.close();
if (wroteSomething == false) {
- mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+ m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
remove(outputFileName.c_str());
- }
-
+ }else { outputNames.push_back(outputFileName); }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "readGroup");
+ m->errorOut(e, "RemoveSeqsCommand", "readGroup");
exit(1);
}
}
//**********************************************************************************************************************
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
-void RemoveSeqsCommand::readAlign(){
+int RemoveSeqsCommand::readAlign(){
try {
if (outputDir == "") { outputDir += hasPath(alignfile); }
- string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+ string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
ofstream out;
openOutputFile(outputFileName, out);
out << endl;
while(!in.eof()){
-
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
in >> name; //read from first column
//if this name is in the accnos file
out << endl;
}else {//still read just don't do anything with it
- names.erase(name);
+ //names.erase(name);
//read rest
for (int i = 0; i < 15; i++) {
out.close();
if (wroteSomething == false) {
- mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+ m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
remove(outputFileName.c_str());
- }
+ }else { outputNames.push_back(outputFileName); }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "readAlign");
+ m->errorOut(e, "RemoveSeqsCommand", "readAlign");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "RemoveSeqsCommand", "readAccnos");
+ m->errorOut(e, "RemoveSeqsCommand", "readAccnos");
exit(1);
}
}
projects / mothur.git / blobdiff