taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
-
+
+ string usedDups = "true";
+ string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
+ dups = isTrue(temp);
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
+
+ if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
+
}
}
try {
m->mothurOut("The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy or alignreport file.\n");
m->mothurOut("It outputs a file containing only the sequences in the .accnos file.\n");
- m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy and alignreport. You must provide accnos and at least one of the other parameters.\n");
+ m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, alignreport and dups. You must provide accnos and at least one of the other parameters.\n");
+ m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n");
m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
m->mothurOut("Example get.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");
if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
- if (fastafile != "") { readFasta(); }
if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
if (alignfile != "") { readAlign(); }
if (listfile != "") { readList(); }
if (name != "") {
//if this name is in the accnos file
- if (names.count(name) == 1) {
+ if (names.count(name) != 0) {
wroteSomething = true;
currSeq.printSequence(out);
binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
//if that name is in the .accnos file, add it
- if (names.count(name) == 1) { newNames += name + ","; }
+ if (names.count(name) != 0) { newNames += name + ","; }
}
//get last name
- if (names.count(binnames) == 1) { newNames += binnames + ","; }
+ if (names.count(binnames) != 0) { newNames += binnames + ","; }
//if there are names in this bin add to new list
if (newNames != "") {
if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
in >> firstCol;
- in >> secondCol;
+ in >> secondCol;
+
+ string hold = "";
+ if (dups) { hold = secondCol; }
vector<string> parsedNames;
//parse second column saving each name
vector<string> validSecond;
for (int i = 0; i < parsedNames.size(); i++) {
- if (names.count(parsedNames[i]) == 1) {
+ if (names.count(parsedNames[i]) != 0) {
validSecond.push_back(parsedNames[i]);
}
}
-
- //if the name in the first column is in the set then print it and any other names in second column also in set
- if (names.count(firstCol) == 1) {
-
+ if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
+ for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
+ out << firstCol << '\t' << hold << endl;
wroteSomething = true;
-
- out << firstCol << '\t';
-
- //you know you have at least one valid second since first column is valid
- for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
- out << validSecond[validSecond.size()-1] << endl;
-
-
- //make first name in set you come to first column and then add the remaining names to second column
}else {
- //you want part of this row
- if (validSecond.size() != 0) {
+ //if the name in the first column is in the set then print it and any other names in second column also in set
+ if (names.count(firstCol) != 0) {
wroteSomething = true;
- out << validSecond[0] << '\t';
-
+ out << firstCol << '\t';
+
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
out << validSecond[validSecond.size()-1] << endl;
+
+
+ //make first name in set you come to first column and then add the remaining names to second column
+ }else {
+ //you want part of this row
+ if (validSecond.size() != 0) {
+
+ wroteSomething = true;
+
+ out << validSecond[0] << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+ }
}
}
-
gobble(in);
}
in.close();
in >> group; //read from second column
//if this name is in the accnos file
- if (names.count(name) == 1) {
+ if (names.count(name) != 0) {
wroteSomething = true;
out << name << '\t' << group << endl;
in >> tax; //read from second column
//if this name is in the accnos file
- if (names.count(name) == 1) {
+ if (names.count(name) != 0) {
wroteSomething = true;
out << name << '\t' << tax << endl;
in >> name; //read from first column
//if this name is in the accnos file
- if (names.count(name) == 1) {
+ if (names.count(name) != 0) {
wroteSomething = true;
out << name << '\t';
projects / mothur.git / blobdiff