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';
set<string> names;
vector<string> outputNames;
string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
- bool abort;
+ bool abort, dups;
int readFasta();
int readName();
if (error != 0) { readOk = error; }
filehandle.close();
+
return readOk;
}
catch(exception& e) {
// ';' means end of tree.
else if((ch=filehandle.peek())==';' || ch=='['){
rooted = 1;
- }
+ }
+
if(rooted != 1){
rc = readNewickInt(filehandle, n, T);
if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
- }
+ }
}
//note: treeclimber had the code below added - not sure why?
else{
lc = rc = -1;
}
- while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}
+ while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}
+
if(rooted != 1){
T->tree[n].setChildren(lc,rc);
T->tree[n].setBranchLength(0);
if(lc!=-1){ T->tree[lc].setParent(n); }
if(rc!=-1){ T->tree[rc].setParent(n); }
}
+
+ //T->printTree(); cout << endl;
return 0;
}
if (m->control_pressed) { return -1; }
int c = readNodeChar(f);
- string k;
-k = c;
- cout << "at beginning = " << k <<endl;
+
if(c == '('){
//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
while(f.peek() != ')'){
int child = readNewickInt(f, n, T);
if (child == -1) { return -1; } //reports an error in reading
-
+ //cout << "child = " << child << endl;
childrenNodes.push_back(child);
//after a child you either have , or ), check for both
if(f.peek()==')'){ break; }
else if (f.peek()==',') { readSpecialChar(f,',',"comma"); }
- else { string k;
- k = f.peek();
- cout << "in here k = " << k << '\t' << f.tellg() <<endl;
- }
+ else {;}
}
- cout << childrenNodes.size() << endl;
+ //cout << childrenNodes.size() << endl;
if (childrenNodes.size() < 2) { m->mothurOut("Error in tree, please correct."); m->mothurOutEndLine(); return -1; }
//then force into 2 node structure
int lc, rc;
if (i == 1) { lc = childrenNodes[i-1]; rc = childrenNodes[i]; }
- else { lc = n; rc = childrenNodes[i]; }
- cout << i << '\t' << lc << '\t' << rc << endl;
+ else { lc = n-1; rc = childrenNodes[i]; }
+ //cout << i << '\t' << lc << '\t' << rc << endl;
T->tree[n].setChildren(lc,rc);
T->tree[lc].setParent(n);
T->tree[rc].setParent(n);
- T->printTree(); cout << endl;
+ //T->printTree(); cout << endl;
n++;
}
//to account for extra ++ in looping
n--;
- //int lc = readNewickInt(f, n, T);
- //if (lc == -1) { return -1; } //reports an error in reading
-
- //readSpecialChar(f,',',"comma");
-
- //int rc = readNewickInt(f, n, T);
- //if (rc == -1) { return -1; } //reports an error in reading
if(f.peek()==')'){
readSpecialChar(f,')',"right parenthesis");
//to pass over labels in trees
c=filehandle.get();
- while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')&& (c!=')')){ c=filehandle.get(); }
filehandle.putback(c);
}
T->tree[n].setBranchLength(0.0);
}
- //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
- /*while(f.peek() == ','){
- string k;
- k = f.peek();
- cout << "in here k = " << k << '\t' << f.tellg() <<endl;
- //force this node to be left child and read new rc
- T->tree[n].setChildren(lc,rc);
- T->tree[lc].setParent(n);
- T->tree[rc].setParent(n);
-
- T->printTree(); cout << endl;
- lc = n;
- n++;
-
- readSpecialChar(f,',',"comma");
-
- rc = readNewickInt(f, n, T);
-
- if (rc == -1) { return -1; } //reports an error in reading
-
- if(f.peek()==')'){
- readSpecialChar(f,')',"right parenthesis");
- //to pass over labels in trees
- c=filehandle.get();
- while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
- filehandle.putback(c);
-
- if(f.peek() == ':'){
- readSpecialChar(f,':',"colon");
-
- if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n"); readOk = -1; return -1; }
-
- T->tree[n].setBranchLength(readBranchLength(f));
- }else{
- T->tree[n].setBranchLength(0.0);
- }
-
- break;
- }
- }*/
-
//T->tree[n].setChildren(lc,rc);
//T->tree[lc].setParent(n);
//T->tree[rc].setParent(n);
name += d;
d=f.get();
}
- cout << name << endl;
+//cout << name << endl;
int blen = 0;
if(d == ':') { blen = 1; }
}
while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') ) {;}
+
f.putback(c);
return n1;
delete globaldata->gTreemap;
return 0;
}
-
+
T[i]->assembleTree();
}
m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy 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, taxonomy, alignreport and dups. You must provide accnos and at least 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 dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. \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");
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(); }
try {
if (outputDir == "") { outputDir += hasPath(namefile); }
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 wroteDups = false;
-
ofstream out;
openOutputFile(outputFileName, out);
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; }
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
in >> firstCol;
in >> secondCol;
}
}
- if ((dups) && (validSecond.size() != parsedNames.size())) {
- wroteDups = true;
- for (int i = 0; i < parsedNames.size(); i++) { out2 << parsedNames[i] << endl; }
+ if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone
+ for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
}else {
//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) {
in.close();
out.close();
- if (dups) { out2.close(); }
- if (wroteDups == false) {
- remove(outputFileName2.c_str());
- }else { outputNames.push_back(outputFileName2); }
-
if (wroteSomething == false) {
m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
remove(outputFileName.c_str());
//cout << " at beginning of while " << k << endl;
if(c == ')') {
//to pass over labels in trees
- string label = readLabel(filehandle);
+ c=filehandle.get();
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ filehandle.putback(c);
}
-
if(c == ';') { return 0; }
if(c == -1) { return 0; }
-
//if you are a name
if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
- name = readName(filehandle);
+ name = "";
+ c = filehandle.get();
+ //k = c;
+//cout << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ //k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
globaldata->Treenames.push_back(name);
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
}
if(c == ':') { //read until you reach the end of the branch length
- string bl = readBranchLength(filehandle);
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+ c = filehandle.get();
+ //k = c;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
}
c = filehandle.get();
}
/*******************************************************/
-string Tree::readLabel(ifstream& filehandle) {
- try {
-
- string label = "";
-
- //to pass over labels in trees
- int c=filehandle.get();
- while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ label += c; c=filehandle.get(); }
- filehandle.putback(c);
-
- return label;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Tree", "readLabel");
- exit(1);
- }
-}
-/*******************************************************/
-string Tree::readName(ifstream& filehandle) {
- try {
-
- string name = "";
- int c = filehandle.get();
-
- while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
- name += c;
- c = filehandle.get();
- }
-
-//cout << "name = " << name << endl;
- filehandle.putback(c);
-
- return name;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Tree", "readName");
- exit(1);
- }
-}
-/*******************************************************/
-string Tree::readBranchLength(ifstream& filehandle) {
- try {
-
- string br = "";
- int c;
- while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
- br += c;
- c = filehandle.get();
- }
- filehandle.putback(c);
-
- return br;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Tree", "readBranchLength");
- exit(1);
- }
-}
/*******************************************************/
-/*******************************************************/
//not included in the tree.
//only takes names from the first tree in the tree file and assumes that all trees use the same names.
int readTreeString(ifstream&);
- string readLabel(ifstream&);
- string readName(ifstream&);
- string readBranchLength(ifstream&);
-
+
MothurOut* m;
};
projects / mothur.git / commitdiff