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Adds mothur location and skip blank files option to make.contigs 

#233
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1 parent 8690a90 commit 5ae7e78c96c3042e8044721fda4e019892d351d2 @mothur-westcott mothur-westcott committed Jul 13, 2016
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Showing with 68 additions and 12 deletions.
  1. +68 −12 source/commands/makecontigscommand.cpp
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80 source/commands/makecontigscommand.cpp
@@ -2927,6 +2927,7 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
if (m->control_pressed) { return files; }
+ bool skip = false;
string line = m->getline(in); m->gobble(in);
vector<string> pieces = m->splitWhiteSpace(line);
@@ -2975,16 +2976,21 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
}
}
-
+ //look for mothur exe
+ string mpath = m->argv;
+ string tempPath = mpath;
+ for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
+ mpath = mpath.substr(0, (tempPath.find_last_of('m')));
//check to make sure both are able to be opened
ifstream in2;
int openForward = m->openInputFile(forward, in2, "noerror");
+ string tryPath = forward;
//if you can't open it, try default location
if (openForward == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(forward);
+ tryPath = m->getDefaultPath() + m->getSimpleName(forward);
m->mothurOut("Unable to open " + forward + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in3;
openForward = m->openInputFile(tryPath, in3, "noerror");
@@ -2996,7 +3002,7 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
//if you can't open it, try output location
if (openForward == 1) {
if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(forward);
+ tryPath = m->getOutputDir() + m->getSimpleName(forward);
m->mothurOut("Unable to open " + forward + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in4;
openForward = m->openInputFile(tryPath, in4, "noerror");
@@ -3005,17 +3011,31 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
}
}
+ //if you can't open it, try mothur's location
+ if (openForward == 1) {
+ tryPath = mpath + m->getSimpleName(forward);
+ m->mothurOut("Unable to open " + forward + ". Trying mothur's executable directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openForward = m->openInputFile(tryPath, in4, "noerror");
+ forward = tryPath;
+ in4.close();
+ }
+
if (openForward == 1) { //can't find it
m->mothurOut("[WARNING]: can't find " + forward + ", ignoring pair.\n");
- }else{ in2.close(); }
+ }else{
+ if (m->isBlank(tryPath)) { m->mothurOut("[WARNING]: " + forward + " is blank, skipping.\n"); skip=true; }
+ in2.close();
+ }
ifstream in3;
int openReverse = m->openInputFile(reverse, in3, "noerror");
+ tryPath = reverse;
//if you can't open it, try default location
if (openReverse == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(reverse);
+ tryPath = m->getDefaultPath() + m->getSimpleName(reverse);
m->mothurOut("Unable to open " + reverse + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in3;
openReverse = m->openInputFile(tryPath, in3, "noerror");
@@ -3024,10 +3044,20 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
}
}
+ //if you can't open it, try mothur's location
+ if (openReverse == 1) {
+ tryPath = mpath + m->getSimpleName(reverse);
+ m->mothurOut("Unable to open " + reverse + ". Trying mothur's executable directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openForward = m->openInputFile(tryPath, in4, "noerror");
+ reverse = tryPath;
+ in4.close();
+ }
+
//if you can't open it, try output location
if (openReverse == 1) {
if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(reverse);
+ tryPath = m->getOutputDir() + m->getSimpleName(reverse);
m->mothurOut("Unable to open " + reverse + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in4;
openReverse = m->openInputFile(tryPath, in4, "noerror");
@@ -3038,17 +3068,18 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
if (openReverse == 1) { //can't find it
m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n");
- }else{ in3.close(); }
+ }else{ if (m->isBlank(tryPath)) { m->mothurOut("[WARNING]: " + reverse + " is blank, skipping.\n"); skip=true; } in3.close(); }
int openFindex = 0;
if ((findex != "") && (findex != "NONE")){
ifstream in4;
openFindex = m->openInputFile(findex, in4, "noerror"); in4.close();
+ tryPath = findex;
//if you can't open it, try default location
if (openFindex == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(findex);
+ tryPath = m->getDefaultPath() + m->getSimpleName(findex);
m->mothurOut("Unable to open " + findex + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in5;
openFindex = m->openInputFile(tryPath, in5, "noerror");
@@ -3057,10 +3088,20 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
}
}
+ //if you can't open it, try mothur's location
+ if (openFindex == 1) {
+ tryPath = mpath + m->getSimpleName(findex);
+ m->mothurOut("Unable to open " + findex + ". Trying mothur's executable directory " + tryPath); m->mothurOutEndLine();
+ ifstream in14;
+ openForward = m->openInputFile(tryPath, in14, "noerror");
+ findex = tryPath;
+ in14.close();
+ }
+
//if you can't open it, try output location
if (openFindex == 1) {
if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(findex);
+ tryPath = m->getOutputDir() + m->getSimpleName(findex);
m->mothurOut("Unable to open " + findex + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in6;
openFindex = m->openInputFile(tryPath, in6, "noerror");
@@ -3071,18 +3112,21 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
if (openFindex == 1) { //can't find it
m->mothurOut("[WARNING]: can't find " + findex + ", ignoring pair.\n");
+ }else{
+ if (m->isBlank(tryPath)) { m->mothurOut("[WARNING]: " + findex + " is blank, skipping.\n"); skip=true; }
}
}
int openRindex = 0;
if ((rindex != "") && (rindex != "NONE")) {
ifstream in7;
openRindex = m->openInputFile(rindex, in7, "noerror"); in7.close();
+ tryPath = rindex;
//if you can't open it, try default location
if (openRindex == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(rindex);
+ tryPath = m->getDefaultPath() + m->getSimpleName(rindex);
m->mothurOut("Unable to open " + rindex + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in8;
openRindex = m->openInputFile(tryPath, in8, "noerror");
@@ -3091,10 +3135,20 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
}
}
+ //if you can't open it, try mothur's location
+ if (openFindex == 1) {
+ tryPath = mpath + m->getSimpleName(rindex);
+ m->mothurOut("Unable to open " + rindex + ". Trying mothur's executable directory " + tryPath); m->mothurOutEndLine();
+ ifstream in14;
+ openForward = m->openInputFile(tryPath, in14, "noerror");
+ rindex = tryPath;
+ in14.close();
+ }
+
//if you can't open it, try output location
if (openRindex == 1) {
if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(rindex);
+ tryPath = m->getOutputDir() + m->getSimpleName(rindex);
m->mothurOut("Unable to open " + rindex + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in9;
openRindex = m->openInputFile(tryPath, in9, "noerror");
@@ -3105,12 +3159,14 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
if (openRindex == 1) { //can't find it
m->mothurOut("[WARNING]: can't find " + rindex + ", ignoring pair.\n");
+ }else{
+ if (m->isBlank(tryPath)) { m->mothurOut("[WARNING]: " + rindex + " is blank, skipping.\n"); skip=true; }
}
}
- if ((openForward != 1) && (openReverse != 1) && (openFindex != 1) && (openRindex != 1)) { //good pair
+ if ((openForward != 1) && (openReverse != 1) && (openFindex != 1) && (openRindex != 1) && (!skip)) { //good pair
file2Group[files.size()] = group;
vector<string> pair;
#ifdef USE_BOOST

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