outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
path += "lookupFiles\\";
#endif
lookupFileName = m->getFullPathName(path) + "LookUp_Titanium.pat";
-
- int ableToOpen;
- ifstream in;
- ableToOpen = m->openInputFile(lookupFileName, in, "noerror");
- in.close();
-
- //if you can't open it, try input location
- if (ableToOpen == 1) {
- if (inputDir != "") { //default path is set
- string tryPath = inputDir + m->getSimpleName(lookupFileName);
- m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- lookupFileName = tryPath;
- }
- }
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(lookupFileName);
- m->mothurOut("Unable to open " + lookupFileName + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- lookupFileName = tryPath;
- }
- }
-
- //if you can't open it its not in current working directory or inputDir, try mothur excutable location
- if (ableToOpen == 1) {
- string exepath = m->argv;
- string tempPath = exepath;
- for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- exepath = exepath.substr(0, (tempPath.find_last_of('m')));
-
- string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
- m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- lookupFileName = tryPath;
- }
-
- if (ableToOpen == 1) { m->mothurOut("Unable to open " + lookupFileName + "."); m->mothurOutEndLine(); abort=true; }
- }
- else if(temp == "not open") {
+ bool ableToOpen = m->checkLocations(lookupFileName, inputDir);
+ if (!ableToOpen) { abort=true; }
+ }else if(temp == "not open") {
lookupFileName = validParameter.validFile(parameters, "lookup", false);
vector<string> sffFiles, oligosFiles;
readFile(sffFiles, oligosFiles);
- outputDir = m->hasPath(filename);
- string fileroot = outputDir + m->getRootName(m->getSimpleName(filename));
+ string thisOutputDir = outputDir;
+ if (thisOutputDir == "") { thisOutputDir = m->hasPath(filename); }
+ string fileroot = thisOutputDir + m->getRootName(m->getSimpleName(filename));
map<string, string> variables;
variables["[filename]"] = fileroot;
string fasta = getOutputFileName("fasta",variables);
if (makeGroup) { outputNames.push_back(group); outputTypes["group"].push_back(group); m->setGroupFile(group); }
}
+ m->setProcessors(toString(processors));
+
//report output filenames
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
in >> sff;
- sff = m->getFullPathName(sff);
-
//ignore file pairing
if(sff[0] == '#'){ while (!in.eof()) { char c = in.get(); if (c == 10 || c == 13){ break; } } m->gobble(in); }
else { //check for oligos file
+ bool ableToOpenSff = m->checkLocations(sff, inputDir);
+
oligos = "";
// get rest of line in case there is a oligos filename
if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { oligos += c; }
- }
- sffFiles.push_back(sff);
- if (oligos != "") { oligos = m->getFullPathName(oligos); allBlank = false; }
- if (oligos == "") { allFull = false; }
- oligosFiles.push_back(oligos); //will push a blank if there is not an oligos for this sff file
+ }
+
+ if (ableToOpenSff) {
+ sffFiles.push_back(sff);
+ if (oligos != "") {
+ bool ableToOpenOligos = m->checkLocations(oligos, inputDir);
+ if (ableToOpenOligos) { allBlank = false; }
+ else { m->mothurOut("Can not find " + oligos + ". Ignoring.\n"); oligos = ""; }
+ }
+ if (oligos == "") { allFull = false; }
+ oligosFiles.push_back(oligos); //will push a blank if there is not an oligos for this sff file
+ }else { m->mothurOut("Can not find " + sff + ". Ignoring.\n"); }
}
m->gobble(in);
}
m->mothurOut("\n>>>>>\tProcessing " + sff + " (file " + toString(s+1) + " of " + toString(sffFiles.size()) + ")\t<<<<<\n");
//run sff.info
+ string redirects = "";
+ if (inputDir != "") { redirects += ", inputdir=" + inputDir; }
+ if (outputDir != "") { redirects += ", outputdir=" + outputDir; }
string inputString = "sff=" + sff + ", flow=T";
if (trim) { inputString += ", trim=T"; }
+ if (redirects != "") { inputString += redirects; }
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: sffinfo(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
m->mothurCalling = false;
m->mothurOutEndLine();
+ redirects = "";
+ if (outputDir != "") { redirects += ", outputdir=" + outputDir; }
+
//run summary.seqs on the fasta file
string fastaFile = "";
map<string, vector<string> >::iterator it = filenames.find("fasta");
else { m->mothurOut("[ERROR]: sffinfo did not create a fasta file, quitting.\n"); m->control_pressed = true; break; }
inputString = "fasta=" + fastaFile + ", processors=1";
+ if (redirects != "") { inputString += redirects; }
m->mothurOutEndLine();
m->mothurOut("Running command: summary.seqs(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
inputString += ", maxhomop=" + toString(maxHomoP) + ", maxflows=" + toString(maxFlows) + ", minflows=" + toString(minFlows);
inputString += ", pdiffs=" + toString(pdiffs) + ", bdiffs=" + toString(bdiffs) + ", ldiffs=" + toString(ldiffs) + ", sdiffs=" + toString(sdiffs);
inputString += ", tdiffs=" + toString(tdiffs) + ", signal=" + toString(signal) + ", noise=" + toString(noise) + ", order=" + flowOrder + ", processors=1";
-
+ if (redirects != "") { inputString += redirects; }
m->mothurOutEndLine();
m->mothurOut("Running command: trim.flows(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
inputString += ", sigma=" +toString(sigma);
inputString += ", mindelta=" + toString(minDelta);
inputString += ", order=" + flowOrder + ", processors=1";
-
+ if (redirects != "") { inputString += redirects; }
//run shhh.flows
m->mothurOutEndLine();
m->mothurOut("Running command: shhh.flows(" + inputString + ")"); m->mothurOutEndLine();
if (keepFirst != 0) { inputString += ", keepfirst=" + toString(keepFirst); }
if (removeLast != 0) { inputString += ", removelast=" + toString(removeLast); }
inputString += ", processors=1";
-
+ if (redirects != "") { inputString += redirects; }
//run trim.seqs
m->mothurOutEndLine();
m->mothurOut("Running command: trim.seqs(" + inputString + ")"); m->mothurOutEndLine();
}
inputString = "fasta=" + fastaFile + ", processors=1, name=" + nameFile;
+ if (redirects != "") { inputString += redirects; }
m->mothurOutEndLine();
m->mothurOut("Running command: summary.seqs(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
m->appendFiles(nameFile, name);
if (makeGroup) { m->appendFiles(groupFile, group); }
}
- count++;
+
for (it = filenames.begin(); it != filenames.end(); it++) {
for (int i = 0; i < (it->second).size(); i++) {
outputNames.push_back((it->second)[i]); outputTypes[it->first].push_back((it->second)[i]);
}
}
+ count++;
}
return count;
projects / mothur.git / blobdiff