else {
//valid paramters for this command
- string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold"};
+ string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ 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);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("template");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["template"] = inputDir + it->second; }
+ }
+ }
+
//check for required parameters
templateFileName = validParameter.validFile(parameters, "template", true);
if (templateFileName == "not found") {
mothurOut("template is a required parameter for the align.seqs command.");
mothurOutEndLine();
abort = true;
- }
- else if (templateFileName == "not open") { abort = true; }
+ }else if (templateFileName == "not open") { abort = true; }
candidateFileName = validParameter.validFile(parameters, "candidate", false);
if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true; }
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < candidateFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(candidateFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
+ }
+
int ableToOpen;
ifstream in;
ableToOpen = openInputFile(candidateFileNames[i], in);
mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
- mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse compement if a sequence falls below the threshold. The default is false.\n");
- mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. \n");
+ mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n");
+ mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
mothurOut("The align.seqs command should be in the following format: \n");
for (int s = 0; s < candidateFileNames.size(); s++) {
mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
- string alignFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "align";
- string reportFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "align.report";
- string accnosFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "flip.accnos";
+ if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
+ string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
+ string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
+ string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
int numFastaSeqs = 0;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
}
#else
ifstream inFASTA;
- openInputFile(candidateFileName[s], inFASTA);
+ openInputFile(candidateFileNames[s], inFASTA);
numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
inFASTA.close();
lines.push_back(new linePair(0, numFastaSeqs));
- driver(lines[0], alignFileName, reportFileName, accnosFileName);
+ driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
//delete accnos file if its blank else report to user
if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); }
projects / mothur.git / blobdiff