*/
#include "makegroupcommand.h"
+#include "sequence.hpp"
//**********************************************************************************************************************
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
+ filename = outputDir;
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
in.close();
if (ableToOpen == 1) {
- m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
- }
+ }else{ filename += getRootName(getSimpleName(fastaFileNames[i])); }
}
+ filename += "groups";
+
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
-
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
+ else { splitAtDash(groups, groupsNames); }
+
+ if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; }
}
}
void MakeGroupCommand::help(){
try {
- m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
- m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
- m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
- m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
- m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
- m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
- m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
- m->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");
- m->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");
- m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
- m->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");
- m->mothurOut("The align.seqs command should be in the following format: \n");
- m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
- m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
+ m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
+ m->mothurOut("The make.group command parameters are fasta and groups, both are required.\n");
+ m->mothurOut("The make.group command should be in the following format: \n");
+ m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups. \n");
+ m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "help");
try {
if (abort == true) { return 0; }
+ ofstream out;
+ openOutputFile(filename, out);
+
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+
+ ifstream in;
+ openInputFile(fastaFileNames[i], in);
+
+ while (!in.eof()) {
+
+ Sequence seq(in); gobble(in);
+
+ if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
+ }
+ in.close();
+ }
+
+ out.close();
m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- //for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
exit(1);
}
}
+//**********************************************************************************************************************
+
projects / mothur.git / blobdiff