CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp);
CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch);
- CommandParameter pinclude("include", "Multiple", "greater-greaterequal-all", "greater", "", "", "",false,false); parameters.push_back(pinclude);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prealign);
CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
- helpString += "The include parameter is used when template=self and allows you to choose which sequences will make up the \"template\". Options are greater, greaterequal and all, default=greater, meaning sequences with greater abundance than the query sequence. \n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
#ifdef USE_MPI
helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
m->setProcessors(temp);
convert(temp, processors);
- includeAbunds = validParameter.validFile(parameters, "include", false); if (includeAbunds == "not found") { includeAbunds = "greater"; }
- if ((includeAbunds != "greater") && (includeAbunds != "greaterequal") && (includeAbunds != "all")) { includeAbunds = "greater"; m->mothurOut("Invalid include setting. options are greater, greaterequal or all. using greater."); m->mothurOutEndLine(); }
-
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
convert(temp, ksize);
if (templatefile != "self") { //you want to run slayer with a refernce template
chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
}else {
+ if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
+ string nameFile = "";
if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFileNames[s], search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
+ nameFile = nameFileNames[s];
}else {
-
m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
//use unique.seqs to create new name and fastafile
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
- string nameFile = filenames["name"][0];
+ nameFile = filenames["name"][0];
fastaFileNames[s] = filenames["fasta"][0];
-
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
}
+
+ //sort fastafile by abundance, returns new sorted fastafile name
+ m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
+ fastaFileNames[s] = sortFastaFile(fastaFileNames[s], nameFile);
+ m->mothurOut("Done."); m->mothurOutEndLine();
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+
+ chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
}
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
exit(1);
}
}
+/**************************************************************************************************/
+
+string ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
+ try {
+
+ //read through fastafile and store info
+ map<string, string> seqs;
+ ifstream in;
+ m->openInputFile(fastaFile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return ""; }
+
+ Sequence seq(in); m->gobble(in);
+ seqs[seq.getName()] = seq.getAligned();
+ }
+
+ in.close();
+
+ //read namefile
+ vector<seqPriorityNode> nameMapCount;
+ int error = m->readNames(nameFile, nameMapCount, seqs);
+
+ if (m->control_pressed) { return ""; }
+
+ if (error == 1) { m->control_pressed = true; return ""; }
+ if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return ""; }
+
+ sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
+
+ string newFasta = fastaFile + ".temp";
+ ofstream out;
+ m->openOutputFile(newFasta, out);
+
+ //print new file in order of
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
+ }
+ out.close();
+
+ rename(newFasta.c_str(), fastaFile.c_str());
+
+ return fastaFile;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
+ exit(1);
+ }
+}
/**************************************************************************************************/
projects / mothur.git / blobdiff