#include "listseqscommand.h"
#include "sequence.hpp"
#include "listvector.hpp"
+#include "counttable.h"
//**********************************************************************************************************************
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
string ListSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
- helpString += "The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport. You must provide one of these parameters.\n";
+ helpString += "The list.seqs command reads a fasta, name, group, count, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+ helpString += "The list.seqs command parameters are fasta, name, group, count, list, taxonomy and alignreport. You must provide one of these parameters.\n";
helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
helpString += "Example list.seqs(fasta=amazon.fasta).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
//check for required parameters
if (taxfile == "not open") { abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
else { m->setTaxonomyFile(taxfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
- if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == "")) { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
+ if ((countfile == "") && (fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == "")) { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
int okay = 1;
if (outputDir != "") { okay++; }
else if (alignfile != "") { inputFileName = alignfile; readAlign(); }
else if (listfile != "") { inputFileName = listfile; readList(); }
else if (taxfile != "") { inputFileName = taxfile; readTax(); }
+ else if (countfile != "") { inputFileName = countfile; readCount(); }
if (m->control_pressed) { outputTypes.clear(); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
- //if (lastName == "") { lastName = name; }
- //if (name != lastName) { count = 1; }
- // lastName = name;
-
- //Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
- //newSeq.printSequence(out);
if (name != "") { names.push_back(name); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+int ListSeqsCommand::readCount(){
+ try {
+ CountTable ct;
+ ct.readTable(countfile);
+
+ if (m->control_pressed) { return 0; }
+
+ names = ct.getNamesOfSeqs();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readCount");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
int ListSeqsCommand::readAlign(){