#include "binsequencecommand.h"
//**********************************************************************************************************************
-BinSeqCommand::BinSeqCommand(string option){
+BinSeqCommand::BinSeqCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
//make sure the user has already run the read.otu command
if (globaldata->getListFile() == "") {
- mothurOut("You must read a listfile before running the bin.seqs command.");
- mothurOutEndLine();
+ m->mothurOut("You must read a listfile before running the bin.seqs command.");
+ m->mothurOutEndLine();
abort = true;
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the bin.seqs command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the bin.seqs command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
//check for optional parameter and set defaults
}
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "BinSeqCommand");
+ m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
exit(1);
}
}
void BinSeqCommand::help(){
try {
- mothurOut("The bin.seqs command can only be executed after a successful read.otu command of a listfile.\n");
- mothurOut("The bin.seqs command parameters are fasta, name, label and group. The fasta parameter is required.\n");
- mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
- mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
- mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n");
- mothurOut("The default value for label is all lines in your inputfile.\n");
- mothurOut("The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n");
- mothurOut("If you provide a groupfile, then it also appends the sequences group to the name.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ m->mothurOut("The bin.seqs command can only be executed after a successful read.otu command of a listfile.\n");
+ m->mothurOut("The bin.seqs command parameters are fasta, name, label and group. The fasta parameter is required.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
+ m->mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
+ m->mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n");
+ m->mothurOut("The default value for label is all lines in your inputfile.\n");
+ m->mothurOut("The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n");
+ m->mothurOut("If you provide a groupfile, then it also appends the sequences group to the name.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "help");
+ m->errorOut(e, "BinSeqCommand", "help");
exit(1);
}
}
readNamesFile();
}
+
//read list file
read = new ReadOTUFile(globaldata->getListFile());
read->read(&*globaldata);
list = globaldata->gListVector;
string lastLabel = list->getLabel();
+ if (m->control_pressed) { return 0; }
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
if(allLines == 1 || labels.count(list->getLabel()) == 1){
error = process(list);
- if (error == 1) { return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector();
}
-
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
delete list;
}
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+
return 0;
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "execute");
+ m->errorOut(e, "BinSeqCommand", "execute");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "readNamesFile");
+ m->errorOut(e, "BinSeqCommand", "readNamesFile");
exit(1);
}
}
string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
openOutputFile(outputFileName, out);
+
+ //save to output list of output file names
+ outputNames.push_back(outputFileName);
- mothurOut(list->getLabel()); mothurOutEndLine();
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
//for each bin in the list vector
for (int i = 0; i < list->size(); i++) {
-
+
+ if (m->control_pressed) { return 1; }
+
binnames = list->get(i);
while (binnames.find_first_of(',') != -1) {
name = binnames.substr(0,binnames.find_first_of(','));
}else {//if you do have groups
string group = groupMap->getGroup(name);
if (group == "not found") {
- mothurOut(name + " is missing from your group file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
return 1;
}else{
name = name + "|" + group + "|" + toString(i+1);
}
}
}else {
- mothurOut(name + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
return 1;
}
}else {//if you do have groups
string group = groupMap->getGroup(binnames);
if (group == "not found") {
- mothurOut(binnames + " is missing from your group file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
return 1;
}else{
binnames = binnames + "|" + group + "|" + toString(i+1);
}
}
}else {
- mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
return 1;
}
}
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "process");
+ m->errorOut(e, "BinSeqCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff