//***************************************************************************************************************
-ScreenSeqsCommand::ScreenSeqsCommand(string option){
+ScreenSeqsCommand::ScreenSeqsCommand(string option) {
try {
abort = false;
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
groupfile = validParameter.validFile(parameters, "group", true);
}
catch(exception& e) {
- errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
+ m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
exit(1);
}
}
void ScreenSeqsCommand::help(){
try {
- mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
- mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group.\n");
- mothurOut("The fasta parameter is required.\n");
- mothurOut("The start parameter .... The default is -1.\n");
- mothurOut("The end parameter .... The default is -1.\n");
- mothurOut("The maxambig parameter .... The default is -1.\n");
- mothurOut("The maxhomop parameter .... The default is -1.\n");
- mothurOut("The minlength parameter .... The default is -1.\n");
- mothurOut("The maxlength parameter .... The default is -1.\n");
- mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
- mothurOut("The screen.seqs command should be in the following format: \n");
- mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
- mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
- mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
+ m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group.\n");
+ m->mothurOut("The fasta parameter is required.\n");
+ m->mothurOut("The start parameter .... The default is -1.\n");
+ m->mothurOut("The end parameter .... The default is -1.\n");
+ m->mothurOut("The maxambig parameter .... The default is -1.\n");
+ m->mothurOut("The maxhomop parameter .... The default is -1.\n");
+ m->mothurOut("The minlength parameter .... The default is -1.\n");
+ m->mothurOut("The maxlength parameter .... The default is -1.\n");
+ m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
+ m->mothurOut("The screen.seqs command should be in the following format: \n");
+ m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
+ m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
+ m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- errorOut(e, "ScreenSeqsCommand", "help");
+ m->errorOut(e, "ScreenSeqsCommand", "help");
exit(1);
}
}
ofstream badSeqOut; openOutputFile(badSeqFile, badSeqOut);
while(!inFASTA.eof()){
+ if (m->control_pressed) { goodSeqOut.close(); badSeqOut.close(); inFASTA.close(); remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
Sequence currSeq(inFASTA);
if (currSeq.getName() != "") {
bool goodSeq = 1; // innocent until proven guilty
}
}
gobble(inFASTA);
- }
- if(namefile != "" && groupfile != "") { screenNameGroupFile(badSeqNames); } // this screens both names and groups
- else if(namefile != "") { screenNameGroupFile(badSeqNames); }
- else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the groups
+ }
+
+ if(namefile != "" && groupfile != "") {
+ screenNameGroupFile(badSeqNames);
+ if (m->control_pressed) { goodSeqOut.close(); badSeqOut.close(); inFASTA.close(); remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ }else if(namefile != "") {
+ screenNameGroupFile(badSeqNames);
+ if (m->control_pressed) { goodSeqOut.close(); badSeqOut.close(); inFASTA.close(); remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
+
+ if (m->control_pressed) { goodSeqOut.close(); badSeqOut.close(); inFASTA.close(); remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
if(alignreport != "") { screenAlignReport(badSeqNames); }
goodSeqOut.close();
badSeqOut.close();
inFASTA.close();
+
+
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(goodSeqFile); m->mothurOutEndLine();
+ m->mothurOut(badSeqFile); 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, "ScreenSeqsCommand", "execute");
+ m->errorOut(e, "ScreenSeqsCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
-void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
ifstream inputNames;
openInputFile(namefile, inputNames);
string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
+ outputNames.push_back(goodNameFile); outputNames.push_back(badNameFile);
+
ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
while(!inputNames.eof()){
+ if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
+
inputNames >> seqName >> seqList;
it = badSeqNames.find(seqName);
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
- mothurOutEndLine();
+ m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
}
}
string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
+ outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
+
ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
while(!inputGroups.eof()){
+ if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+
inputGroups >> seqName >> group;
it = badSeqGroups.find(seqName);
//we were unable to remove some of the bad sequences
if (badSeqGroups.size() != 0) {
for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
- mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
- mothurOutEndLine();
+ m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
}
}
}
+
+ return 0;
+
}
//***************************************************************************************************************
-void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
ifstream inputGroups;
openInputFile(groupfile, inputGroups);
string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
+ outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
+
ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
while(!inputGroups.eof()){
+ if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+
inputGroups >> seqName >> group;
it = badSeqNames.find(seqName);
gobble(inputGroups);
}
+ if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
- mothurOutEndLine();
+ m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
}
}
goodGroupOut.close();
badGroupOut.close();
+ if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); }
+
+
+ return 0;
+
}
//***************************************************************************************************************
-void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
+int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
ifstream inputAlignReport;
openInputFile(alignreport, inputAlignReport);
string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
+ outputNames.push_back(goodAlignReportFile); outputNames.push_back(badAlignReportFile);
+
ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
}
while(!inputAlignReport.eof()){
+ if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+
inputAlignReport >> seqName;
it = badSeqNames.find(seqName);
string line;
gobble(inputAlignReport);
}
+ if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- mothurOut("Your file does not include the sequence " + *it + " please correct.");
- mothurOutEndLine();
+ m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
}
}
inputAlignReport.close();
goodAlignReportOut.close();
badAlignReportOut.close();
+
+ if (m->control_pressed) { remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+
+ return 0;
+
}
projects / mothur.git / blobdiff