helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
}
catch(exception& e) {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(fastafile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
- convert(temp, numbases);
+ m->mothurConvert(temp, numbases);
temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
countGaps = m->isTrue(temp);
Sequence seq(in);
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0; }
if (seq.getName() != "") {
string newSeqString = getChopped(seq);
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
- else { remove(outputFileNameAccnos.c_str()); }
+ else { m->mothurRemove(outputFileNameAccnos); }
m->mothurOutEndLine();
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+ if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
numBasesCounted++;
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ else { temp = temp.substr(0, stopSpot+1); }
}else {
if (!Short) { temp = ""; } //sequence too short
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+ if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
numBasesCounted++;
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
+ temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ else { temp = temp.substr(0, stopSpot+1); }
}else {
if (!Short) { temp = ""; } //sequence too short
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
+ temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(stopSpot+1); }
+ else { temp = temp.substr(stopSpot); }
}else {
if (!Short) { temp = ""; } //sequence too short
}