CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "",false,false); parameters.push_back(pnomatch);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
string PcrSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The pcr.seqs command reads a fasta file ...\n";
-
+ helpString += "The pcr.seqs command reads a fasta file.\n";
+ helpString += "The pcr.seqs command parameters are fasta, oligos, name, group, taxonomy, ecoli, start, end, nomatch, processors, keepprimer and keepdots.\n";
+ helpString += "The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence.\n";
+ helpString += "The start parameter allows you to provide a starting position to trim to.\n";
+ helpString += "The end parameter allows you to provide a ending position to trim from.\n";
+ helpString += "The nomatch parameter allows you to decide what to do with sequences where the primer is not found. Default=reject, meaning remove from fasta file. if nomatch=true, then do nothing to sequence.\n";
+ helpString += "The processors parameter allows you to use multiple processors.\n";
+ helpString += "The keepprimer parameter allows you to keep the primer, default=false.\n";
+ helpString += "The keepdots parameter allows you to keep the leading and trailing .'s, default=true.\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Pcr.seqs .\n";
return helpString;
}
- //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 = ""; }
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
}else if (fastafile == "not open") { fastafile = ""; 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); }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
if (taxfile == "not found"){ taxfile = ""; }
else if(taxfile == "not open"){ taxfile = ""; abort = true; }
else { m->setTaxonomyFile(taxfile); }
-
- temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
- m->mothurConvert(temp, pdiffs);
-
+
temp = validParameter.validFile(parameters, "start", false); if (temp == "not found") { temp = "-1"; }
m->mothurConvert(temp, start);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pcr.scrap.fasta";
- outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile);
+
length = 0;
if(oligosfile != ""){ readOligos(); } if (m->control_pressed) { return 0; }
//don't write or keep if blank
if (badNames.size() != 0) { writeAccnos(badNames); }
if (m->isBlank(badSeqFile)) { m->mothurRemove(badSeqFile); }
+ else { outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (namefile != "") { readName(badNames); }
}
}
}
-
+
+ //trimming removed all bases
+ if (currSeq.getUnaligned() == "") { goodSeq = false; }
+
if(goodSeq == 1) { currSeq.printSequence(goodFile); }
else {
badSeqNames.insert(currSeq.getName());