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rename the parameter
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@elileka
elileka committed May 1, 2024
1 parent 4048af4 commit e5d8d80
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Showing 2 changed files with 29 additions and 29 deletions.
12 changes: 6 additions & 6 deletions src/commons/LocalParameters.h
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Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,8 @@ class LocalParameters : public Parameters {
PARAMETER(PARAM_WRITE_FRAG_COORDS)
int writeFragCoords;

PARAMETER(PARAM_LEN_SEARCH_START)
int lenSearchStart;
PARAMETER(PARAM_LEN_SCAN_FOR_START)
int lenScanForStart;

private:
LocalParameters() :
Expand All @@ -87,7 +87,7 @@ class LocalParameters : public Parameters {
PARAM_ALLOW_OVERLAP(PARAM_ALLOW_OVERLAP_ID,"--overlap", "allow same-strand overlaps", "allow predictions to overlap another on the same strand. when not allowed (default), only the prediction with better E-value will be retained [0,1]", typeid(int), (void *) &overlapAllowed, "^[0-1]{1}$"),
PARAM_WRITE_TKEY(PARAM_WRITE_TKEY_ID,"--target-key", "write target key instead of accession", "write the target key (internal DB identifier) instead of its accession. By default (0) target accession will be written [0,1]", typeid(int), (void *) &writeTargetKey, "^[0-1]{1}$"),
PARAM_WRITE_FRAG_COORDS(PARAM_WRITE_FRAG_COORDS_ID,"--write-frag-coords", "write fragment contig coords", "write the contig coords of the stop-to-stop fragment in which putative exon lies. By default (0) only putative exon coords will be written [0,1]", typeid(int), (void *) &writeFragCoords, "^[0-1]{1}$"),
PARAM_LEN_SEARCH_START(PARAM_LEN_SEARCH_START_ID,"--len-search-start", "length to search for start codon", "length to search for a start codon before the first exon and in the same frame. By default (0) no search", typeid(int), (void *) &lenSearchStart, "^[0-9]+$")
PARAM_LEN_SCAN_FOR_START(PARAM_LEN_SCAN_FOR_START_ID,"--len-scan-for-start", "length to scan for start codon", "length to scan for a start codon before the first exon and in the same frame. By default (0) no scan", typeid(int), (void *) &lenScanForStart, "^[0-9]+$")

{
collectoptimalset.push_back(&PARAM_METAEUK_EVAL_THR);
Expand Down Expand Up @@ -119,7 +119,7 @@ class LocalParameters : public Parameters {
unitesetstofasta.push_back(&PARAM_TRANSLATION_TABLE);
unitesetstofasta.push_back(&PARAM_WRITE_TKEY);
unitesetstofasta.push_back(&PARAM_WRITE_FRAG_COORDS);
unitesetstofasta.push_back(&PARAM_LEN_SEARCH_START);
unitesetstofasta.push_back(&PARAM_LEN_SCAN_FOR_START);
unitesetstofasta.push_back(&PARAM_MAX_SEQ_LEN);
unitesetstofasta.push_back(&PARAM_THREADS);
unitesetstofasta.push_back(&PARAM_V);
Expand Down Expand Up @@ -155,8 +155,8 @@ class LocalParameters : public Parameters {
// default value 0 means only coords of putative exon are written
writeFragCoords = 0;

// default value 0 means no searching before the first exon
lenSearchStart = 0;
// default value 0 means no scanning before the first exon
lenScanForStart = 0;

citations.emplace(CITATION_METAEUK, "Levy Karin E, Mirdita M, Soeding J: MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics. biorxiv, 851964 (2019).");
}
Expand Down
46 changes: 23 additions & 23 deletions src/exonpredictor/unitesetstofasta.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ int findStartInString (const std::string & seq) {
return(lastPosOfClosestStart);
}

int searchForStartBeforeFirstExon(Prediction & pred, const char* contigData, std::ostringstream & joinedExonsStream, const int searchLen) {
int scanForStartBeforeFirstExon(Prediction & pred, const char* contigData, std::ostringstream & joinedExonsStream, const int scanLen) {
// check if first exon's first codon is start and if so return 0 - already a start codon
if (pred.strand == PLUS) {
std::string firstCodon(&contigData[pred.lowContigCoord], 3);
Expand All @@ -53,34 +53,34 @@ int searchForStartBeforeFirstExon(Prediction & pred, const char* contigData, std
}
}

int seachLenLegal = searchLen - (searchLen % 3);
int scanLenLegal = scanLen - (scanLen % 3);

// case PLUS
int coordToStartSearch = pred.lowContigCoord - seachLenLegal;
int coordToBeginScan = pred.lowContigCoord - scanLenLegal;
int posAfterStopCodon = pred.optimalExonSet[0].potentialExonContigStartBeforeTrim;
// case MINUS
if (pred.strand == MINUS) {
coordToStartSearch = pred.highContigCoord + 1;
coordToBeginScan = pred.highContigCoord + 1;
posAfterStopCodon = pred.optimalExonSet[0].potentialExonContigEndBeforeTrim;
}

// be careful at the edge of the first exon - don't go over stop
// case PLUS
if ((pred.strand == PLUS) && (coordToStartSearch < posAfterStopCodon)) {
coordToStartSearch = posAfterStopCodon;
seachLenLegal = pred.lowContigCoord - coordToStartSearch;
if ((pred.strand == PLUS) && (coordToBeginScan < posAfterStopCodon)) {
coordToBeginScan = posAfterStopCodon;
scanLenLegal = pred.lowContigCoord - coordToBeginScan;
}
// case MINUS
if ((pred.strand == MINUS) && ((posAfterStopCodon - pred.highContigCoord) < (size_t)seachLenLegal)) {
seachLenLegal = (posAfterStopCodon - pred.highContigCoord);
if (seachLenLegal % 3 != 0) {
Debug(Debug::ERROR) << "ERROR: seachLenLegal mod 3 is not 0.\n";
if ((pred.strand == MINUS) && ((posAfterStopCodon - pred.highContigCoord) < (size_t)scanLenLegal)) {
scanLenLegal = (posAfterStopCodon - pred.highContigCoord);
if (scanLenLegal % 3 != 0) {
Debug(Debug::ERROR) << "ERROR: scanLenLegal mod 3 is not 0.\n";
EXIT(EXIT_FAILURE);
}
}

// extract the segment from the contig:
std::string beforeFirstExonSeq(&contigData[coordToStartSearch], (size_t)seachLenLegal);
std::string beforeFirstExonSeq(&contigData[coordToBeginScan], (size_t)scanLenLegal);
std::string beforeFirstExonSeqRevCompSeq(beforeFirstExonSeq);
if (pred.strand == MINUS) {
reverseComplement (beforeFirstExonSeq, beforeFirstExonSeqRevCompSeq);
Expand Down Expand Up @@ -114,7 +114,7 @@ int searchForStartBeforeFirstExon(Prediction & pred, const char* contigData, std

void preparePredDataAndHeader (Prediction & pred, const std::string & targetHeaderAcc, const std::string & contigHeaderAcc,
const char* contigData, std::ostringstream & joinedHeaderStream, std::ostringstream & joinedExonsStream,
const int writeFragCoords, const int lenSearchStart, const size_t contigLen) {
const int writeFragCoords, const int lenScanForStart, const size_t contigLen) {

// clear streams:
joinedHeaderStream.str("");
Expand All @@ -134,13 +134,13 @@ void preparePredDataAndHeader (Prediction & pred, const std::string & targetHead
joinedHeaderStream << "-|";
}
joinedHeaderStream << pred.totalBitscore << "|" << pred.combinedEvalue << "|" << pred.numExons << "|";
if (lenSearchStart == 0) {
// default case: user doesn't want to search for start codon before the first exon:
if (lenScanForStart == 0) {
// default case: user doesn't want to scan for start codon before the first exon:
joinedHeaderStream << pred.lowContigCoord << "|" << pred.highContigCoord;
} else {
// special case: user wants to search for start codon before the first exon:
// special case: user wants to scan for start codon before the first exon:
// if found - padd it up/downstream and indicate the padding != 0 in []
int numNucsAdded = searchForStartBeforeFirstExon(pred, contigData, joinedExonsStream, lenSearchStart);
int numNucsAdded = scanForStartBeforeFirstExon(pred, contigData, joinedExonsStream, lenScanForStart);
if (pred.strand == PLUS) {
joinedHeaderStream << pred.lowContigCoord << "[" << numNucsAdded << "]" << "|" << pred.highContigCoord;
} else {
Expand Down Expand Up @@ -385,8 +385,8 @@ int unitesetstofasta(int argn, const char **argv, const Command& command) {

// for the translated result
TranslateNucl translateNucl(static_cast<TranslateNucl::GenCode>(par.translationTable));
if ((par.translationTable != 1) && (par.lenSearchStart > 0)) {
Debug(Debug::WARNING) << "Selected translation table is not canonical and search for start is turned on. Please note that only ATG/atg is considered a start codon for the search!\n";
if ((par.translationTable != 1) && (par.lenScanForStart > 0)) {
Debug(Debug::WARNING) << "Selected translation table is not canonical and scan for start is turned on. Please note that only ATG/atg is considered a start codon for the scan!\n";
}
// for now, opting to use only ATG/atg as start codon because:
// In Euks ATG is super dominant, unlike proks
Expand Down Expand Up @@ -482,7 +482,7 @@ int unitesetstofasta(int argn, const char **argv, const Command& command) {
}

if (plusPred.optimalExonSet.size() > 0) {
preparePredDataAndHeader(plusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenSearchStart, contigLen);
preparePredDataAndHeader(plusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenScanForStart, contigLen);
std::string result = ">" + joinedHeaderStream.str();
fastaAaWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
fastaCodonWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
Expand Down Expand Up @@ -514,7 +514,7 @@ int unitesetstofasta(int argn, const char **argv, const Command& command) {
fastaCodonWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
}
if (minusPred.optimalExonSet.size() > 0) {
preparePredDataAndHeader(minusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenSearchStart, contigLen);
preparePredDataAndHeader(minusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenScanForStart, contigLen);
std::string result = ">" + joinedHeaderStream.str();
fastaAaWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
fastaCodonWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
Expand Down Expand Up @@ -576,7 +576,7 @@ int unitesetstofasta(int argn, const char **argv, const Command& command) {
}

if (plusPred.optimalExonSet.size() > 0) {
preparePredDataAndHeader(plusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenSearchStart, contigLen);
preparePredDataAndHeader(plusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenScanForStart, contigLen);
std::string result = ">" + joinedHeaderStream.str();
fastaAaWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
fastaCodonWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
Expand Down Expand Up @@ -608,7 +608,7 @@ int unitesetstofasta(int argn, const char **argv, const Command& command) {
fastaCodonWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
}
if (minusPred.optimalExonSet.size() > 0) {
preparePredDataAndHeader(minusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenSearchStart, contigLen);
preparePredDataAndHeader(minusPred, targetHeaderAcc, contigHeaderAcc, contigData, joinedHeaderStream, joinedExonsStream, par.writeFragCoords, par.lenScanForStart, contigLen);
std::string result = ">" + joinedHeaderStream.str();
fastaAaWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
fastaCodonWriter.writeData(result.c_str(), result.size(), 0, thread_idx, false, false);
Expand Down

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