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Merge pull request #76 from xiaodli/master
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final pro
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@baoxingsong
baoxingsong authored Sep 23, 2024
2 parents 1a599ce + 739e9d0 commit 6b2b2d5
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Showing 3 changed files with 1,337 additions and 244 deletions.
245 changes: 145 additions & 100 deletions src/controlLayer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1484,19 +1484,18 @@ int geno(int argc, char **argv) {
}




int pro(int argc, char **argv) {
double MIN_ALIGNMENT_SCORE = 2;
double GAP_OPEN_PENALTY = -0.02;
double GAP_EXTENSION_PENALTY = -0.005;
int MAX_DIST_BETWEEN_MATCHES = 25;
int refMaximumTimes = 1;
int queryMaximumTimes = 1;
int OVER_LAP_WINDOW = 5;
int delete_tandem = 0;
int OVER_LAP_WINDOW = 0;
int delete_tandem_length = 0;
int get_all_collinear_gene_pair = 0;
int count_style = 1;
int strict_strand = 1;

std::stringstream usage;

Expand All @@ -1512,14 +1511,14 @@ int pro(int argc, char **argv) {
" -E DOUBLE chain gap extend penalty (default: " << GAP_EXTENSION_PENALTY << ")" << std::endl <<
" -I DOUBLE minimum chain score (default: " << MIN_ALIGNMENT_SCORE << ")" << std::endl <<
" -D INT maximum gap size for chain (default: " << MAX_DIST_BETWEEN_MATCHES << ")" << std::endl <<
" -m INT Specify whether to delete tandem gene pairs in the input file (default: " << delete_tandem << ")" << std::endl <<
" Options: 0 to retain tandem gene pairs; 1 or any other integer to delete them." << std::endl <<
" -W INT When -m is set to delete tandem gene pairs(1 or any other integer), " << std::endl <<
" specify the maximum distance allowed between two homologous gene pairs before they are considered for deletion" << "(default: " << OVER_LAP_WINDOW << ")" << std::endl <<
" This parameter is ignored if -m is not set to delete tandem gene pairs(set 0)." << std::endl <<
" -m INT Specify whether to delete tandem gene pairs in the input file (default: " << delete_tandem_length << ")" << std::endl <<
" Options: 0 means retain tandem gene pairs; 1 or any other integer means delete gene pairs with length less than this value)." << std::endl <<
" When you are doing self vs self synteny alignment, we recommend you to delete tandem gene pairs."<< std::endl <<
" -W INT Collapse BLAST matches. Specify the maximum distance allowed, and only retain best homology pair" << "(default: " << OVER_LAP_WINDOW << ")" << std::endl <<
" -a INT Enable this flag to get all collinear results and disable the R and Q parameters (default: " << get_all_collinear_gene_pair << ")" << std::endl <<
" Options: 0:enable R Q parameter; 1 or other integer: all collinear result" << std::endl <<
" -c INT For R Q count, 0: gene number count; 1 or other integer: block count (default: " << count_style << ")"
" -c INT For R Q count, 0: gene number count; 1 or other integer: block count (default: " << count_style << ")" << std::endl <<
" -s INT Specify whether the direction of the gene pair is the same as the block direction (default: "<< strict_strand << ")"
<< std::endl;

InputParser inputParser(argc, argv);
Expand Down Expand Up @@ -1560,10 +1559,16 @@ int pro(int argc, char **argv) {
OVER_LAP_WINDOW = std::stoi(inputParser.getCmdOption("-W"));
}
if (inputParser.cmdOptionExists("-m")) {
delete_tandem = std::stoi(inputParser.getCmdOption("-m"));
delete_tandem_length = std::stoi(inputParser.getCmdOption("-m"));
}
if (inputParser.cmdOptionExists("-s")) {
strict_strand = std::stoi(inputParser.getCmdOption("-s"));
}
if (inputParser.cmdOptionExists("-c")) {
count_style = std::stoi(inputParser.getCmdOption("-c"));
}


std::vector<double> block_score;
std::vector<std::vector<AlignmentMatch>> alignmentMatchsMap;
std::vector<AlignmentMatch> alignmentMatchsMapT;
std::ifstream infile(fakeBlastpResultFile);
Expand All @@ -1572,6 +1577,7 @@ int pro(int argc, char **argv) {
exit(1);
}
std::string line;
int flag = 0;
// prepare data in RAM begin
while (std::getline(infile, line)) {
std::vector<std::string> elems;
Expand All @@ -1596,6 +1602,11 @@ int pro(int argc, char **argv) {
}

if (refGene == queryGene) {
flag = 1;
continue;
}

if (refChr == queryChr && delete_tandem_length != 0 && std::abs(refId -queryId) <= delete_tandem_length && flag == 1) {
continue;
}

Expand All @@ -1608,83 +1619,9 @@ int pro(int argc, char **argv) {
alignmentMatchsMapT.push_back(orthologPair);
}
infile.close();
// prepare data in RAM end
if (delete_tandem !=0 ) {
// sort by querychr refchr querystart(query gene name) and identity/100,respectively.
orthologPairSortQuery(alignmentMatchsMapT);
// filter ref tandem gene by threshold five. This thought comes from MCScanX.
std::vector<AlignmentMatch>::const_iterator it1, prev_pair1;
std::vector<AlignmentMatch> alignmentMatchsMapT_cpy1;
std::vector<AlignmentMatch> match_bin1;
prev_pair1 = it1 = alignmentMatchsMapT.begin();
it1++;
// insert first pair
match_bin1.push_back(*prev_pair1);
// match_bin1[0] has a maximum identity value in the match_bin by orthologPairSortQuery function.
// std::cout << "\t" << "line1606" << "\t" << alignmentMatchsMapT.size() << std::endl;
for (; it1 != alignmentMatchsMapT.end(); it1++) {
if (it1->getRefChr() == prev_pair1->getRefChr() && it1->getQueryChr() == prev_pair1->getQueryChr()) {
if ((it1->getQueryId() != prev_pair1->getQueryId()) ||
(std::abs(it1->getRefId() - prev_pair1->getRefId()) > OVER_LAP_WINDOW)) {
alignmentMatchsMapT_cpy1.push_back(match_bin1[0]);
match_bin1.clear();
}
match_bin1.push_back(*it1);
} else if (it1->getRefChr() != prev_pair1->getRefChr() ||
it1->getQueryChr() != prev_pair1->getQueryChr()) {
alignmentMatchsMapT_cpy1.push_back(match_bin1[0]);
match_bin1.clear();
prev_pair1 = it1;
match_bin1.push_back(*prev_pair1);
continue;
}
prev_pair1 = it1;
}
alignmentMatchsMapT_cpy1.push_back(match_bin1[0]); //the last bin
alignmentMatchsMapT.clear();
alignmentMatchsMapT = alignmentMatchsMapT_cpy1;
// std::cout << "\t" << "line1628" << "\t" << alignmentMatchsMapT.size() << std::endl;
alignmentMatchsMapT_cpy1.clear();

// sort by querychr refchr refstart(ref gene name) and identity/100,respectively.
orthologPairSortReference(alignmentMatchsMapT);
// filter query tandem gene by threshold five. This thought comes from MCScanX.
std::vector<AlignmentMatch>::const_iterator it2, prev_pair2;
std::vector<AlignmentMatch> alignmentMatchsMapT_cpy2;
std::vector<AlignmentMatch> match_bin2;
prev_pair2 = it2 = alignmentMatchsMapT.begin();
it2++;
// insert first pair
match_bin2.push_back(*prev_pair2);
// match_bin2[0] has a maximum identity value in the match_bin by orthologPairSortReference.
// std::cout << "\t" << "line1642" << "\t" << alignmentMatchsMapT.size() << std::endl;
for (; it2 != alignmentMatchsMapT.end(); it2++) {
if (it2->getRefChr() == prev_pair2->getRefChr() && it2->getQueryChr() == prev_pair2->getQueryChr()) {
if ((it2->getRefId() != prev_pair2->getRefId()) ||
(std::abs(it2->getQueryId() - prev_pair2->getQueryId()) > OVER_LAP_WINDOW)) {
alignmentMatchsMapT_cpy2.push_back(match_bin2[0]);
match_bin2.clear();
}
match_bin2.push_back(*it2);
} else if (it1->getRefChr() != prev_pair1->getRefChr() ||
it1->getQueryChr() != prev_pair1->getQueryChr()) {
alignmentMatchsMapT_cpy2.push_back(match_bin2[0]);
match_bin2.clear();
prev_pair2 = it2;
match_bin2.push_back(*prev_pair2);
continue;
}
prev_pair2 = it2;
}
alignmentMatchsMapT_cpy2.push_back(match_bin2[0]);
alignmentMatchsMapT.clear();
alignmentMatchsMapT = alignmentMatchsMapT_cpy2;
// std::cout << "\t" << "line1664" << "\t" << alignmentMatchsMapT.size() << std::endl;
alignmentMatchsMapT_cpy2.clear();
}

// begin setting index, they are necessary in the longest path approach
std::map<std::string, std::map<int, std::string>> queryIndexMap; // chr : index : queryGeneName
std::map <std::string, std::map<int, std::string>> queryIndexMap; // chr : index : queryGeneName
for (const auto &ii: alignmentMatchsMapT) {
if (queryIndexMap.find(ii.getQueryChr()) == queryIndexMap.end()) {
queryIndexMap[ii.getQueryChr()] = std::map<int, std::string>();
Expand All @@ -1697,7 +1634,7 @@ int pro(int argc, char **argv) {
}
}

std::map<std::string, std::map<int, std::string>> refIndexMap; // chr : index : refGeneName
std::map <std::string, std::map<int, std::string>> refIndexMap; // chr : index : refGeneName
for (const auto &ii: alignmentMatchsMapT) {
if (refIndexMap.find(ii.getRefChr()) == refIndexMap.end()) {
refIndexMap[ii.getRefChr()] = std::map<int, std::string>();
Expand All @@ -1710,16 +1647,124 @@ int pro(int argc, char **argv) {
}
}

orthologPairSortPosition(alignmentMatchsMapT);
// std::cout << "\t" << "line1739" << "\t" << alignmentMatchsMapT.size() << std::endl;
std::vector<double> block_score;
// for (AlignmentMatch &ortholog_pair: alignmentMatchsMapT) {
// std::cout << "line1746" << "\t" << ortholog_pair.getQueryChr() << "\t" << ortholog_pair.getQueryGeneName() << "\t" << ortholog_pair.getQueryId() << "\t" << ortholog_pair.getRefChr() << "\t" << ortholog_pair.getReferenceGeneName() << "\t" << ortholog_pair.getRefId() << "\t" << ortholog_pair.getScore() << std::endl;
// }
// exit(1);
longestPathQuotaGene(alignmentMatchsMapT, alignmentMatchsMap, refIndexMap, queryIndexMap,
GAP_EXTENSION_PENALTY, GAP_OPEN_PENALTY, MIN_ALIGNMENT_SCORE, MAX_DIST_BETWEEN_MATCHES,
refMaximumTimes, queryMaximumTimes, block_score, count_style, get_all_collinear_gene_pair);
std::map<std::string, int64_t> refTimes; // key is the gene name
std::map<std::string, int64_t> queryTimes; // key is the gene name
std::map<std::string, std::vector<AlignmentMatch>> groupedMapAlignmentMatch;
std::string kKey="pass";
if (get_all_collinear_gene_pair != 0) {
for (const auto &match : alignmentMatchsMapT){
groupedMapAlignmentMatch[match.getRefChr() + "_" + match.getQueryChr()].push_back(match);
}
alignmentMatchsMapT.clear();
}
else{
for (const auto &match : alignmentMatchsMapT){
groupedMapAlignmentMatch[kKey].push_back(match);
}
alignmentMatchsMapT.clear();
}

for (const auto &subAlignmentMatchT : groupedMapAlignmentMatch) {
alignmentMatchsMapT = subAlignmentMatchT.second;

// prepare data in RAM end
if (OVER_LAP_WINDOW != 0) {
orthologPairSortQuery(alignmentMatchsMapT);
// filter ref fake tandem gene by threshold five. This thought comes from MCScanX.
std::vector<AlignmentMatch>::const_iterator it1, prev_pair1;
std::vector <AlignmentMatch> alignmentMatchsMapT_cpy1;
std::vector <AlignmentMatch> match_bin1;
prev_pair1 = it1 = alignmentMatchsMapT.begin();
it1++;
// insert first pair
match_bin1.push_back(*prev_pair1);
// match_bin1[0] has a maximum identity value in the match_bin.
for (; it1 != alignmentMatchsMapT.end(); it1++) {
if (it1->getRefChr() == prev_pair1->getRefChr() &&
it1->getQueryChr() == prev_pair1->getQueryChr()) {
if ((it1->getQueryId() != prev_pair1->getQueryId()) ||
(std::abs(it1->getRefId() - prev_pair1->getRefId()) > OVER_LAP_WINDOW)) {
orthologPairSortMatchBin(match_bin1);

alignmentMatchsMapT_cpy1.push_back(match_bin1[0]);
match_bin1.clear();
}
match_bin1.push_back(*it1);
} else if (it1->getRefChr() != prev_pair1->getRefChr() ||
it1->getQueryChr() != prev_pair1->getQueryChr()) {
orthologPairSortMatchBin(match_bin1);

alignmentMatchsMapT_cpy1.push_back(match_bin1[0]);
match_bin1.clear();
prev_pair1 = it1;
match_bin1.push_back(*prev_pair1);
continue;
}
prev_pair1 = it1;
}
orthologPairSortMatchBin(match_bin1);

alignmentMatchsMapT_cpy1.push_back(match_bin1[0]);
alignmentMatchsMapT.clear();
alignmentMatchsMapT = alignmentMatchsMapT_cpy1;
alignmentMatchsMapT_cpy1.clear();


orthologPairSortReference(alignmentMatchsMapT);
// filter query fake tandem gene by threshold five. This thought comes from MCScanX.
std::vector<AlignmentMatch>::const_iterator it2, prev_pair2;
std::vector <AlignmentMatch> alignmentMatchsMapT_cpy2;
std::vector <AlignmentMatch> match_bin2;
prev_pair2 = it2 = alignmentMatchsMapT.begin();
it2++;
// insert first pair
match_bin2.push_back(*prev_pair2);
// match_bin2[0] has a maximum identity value in the match_bin.
for (; it2 != alignmentMatchsMapT.end(); it2++) {
if (it2->getRefChr() == prev_pair2->getRefChr() &&
it2->getQueryChr() == prev_pair2->getQueryChr()) {
if ((it2->getRefId() != prev_pair2->getRefId()) ||
(std::abs(it2->getQueryId() - prev_pair2->getQueryId()) > OVER_LAP_WINDOW)) {
orthologPairSortMatchBin(match_bin2);

alignmentMatchsMapT_cpy2.push_back(match_bin2[0]);
match_bin2.clear();
}
match_bin2.push_back(*it2);
} else if (it1->getRefChr() != prev_pair1->getRefChr() ||
it1->getQueryChr() != prev_pair1->getQueryChr()) {
orthologPairSortMatchBin(match_bin2);

alignmentMatchsMapT_cpy2.push_back(match_bin2[0]);
match_bin2.clear();
prev_pair2 = it2;
match_bin2.push_back(*prev_pair2);
continue;
}
prev_pair2 = it2;
}
orthologPairSortMatchBin(match_bin2);

alignmentMatchsMapT_cpy2.push_back(match_bin2[0]);
alignmentMatchsMapT.clear();
alignmentMatchsMapT = alignmentMatchsMapT_cpy2;
alignmentMatchsMapT_cpy2.clear();
}


orthologPairSortPosition(alignmentMatchsMapT);
if (strict_strand != 0) {
longestPathQuotaGene(alignmentMatchsMapT, alignmentMatchsMap, refIndexMap, queryIndexMap,
GAP_EXTENSION_PENALTY, GAP_OPEN_PENALTY, MIN_ALIGNMENT_SCORE,
MAX_DIST_BETWEEN_MATCHES,refMaximumTimes, queryMaximumTimes,
block_score, count_style, get_all_collinear_gene_pair, refTimes, queryTimes);
} else {
longestPathQuotaGeneNonStrand(alignmentMatchsMapT, alignmentMatchsMap, refIndexMap, queryIndexMap,
GAP_EXTENSION_PENALTY, GAP_OPEN_PENALTY, MIN_ALIGNMENT_SCORE,
MAX_DIST_BETWEEN_MATCHES,refMaximumTimes, queryMaximumTimes,
block_score, count_style, get_all_collinear_gene_pair, refTimes, queryTimes);
}
}
// output anchors file.
if (inputParser.cmdOptionExists("-o")) {
std::string wholeCommand = argv[0];
Expand Down Expand Up @@ -1749,7 +1794,7 @@ int pro(int argc, char **argv) {
for (std::vector<AlignmentMatch> v_am: alignmentMatchsMap) {
// if (v_am.size() >= 4) {
std::string plus_minus = "NEGATIVE";
if (v_am[0].getStrand() == POSITIVE) {
if (v_am[0].getQueryId() < v_am[1].getQueryId()) {
plus_minus = "POSITIVE";
}
offile << "##Alignment" << "\t" << blockIndex << "\t" << "N=" << v_am.size() << "\t"
Expand Down Expand Up @@ -1777,7 +1822,6 @@ int pro(int argc, char **argv) {
<< i.getScore() << std::endl;
totalAnchors++;
}
// }
}
offile.close();
std::cout << "totalAnchors:" << totalAnchors << std::endl;
Expand All @@ -1788,3 +1832,4 @@ int pro(int argc, char **argv) {
}
return 0;
}

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