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#include <string>
#include "base/CommandLineParser.h"
#include "analysis/DNAVector.h"
#include "base/FileParser.h"
#include "aligns/KmerAlignCore.h"
int main(int argc,char** argv)
{
commandArg<string> aStringCmmd("-t","fasta transcript file");
commandArg<string> bStringCmmd("-i","inchworm file");
commandArg<string> oStringCmmd("-o","output fasta file");
commandLineParser P(argc,argv);
P.SetDescription("Maps chrysalis components to a reference.");
P.registerArg(aStringCmmd);
P.registerArg(bStringCmmd);
P.registerArg(oStringCmmd);
P.parse();
string aString = P.GetStringValueFor(aStringCmmd);
string bString = P.GetStringValueFor(bStringCmmd);
string outFile = P.GetStringValueFor(oStringCmmd);
vecDNAVector ref;
vecDNAVector iworm;
vecDNAVector out;
cout << "Reading files..." << endl;
ref.Read(aString);
iworm.Read(bString);
cout << "done!" << endl;
//test.ReverseComplement();
TranslateBasesToNumberExact trans;
KmerAlignCore core;
core.SetTranslator(&trans);
core.SetNumTables(2);
core.AddData(ref);
//core.SortAll();
size_t i, j;
int min = 24;
int k = 24;
for (i=0; i<iworm.size(); i++) {
const DNAVector & d = iworm[i];
//if (d.isize() > 300)
// continue;
vec<KmerAlignCoreRecord> matchesLeft, matchesRight, matchesMiddle;
int l = d.isize();
core.GetMatches(matchesMiddle, d, l/2-k/2);
if (matchesMiddle.isize() != 0) {
//cout << "Middle match." << endl;
continue;
}
core.GetMatches(matchesLeft, d, 0);
core.GetMatches(matchesRight, d, l-k);
//cout << "left=" << matchesLeft.isize() << " right=" << matchesRight.isize() << endl;
if (matchesLeft.isize() == 0 || matchesRight.isize() == 0)
continue;
if (matchesLeft.isize() > 8 || matchesRight.isize() > 8)
continue;
bool bBad = false;
svec<int> matches;
svec<int> posLeft;
svec<int> posRight;
int diff = d.isize()-k;
for (j=0; j<matchesLeft.isize(); j++) {
int c = matchesLeft[j].GetContig();
int p = matchesLeft[j].GetPosition();
for (int x = 0; x<matchesRight.isize(); x++) {
int cR = matchesRight[x].GetContig();
int pR = matchesRight[x].GetPosition();
if (c != cR)
continue;
//if (iworm.Name(i) == ref.Name(c))
//continue;
int cDiff = pR-p;
int dist = cDiff - diff;
if (dist < 0)
dist = -dist;
if (dist < min) {
bBad = true;
break;
} else {
//cout << "Found dist=" << dist << endl;
matches.push_back(c);
posLeft.push_back(p);
posRight.push_back(pR);
}
}
}
if (bBad)
continue;
if (matches.isize() == 0)
continue;
for (j=0; j<matches.isize(); j++) {
//if (j == 1)
//break;
cout << ref.Name(matches[j]) << "_alt" << endl;
const DNAVector & orig = ref[matches[j]];
DNAVector nn;
nn.resize(orig.isize() + d.isize() - 2*k);
int c = 0;
for (int y=0; y<posLeft[j]; y++) {
cout << orig[y];
//nn[c] = orig[y];
//c++;
}
for (int y=0; y<d.isize(); y++) {
cout << d[y];
//nn[c] = d[y];
//c++;
}
for (int y=posRight[j]+k; y<orig.isize(); y++) {
cout << orig[y];
//nn[c] = orig[y];
//c++;
}
cout << endl;
//out.push_back(nn, ref.Name(matches[j])+"_alt");
}
}
out.Write(outFile);
return 0;
}
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