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// comments added a posteriori, 1 year later:
// script that keeps reads if they match at least one kmer from a contig file
// probably this was done for multi-k optimization?
// to compile it is a bit tricky: go to dsk repository, put that script in dsk/utils folder and use that CMakeLists file: https://github.com/GATB/dsk/blob/12de3e1f49e04f372b80773e7c4bc829c28e5657/utils/CMakeLists.txt
#include <gatb/gatb_core.hpp>
#include <fstream>
#include <set>
// We use the required packages
using namespace std;
static /* probably important that it's static here too */
char revcomp (char s) {
if (s == 'A') return 'T';
else if (s == 'C') return 'G';
else if (s == 'G') return 'C';
else if (s == 'T') return 'A';
else if (s == 'a') return 't';
else if (s == 'c') return 'g';
else if (s == 'g') return 'c';
else if (s == 't') return 'a';
return 'X';
}
static string revcomp (const string &s) {
string rc;
for (signed int i = s.length() - 1; i >= 0; i--) {rc += revcomp(s[i]);}
return rc;
}
/********************************************************************************/
class FilterByPreviousContigs : public Tool
{
public:
/** */
FilterByPreviousContigs () : Tool ("filter_by_previous_contigs")
{
getParser()->push_front (new OptionOneParam ("-previous-contigs", "previous contigs" , true));
getParser()->push_front (new OptionOneParam ("-reads", "reads" , true));
getParser()->push_front (new OptionOneParam (STR_KMER_SIZE, "k-mer size used to generate previous contigs" , true));
getParser()->push_front (new OptionOneParam ("-out", "output file that will contain filtered reads", true));
}
/** */
void execute ()
{
size_t kmerSize = getInput()->getInt (STR_KMER_SIZE);
Integer::apply<Functor,Parameter> (kmerSize, Parameter(*this, kmerSize));
}
struct Parameter
{
Parameter (FilterByPreviousContigs& tool, size_t kmerSize) : tool(tool), kmerSize(kmerSize) {}
FilterByPreviousContigs& tool;
size_t kmerSize;
};
template<size_t span> struct Functor { void operator () (Parameter parameter)
{
FilterByPreviousContigs& tool = parameter.tool;
size_t kmerSize = parameter.kmerSize;
unsigned int k = kmerSize;
typedef typename Kmer<span>::Count Count;
typename Kmer<span>::ModelCanonical model (kmerSize);
BankFasta bank(tool.getInput()->getStr("-previous-contigs"));
IBank* bankReads = Bank::open(tool.getInput()->getStr("-reads"));
BankFasta bankOut(tool.getInput()->getStr("-out"));
BankFasta::Iterator itCtg (bank);
set<string> kmers;
std::cout << "indexing previous contigs" << std::endl;
for (itCtg.first(); !itCtg.isDone(); itCtg.next())
{
string seq = itCtg->toString();
string kmerBegin = seq.substr(0, k );
string kmerEnd = seq.substr(seq.size() - k , k );
kmers.insert(kmerBegin);
kmers.insert(kmerEnd);
kmers.insert(revcomp(kmerBegin));
kmers.insert(revcomp(kmerEnd));
}
std::cout << "filtering reads" << std::endl;
Iterator<Sequence>* itReads = bankReads->iterator();
uint64_t nb_reads = 0, nb_kept = 0;
for (itReads->first(); !itReads->isDone(); itReads->next())
{
bool contains = false;
string seq = (*itReads)->toString();
nb_reads++;
int found_pos = 0;
for (int i = 0; i < seq.size() - k; i++)
{
string kmer = seq.substr(i, k );
contains = (kmers.find(kmer) != kmers.end());
if (contains)
{
found_pos = i;
break;
}
}
if (contains)
{
Sequence s (Data::ASCII);
s.getData().setRef ((char*)seq.c_str(), seq.size());
s._comment = (*itReads)->getComment() + " contains previous-k kmer at pos " + to_string(found_pos);
bankOut.insert(s);
nb_kept++;
}
}
std::cout << "done filtering reads, kept " << nb_kept << "/" << nb_reads << std::endl;
/** We gather some statistics. */
tool.getInfo()->add (1, "stats");
tool.getInfo()->add (2, "kmer_size", "%ld", kmerSize);
}};
};
/********************************************************************************/
/* Dump solid kmers in ASCII format */
/********************************************************************************/
int main (int argc, char* argv[])
{
/* try
{*/
FilterByPreviousContigs().run (argc, argv);
/* }
catch (Exception& e)
{
std::cout << "EXCEPTION: " << e.getMessage() << std::endl;
return EXIT_FAILURE;
}*/
// gdb likes having clean exceptions
}
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