Commit 1911880b by Eric Coissac

Added Code to make sure that if -3 option is given then 3' end must match upto…

Added Code to make sure that if -3 option is given then 3' end must match upto given number of base pairs

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@231 60f365c0-8329-0410-b2a4-ec073aeeaa1d
parent 494791d1
......@@ -777,7 +777,6 @@ int main(int argc, char **argv)
pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
printpairs (pairs, &options,taxonomy);
// closlibman ();
return 0;
}
......@@ -97,8 +97,8 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
params.circular = options->circular;
params.maxerr = options->error_max;
params.omask = (1 << options->strict_three_prime) -1;
// params.omask = 0;
// params.omask = (1 << options->strict_three_prime) -1;
params.omask = 0;
params.patlen = options->primer_length;
positions.val=NULL;
......
......@@ -8,6 +8,7 @@
#include "ecoprimer.h"
#include <string.h>
#include <stdlib.h>
#include "../libthermo/thermostats.h"
static void buildPrimerPairsForOneSeq(uint32_t seqid,
pecodnadb_t seqdb,
......@@ -187,6 +188,9 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
bool_t strand;
//char prmr[50];
//float mtemp;
word_t w1, w1a, omask = (0x1L << options->strict_three_prime) -1;;
word_t w2, w2a, wtmp;
uint32_t bp1,bp2;
//prmr[options->primer_length] = '\0';
......@@ -292,6 +296,42 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
current.asdirect2=bswp;
}
//Code to make sure that if -3 option is given then
//3' end must match upto given number of base pairs
if (options->strict_three_prime > 0)
{
w1 = current.p1->word;
w2 = current.p2->word;
if (!current.asdirect1) //make sure that word is from 5' to 3'
w1=ecoComplementWord(w1,options->primer_length);
if (!current.asdirect2) //make sure that word is from 5' to 3'
w2=ecoComplementWord(w2,options->primer_length);
//now both w1 and w2 are from 5' to 3' end
bp1 = matches[i].position;
bp2 = matches[j].position;
if (!strand)
{
bp1 = matches[j].position;
bp2 = matches[i].position;
}
//get word of first approximate repeat
w1a = extractSite(seqdb[seqid]->SQ,bp1,options->primer_length,strand);
//get word of second approximate repeat
w2a = extractSite(seqdb[seqid]->SQ,bp2,options->primer_length,!strand);
w1 = w1 & omask; //keep only strict_three_prime bases on the right (3') end
w2 = w2 & omask; //keep only strict_three_prime bases on the right (3') end
w1a = w1a & omask; //keep only strict_three_prime bases on the right (3') end
w2a = w2a & omask; //keep only strict_three_prime bases on the right (3') end
//now check that both words and primers of amplifia have same bases on 3' end
if (w1 ^ w1a != 0) continue;
else if (w2 ^ w2a != 0) continue;
}
// Look for the new pair in already seen pairs
......
......@@ -4,8 +4,7 @@
#include <stdlib.h>
#include "thermostats.h"
static word_t extractSite(char* sequence,
size_t begin, size_t length, bool_t strand)
word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand)
{
char *c;
char *start;
......
......@@ -4,5 +4,6 @@
#include "../libecoprimer/ecoprimer.h"
void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand);
#endif
\ No newline at end of file
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