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Patch minimum tm computation

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Add -A option to list all id present in the DB for helping in -R usage

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@228 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-07-18 22:16:18 +00:00
parent 455bf63949
commit 419bda966d
7 changed files with 196 additions and 122 deletions
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70
src/ecoprimer.c
View File

@ -28,36 +28,6 @@ static int cmpprintedpairs(const void* p1,const void* p2);
void* lib_handle = NULL;
float (*calcMelTemp)(char*, char*);
void openlibman ()
{
// Open the library.
char* lib_name = "./libPHunterLib.dylib";
lib_handle = dlopen(lib_name, RTLD_NOW);
if (lib_handle) {
fprintf(stderr, "[%s] dlopen(\"%s\", RTLD_NOW): Successful\n", __FILE__, lib_name);
}
else {
fprintf(stderr, "[%s] Unable to open library: %s\n",
__FILE__, dlerror());
exit(EXIT_FAILURE);
}
// Get the symbol addresses.
calcMelTemp = dlsym(lib_handle, "_Z27calculateMeltingTemperaturePcS_");
if (calcMelTemp) {
fprintf(stderr, "[%s] dlsym(lib_handle, \"addRating\"): Successful\n", __FILE__);
}
else {
fprintf(stderr, "[%s] Unable to get symbol: %s\n",
__FILE__, dlerror());
exit(EXIT_FAILURE);
}
}
void closlibman ()
{
if (lib_handle) dlclose(lib_handle);
}
/* ----------------------------------------------- */
/* printout help */
/* ----------------------------------------------- */
@ -159,6 +129,7 @@ void initoptions(poptions_t options)
strcpy(options->taxonrank, DEFAULTTAXONRANK); /*taxon level for results, species by default*/
options->saltmethod = SALT_METHOD_SANTALUCIA;
options->salt = DEF_SALT;
options->printAC=FALSE;
}
void printapair(int32_t index,ppair_t pair, poptions_t options)
@ -220,16 +191,16 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
printf("%s", p2);
//print primer1 melting temperature
printf ("\t%4.3f", pair->p1temp);
printf ("\t%3.1f", pair->p1temp);
//print minimum melting temperature of approximate versions of primer1
printf ("\t%4.3f", pair->p1mintemp);
printf ("\t%3.1f", pair->p1mintemp);
//print primer2 melting temperature
printf ("\t%4.3f", pair->p2temp);
printf ("\t%3.1f", pair->p2temp);
//print minimum melting temperature of approximate versions of primer2
printf ("\t%4.3f", pair->p2mintemp);
printf ("\t%3.1f", pair->p2mintemp);
//print gc contents of primer1
printf ("\t%d",nparam_CountGCContent(p1));
@ -508,6 +479,13 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
}
/* to get db stats, totals of species, genus etc....*/
static void printAC(pecodnadb_t seqdb,uint32_t seqdbsize)
{
uint32_t i;
for (i=0; i< seqdbsize;i++)
printf("%15s : %s\n",seqdb[i]->AC,seqdb[i]->DE);
}
int main(int argc, char **argv)
{
@ -530,22 +508,11 @@ int main(int argc, char **argv)
int32_t rankdbstats = 0;
//printcurrenttime();
//return 0;
//openlibman ();
//float temp = calculateMeltingTemperature ("GGTCTGAACTCAGATCAC", "CTGTTTACCAAAAACATC");
//float temp = calculateMeltingTemperatureBasic ("CTGTTTACCAAAAACATC");
//printf ("temp = %f\n", temp);
//return 0;
//char *t = "ACGT";
//printf ("\nGETNUMCODE: A=%d, C=%d, G=%d, T=%d\n", GETNUMCODE(t[0]), GETNUMCODE('C'), GETNUMCODE('G'), GETNUMCODE('T'));
//printf ("\nGETREVCODE: A=%d, C=%d, G=%d, T=%d\n", GETREVCODE(t[0]), GETREVCODE('C'), GETREVCODE('G'), GETREVCODE('T'));
//return 0;
CNNParams nnparams;
initoptions(&options);
while ((carg = getopt(argc, argv, "hfvcUDSd:l:L:e:i:r:R:q:3:s:x:t:O:m:a:")) != -1) {
while ((carg = getopt(argc, argv, "hAfvcUDSd:l:L:e:i:r:R:q:3:s:x:t:O:m:a:")) != -1) {
switch (carg) {
/* ---------------------------- */
@ -558,6 +525,12 @@ int main(int argc, char **argv)
case 'f': /* set in single strand mode */
/* ---------------------------- */
options.filtering=FALSE;
break;
/* ---------------------------- */
case 'A': /* set in single strand mode */
/* ---------------------------- */
options.printAC=TRUE;
break;
/* -------------------- */
@ -719,6 +692,11 @@ int main(int argc, char **argv)
seqdb = readdnadb(options.prefix,&seqdbsize);
if (options.printAC)
{
printAC(seqdb,seqdbsize);
exit(0);
}
if (options.reference)
for (i=0; i < seqdbsize;i++)
if (strcmp(seqdb[i]->AC,options.reference)==0)

3
src/libecoprimer/aproxpattern.c
View File

@ -97,7 +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 = (1 << options->strict_three_prime) -1;
params.omask = 0;
params.patlen = options->primer_length;
positions.val=NULL;

8
src/libecoprimer/ecoprimer.h
View File

@ -86,7 +86,8 @@ typedef struct {
typedef union {
uint32_t *pointer;
uint32_t value;
} poslist_t, *ppostlist_t;
} poslist_t, *pposlist_t;
/**
* primer_t structure store fuzzy match positions for a primer
@ -96,10 +97,10 @@ typedef union {
typedef struct {
word_t word; //< code for the primer
uint32_t *directCount; //< Occurrence count on direct strand
ppostlist_t directPos; //< list of position list on direct strand
pposlist_t directPos; //< list of position list on direct strand
uint32_t *reverseCount; //< Occurrence count on reverse strand
ppostlist_t reversePos; //< list of position list on reverse strand
pposlist_t reversePos; //< list of position list on reverse strand
bool_t good; //< primer match more than quorum example and no
// more counterexample quorum.
@ -246,6 +247,7 @@ typedef struct {
}taxontoamp_t, *ptaxontoamp_t;
typedef struct {
bool_t printAC;
bool_t statistics;
bool_t filtering;
uint32_t lmin; //**< Amplifia minimal length

49
src/libthermo/nnparams.c
View File

@ -521,16 +521,57 @@ float nparam_CalcSelfTM(PNNParams nparm, char* seq, int len)
nparam_CleanSeq (seq, nseq, len);
useq = nseq;
int slen = strlen(useq);
//fprintf (stderr,"Primer : %s\n",useq);
for ( i=1;i<slen;i++)
for ( i=1;i<len;i++)
{
c1 = GETREVCODE(useq[i-1]); //nparam_getComplement(seq[i-1],1);
c2 = GETREVCODE(useq[i]); //nparam_getComplement(seq[i],1);
c3 = GETNUMCODE(useq[i-1]);
c4 = GETNUMCODE(useq[i]);
thedH += nparm->dH[c3][c4][c1][c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
}
// printf("------------------\n");
mtemp = nparam_CalcTM(thedS,thedH);
//if (mtemp == 0)
//{
// fprintf(stderr,"Enthalpy: %f, entropy: %f, seq: %s\n", thedH, thedS, useq);
//exit (0);
//}
return mtemp;
}
float nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len)
{
float thedH = 0;
//float thedS = nparam_GetInitialEntropy(nparm);
float thedS = -5.9f+nparm->rlogc;
float mtemp;
char c1;
char c2;
char c3;
char c4;
unsigned int i;
char nseq1[50];
char nseq2[50];
char *useq1;
char *useq2;
nparam_CleanSeq (seq1, nseq1, len);
useq1 = nseq1;
nparam_CleanSeq (seq2, nseq2, len);
useq2 = nseq2;
//fprintf (stderr,"Primer : %s\n",useq);
for ( i=1;i<len;i++)
{
c1 = GETREVCODE(useq2[i-1]); //nparam_getComplement(seq[i-1],1);
c2 = GETREVCODE(useq2[i]); //nparam_getComplement(seq[i],1);
c3 = GETNUMCODE(useq1[i-1]);
c4 = GETNUMCODE(useq1[i]);
//fprintf (stderr,"Primer : %s %f %f %d %d, %d %d %f\n",useq,thedH,thedS,(int)c3,(int)c4,(int)c1,(int)c2,nparam_GetEnthalpy(nparm, c3,c4,c1,c2));
thedH += nparm->dH[c3][c4][c1][c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);

2
src/libthermo/nnparams.h
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@ -63,6 +63,8 @@ float nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
float nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
float nparam_CalcTM(float entropy,float enthalpy);
float nparam_CalcSelfTM(PNNParams nparm, char* seq, int len);
float nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len);
float nparam_GetInitialEntropy(PNNParams nparm) ;
float calculateMeltingTemperatureBasic (char * seq);
//void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);

78
src/libthermo/thermostats.c
View File

@ -4,16 +4,42 @@
#include <stdlib.h>
#include "thermostats.h"
static word_t extractSite(char* sequence,
size_t begin, size_t length, bool_t strand)
{
char *c;
char *start;
uint32_t l;
word_t site = 0;
start=sequence+begin;
if (!strand)
start+=length-1;
for (c=start,
l=0;
l<length;
l++,
c+=(strand)? 1:-1)
site = (site << 2) | ((strand)? (*c):(~*c)&3);
return site;
}
void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options)
{
size_t i, j;
uint32_t begin;
uint32_t end;
size_t i, j,k,l;
uint32_t bp1,bp2;
uint32_t ep1,ep2;
word_t w1;
word_t w2;
bool_t strand;
char *sq;
char prmr[50];
char *sq,*sq1,*sq2,*c;
char prmrd[50];
char prmrr[50];
char sqsite[50];
float mtemp;
for (i = 0; i < count; i++)
@ -27,24 +53,48 @@ void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options)
if (!pairs[i]->asdirect2)
w2=ecoComplementWord(w2,options->primer_length);
pairs[i]->p1temp = nparam_CalcSelfTM (options->pnparm, ecoUnhashWord(w1, options->primer_length), 0) - 273.0;
pairs[i]->p2temp = nparam_CalcSelfTM (options->pnparm, ecoUnhashWord(w2, options->primer_length), 0) - 273.0;
strncpy(prmrd,ecoUnhashWord(w1, options->primer_length),options->primer_length);
strncpy(prmrr,ecoUnhashWord(w2, options->primer_length),options->primer_length);
prmrd[options->primer_length]=0;
prmrr[options->primer_length]=0;
pairs[i]->p1temp = nparam_CalcSelfTM (options->pnparm, prmrd, options->primer_length) - 273.0;
pairs[i]->p2temp = nparam_CalcSelfTM (options->pnparm, prmrr, options->primer_length) - 273.0;
pairs[i]->p1mintemp = 100;
pairs[i]->p2mintemp = 100;
for (j = 0; j < pairs[i]->pcr.ampcount; j++)
{
sq = pairs[i]->pcr.amplifias[j].sequence->SQ;
begin = pairs[i]->pcr.amplifias[j].begin - options->primer_length;
end = pairs[i]->pcr.amplifias[j].end + 1;
strand = pairs[i]->pcr.amplifias[j].strand;
bp1 = pairs[i]->pcr.amplifias[j].begin - options->primer_length;
bp2 = pairs[i]->pcr.amplifias[j].end + 1;
memcpy (prmr, sq + begin, options->primer_length);
mtemp = nparam_CalcSelfTM (options->pnparm, prmr, options->primer_length) - 273.0;
if (!strand)
{
uint32_t tmp;
tmp=bp1;
bp1=bp2;
bp2=tmp;
}
// printf("%s : %s, %c",prmrd,
// ecoUnhashWord(extractSite(sq,bp1,options->primer_length,strand),options->primer_length),
// "rd"[strand]);
mtemp = nparam_CalcTwoTM(options->pnparm,
prmrd,
ecoUnhashWord(extractSite(sq,bp1,options->primer_length,strand),options->primer_length),
options->primer_length) - 273.0;
// printf(" %4.2f %4.2f\n",pairs[i]->p1temp,mtemp);
if (mtemp < pairs[i]->p1mintemp)
pairs[i]->p1mintemp = mtemp;
//fprintf (stderr, "prmr1: %s\n", seqdb[seqid]->SQ);
memcpy (prmr, sq + end, options->primer_length);
mtemp = nparam_CalcSelfTM (options->pnparm, prmr, options->primer_length) - 273.0;
// printf("%s : %s, %c\n",prmrr,ecoUnhashWord(extractSite(sq,bp2,options->primer_length,!strand),options->primer_length),
// "rd"[strand]);
//
mtemp = nparam_CalcTwoTM(options->pnparm,
prmrr,
ecoUnhashWord(extractSite(sq,bp2,options->primer_length,!strand),options->primer_length),
options->primer_length) - 273.0;
if (mtemp < pairs[i]->p2mintemp)
pairs[i]->p2mintemp = mtemp;
}