obitools/ecopcr
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removed the "without temperature" option

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@416 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Céline Mercier
2012-05-04 14:53:33 +00:00
parent 4e5d8893e5
commit 93c530e090
1 changed files with 20 additions and 58 deletions
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78
src/ecopcr.c
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@ -45,8 +45,6 @@ static void PrintHelp()
PP " Taxonomy id are available using the ecofind program.\n");
PP " see its help typing ecofind -h for more information.\n");
PP "-c : Consider that the database sequences are [c]ircular\n");
PP "-t : don't calculate tm (backward compatibility with old ecoPCR\n");
PP " output file format)\n");
PP "-m : Salt correction method for Tm computation (SANTALUCIA : 1\n");
PP " or OWCZARZY:2, default=1)\n\n");
PP "-a : Salt contentration in M for Tm computation (default 0.05 M)\n\n");
@ -107,7 +105,6 @@ static void ExitUsage(stat)
void printRepeat(ecoseq_t *seq,
char* primer1, char* primer2,
char compute_tm,
PNNParams tparm,
PatternPtr o1, PatternPtr o2,
char strand,
@ -267,38 +264,10 @@ void printRepeat(ecoseq_t *seq,
}
if (compute_tm)
{
tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
tm = (tm1 < tm2) ? tm1:tm2;
printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %5.2f | %-32s | %2d | %5.2f | %5d | %s | %s\n",
AC,
seqlength,
taxid,
rank,
species_taxid,
scientificName,
genus_taxid,
genus_name,
family_taxid,
family_name,
superkingdom_taxid,
superkingdom_name,
strand,
oligo1,
error1,
tm1,
oligo2,
error2,
tm2,
amplength - o1->patlen - o2->patlen,
amplifia,
seq->DE
);
}
else
printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %-32s | %2d | %5d | %s | %s\n",
tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
tm = (tm1 < tm2) ? tm1:tm2;
printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %5.2f | %-32s | %2d | %5.2f | %5d | %s | %s\n",
AC,
seqlength,
taxid,
@ -314,12 +283,15 @@ void printRepeat(ecoseq_t *seq,
strand,
oligo1,
error1,
tm1,
oligo2,
error2,
tm2,
amplength - o1->patlen - o2->patlen,
amplifia,
seq->DE
);
}
int main(int argc, char **argv)
@ -377,7 +349,6 @@ int main(int argc, char **argv)
int32_t g=0;
int32_t circular=0;
char compute_tm=1;
int32_t saltmethod=SALT_METHOD_SANTALUCIA;
double salt=0.05;
CNNParams tparm;
@ -453,22 +424,17 @@ int main(int argc, char **argv)
circular = 1;
break;
/* --------------------------- */
case 't': /* compute tm of amplification */
compute_tm = 0; /* --------------------------- */
break;
/* --------------------------------- */
case 'm': /* set salt method */
/* --------------------------------- */
sscanf(optarg,"%d",&(saltmethod));
compute_tm = 1;
break;
/* --------------------------------- */
case 'a': /* set salt */
/* --------------------------------- */
sscanf(optarg,"%lf",&(salt));
compute_tm = 1;
break;
case '?': /* bad option */
@ -509,11 +475,10 @@ int main(int argc, char **argv)
errflag++;
}
if (compute_tm)
nparam_InitParams(&tparm,DEF_CONC_PRIMERS,
DEF_CONC_PRIMERS,
salt,
saltmethod);
nparam_InitParams(&tparm,DEF_CONC_PRIMERS,
DEF_CONC_PRIMERS,
salt,
saltmethod);
if (!oligo1 || !oligo2)
errflag++;
@ -534,17 +499,14 @@ int main(int argc, char **argv)
printf("# reverse strand oligo2 : %-32s ; oligo1c : %32s\n", o2->cpat,o1c->cpat);
printf("# max error count by oligonucleotide : %d\n",error_max);
if (compute_tm)
{
double tm,tm1,tm2;
double tm,tm1,tm2;
tm1=nparam_CalcSelfTM(&tparm,o1->cpat,o1->patlen) - 273.15;
tm2=nparam_CalcSelfTM(&tparm,o2->cpat,o2->patlen) - 273.15;
tm = (tm1 < tm2) ? tm1:tm2;
tm1=nparam_CalcSelfTM(&tparm,o1->cpat,o1->patlen) - 273.15;
tm2=nparam_CalcSelfTM(&tparm,o2->cpat,o2->patlen) - 273.15;
tm = (tm1 < tm2) ? tm1:tm2;
printf("# optimal Tm for primers 1 : %5.2f\n",tm1);
printf("# optimal Tm for primers 2 : %5.2f\n",tm2);
}
printf("# optimal Tm for primers 1 : %5.2f\n",tm1);
printf("# optimal Tm for primers 2 : %5.2f\n",tm2);
printf("# database : %s\n",prefix);
if (lmin && lmax)
@ -646,7 +608,7 @@ int main(int argc, char **argv)
if (length &&
(!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax)))
printRepeat(seq,oligo1,oligo2,compute_tm,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
}
@ -700,7 +662,7 @@ int main(int argc, char **argv)
if (length &&
(!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax)))
printRepeat(seq,oligo1,oligo2,compute_tm,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);
}
}