diff --git a/src/ecopcr.c b/src/ecopcr.c index 04a5148..fe40761 100644 --- a/src/ecopcr.c +++ b/src/ecopcr.c @@ -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); } }