New version 0.2 of ecoPCR, with Tm computation.
Take care file format have change. You must use corresponding version of ecogrep You can use -t option to go back to the old format without tm computation git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@238 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
108
src/ecopcr.c
108
src/ecopcr.c
@ -1,11 +1,13 @@
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#include "libecoPCR/ecoPCR.h"
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#include "libthermo/nnparams.h"
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#include <stdio.h>
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#include <string.h>
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#include <stdlib.h>
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#include <getopt.h>
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#define VERSION "0.1"
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#define VERSION "0.2"
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/* ----------------------------------------------- */
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/* printout help */
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@ -42,7 +44,12 @@ static void PrintHelp()
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PP "-r : [R]estricts the search to the given taxonomic id.\n");
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PP " Taxonomy id are available using the ecofind program.\n");
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PP " see its help typing ecofind -h for more information.\n");
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PP "-c : Consider that the database sequences are [c]ircular");
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PP "-c : Consider that the database sequences are [c]ircular\n");
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PP "-t : don't calculate tm (backward compatibility with old ecoPCR\n");
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PP " output file format)\n");
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PP "-m : Salt correction method for Tm computation (SANTALUCIA : 1\n");
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PP " or OWCZARZY:2, default=1)\n\n");
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PP "-a : Salt contentration in M for Tm computation (default 0.05 M)\n\n");
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PP "\n");
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PP "------------------------------------------\n");
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PP "first argument : oligonucleotide for direct strand\n\n");
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@ -64,11 +71,13 @@ static void PrintHelp()
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PP "column 13 : strand (direct or reverse)\n");
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PP "column 14 : first oligonucleotide\n");
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PP "column 15 : number of errors for the first strand\n");
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PP "column 16 : second oligonucleotide\n");
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PP "column 17 : number of errors for the second strand\n");
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PP "column 18 : amplification length\n");
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PP "column 19 : sequence\n");
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PP "column 20 : definition\n");
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PP "column 16 : Tm for hybridization of primer 1 at this site\n");
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PP "column 17 : second oligonucleotide\n");
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PP "column 18 : number of errors for the second strand\n");
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PP "column 19 : Tm for hybridization of primer 1 at this site\n");
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PP "column 20 : amplification length\n");
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PP "column 21 : sequence\n");
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PP "column 22 : definition\n");
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PP "------------------------------------------\n");
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PP " http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
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PP "------------------------------------------\n\n");
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@ -97,6 +106,9 @@ static void ExitUsage(stat)
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#undef PP
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void printRepeat(ecoseq_t *seq,
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char* primer1, char* primer2,
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char compute_tm,
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PNNParams tparm,
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PatternPtr o1, PatternPtr o2,
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char strand,
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char kingdom,
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@ -128,6 +140,8 @@ void printRepeat(ecoseq_t *seq,
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char *amplifia = NULL;
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int32_t amplength;
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double tm1,tm2;
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double tm=0;
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AC = seq->AC;
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seqlength = seq->SQ_length;
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@ -222,7 +236,38 @@ void printRepeat(ecoseq_t *seq,
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ecoComplementSequence(oligo2);
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amplifia[amplength - o2->patlen - o1->patlen]=0;
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printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %-32s | %2d | %5d | %s | %s\n",
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if (compute_tm)
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{
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tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
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tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
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tm = (tm1 < tm2) ? tm1:tm2;
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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",
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AC,
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seqlength,
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taxid,
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rank,
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species_taxid,
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scientificName,
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genus_taxid,
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genus_name,
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family_taxid,
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family_name,
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superkingdom_taxid,
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superkingdom_name,
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strand,
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oligo1,
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error1,
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tm1,
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oligo2,
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error2,
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tm2,
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amplength - o1->patlen - o2->patlen,
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amplifia,
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seq->DE
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);
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}
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else
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printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %-32s | %2d | %5d | %s | %s\n",
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AC,
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seqlength,
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taxid,
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@ -300,8 +345,12 @@ int main(int argc, char **argv)
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int32_t g=0;
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int32_t circular=0;
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char compute_tm=0;
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int32_t saltmethod=SALT_METHOD_SANTALUCIA;
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double salt=0.05;
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CNNParams tparm;
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while ((carg = getopt(argc, argv, "hcd:l:L:e:i:r:k")) != -1) {
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while ((carg = getopt(argc, argv, "hcd:l:L:e:i:r:km:a:t")) != -1) {
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switch (carg) {
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/* -------------------- */
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@ -366,7 +415,25 @@ int main(int argc, char **argv)
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circular = 1;
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break;
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case '?': /* bad option */
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/* --------------------------- */
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case 't': /* compute tm of amplification */
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compute_tm = 1; /* --------------------------- */
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break;
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/* --------------------------------- */
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case 'm': /* set salt method */
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/* --------------------------------- */
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sscanf(optarg,"%d",&(saltmethod));
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compute_tm = 1;
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break;
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/* --------------------------------- */
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case 'a': /* set salt */
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/* --------------------------------- */
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sscanf(optarg,"%lf",&(salt));
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compute_tm = 1;
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break;
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case '?': /* bad option */
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/* -------------------- */
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errflag++;
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}
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@ -404,6 +471,11 @@ int main(int argc, char **argv)
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errflag++;
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}
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if (compute_tm)
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nparam_InitParams(&tparm,DEF_CONC_PRIMERS,
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DEF_CONC_PRIMERS,
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salt,
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saltmethod);
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if (!oligo1 || !oligo2)
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errflag++;
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@ -423,6 +495,18 @@ int main(int argc, char **argv)
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printf("# reverse strand oligo2 : %-32s ; oligo1c : %32s\n", o2->cpat,o1c->cpat);
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printf("# max error count by oligonucleotide : %d\n",error_max);
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if (compute_tm)
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{
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double tm,tm1,tm2;
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tm1=nparam_CalcSelfTM(&tparm,o1->cpat,o1->patlen) - 273.15;
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tm2=nparam_CalcSelfTM(&tparm,o2->cpat,o2->patlen) - 273.15;
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tm = (tm1 < tm2) ? tm1:tm2;
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printf("# optimal Tm for primers 1 : %5.2f\n",tm1);
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printf("# optimal Tm for primers 2 : %5.2f\n",tm2);
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}
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printf("# database : %s\n",prefix);
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if (lmin && lmax)
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printf("# amplifiat length between [%d,%d] bp\n",lmin,lmax);
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@ -523,7 +607,7 @@ int main(int argc, char **argv)
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if (length &&
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(!lmin || (length >= lmin)) &&
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(!lmax || (length <= lmax)))
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printRepeat(seq,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy);
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printRepeat(seq,oligo1,oligo2,compute_tm,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy);
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//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);
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}
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@ -577,7 +661,7 @@ int main(int argc, char **argv)
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if (length &&
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(!lmin || (length >= lmin)) &&
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(!lmax || (length <= lmax)))
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printRepeat(seq,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy);
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printRepeat(seq,oligo1,oligo2,compute_tm,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy);
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//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);
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}
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}
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