add a -k option to the ecoPCR binary to substitute superkingdom column by a kingdom column

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@11 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/ecopcr.c

@@ -135,6 +135,7 @@ static void ExitUsage(stat)
 void printRepeat(ecoseq_t *seq,
                  PatternPtr o1, PatternPtr o2,
                  char strand, 
+                 char kingdom,
                  int32_t pos1, int32_t pos2,
                  int32_t err1, int32_t err2,
                  ecotaxonomy_t *taxonomy)
@@ -204,7 +205,11 @@ void printRepeat(ecoseq_t *seq,
 			family_name  = "###";
 		}
 	
+	if (kingdom)
+		taxon         = eco_getkingdom((taxon) ? taxon:main_taxon,taxonomy);
+	else
 		taxon         = eco_getsuperkingdom((taxon) ? taxon:main_taxon,taxonomy);
+		
 	if (taxon)
 		{
 			superkingdom_taxid = taxon->taxid;
@@ -299,6 +304,7 @@ int main(int argc, char **argv)
 	int32_t       lmax=0;
 	int32_t       error_max=0;
 	int32_t       errflag=0;
+	char          kingdom_mode=0;
 	
 	char          *prefix;
 	
@@ -325,7 +331,7 @@ int main(int argc, char **argv)
 	int32_t		  errj;
 	
 	
-    while ((carg = getopt(argc, argv, "h1:2:l:L:e:")) != -1) {
+    while ((carg = getopt(argc, argv, "h1:2:l:L:e:k")) != -1) {
 
      switch (carg) {
                                 /* -------------------- */
@@ -368,6 +374,11 @@ int main(int argc, char **argv)
         case 'e':               /* error max            */
                                 /* -------------------- */
           sscanf(optarg,"%d",&error_max);
+          break;
+          
+        case 'k':               /* error max            */
+                                /* -------------------- */
+          kingdom_mode = 1;
           break;
           
                                 /* -------------------- */
@@ -462,7 +473,7 @@ int main(int argc, char **argv)
 						
 						if ((!lmin || (length >= lmin)) &&
 						    (!lmax || (length <= lmax)))
-						    printRepeat(seq,o1,o2c,'D',posi,posj,erri,errj,taxonomy);
+						    printRepeat(seq,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy);
 							//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);
 					}
 				}
@@ -495,7 +506,7 @@ int main(int argc, char **argv)
 						
 						if ((!lmin || (length >= lmin)) &&
 						    (!lmax || (length <= lmax)))
-						    printRepeat(seq,o2,o1c,'R',posi,posj,erri,errj,taxonomy);
+						    printRepeat(seq,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy);
 							//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);
 					}
 				}

src/libecoPCR/ecoPCR.h

@@ -224,6 +224,7 @@ char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
 ecotx_t *eco_getspecies(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getgenus(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
+ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 
 #endif /*ECOPCR_H_*/

src/libecoPCR/ecotax.c

@@ -215,6 +215,24 @@ ecotx_t *eco_getfamily(ecotx_t *taxon,
 	return eco_findtaxonatrank(taxon,rankindex,tax);
 }
 
+ecotx_t *eco_getkingdom(ecotx_t *taxon,
+						ecotaxonomy_t *taxonomy)
+{
+	static ecotaxonomy_t *tax=NULL;
+	static int32_t		 rankindex=-1;
+	
+	if (taxonomy && tax!=taxonomy)
+	{
+		rankindex = rank_index("kingdom",taxonomy->ranks);
+		tax=taxonomy;
+	}
+		
+	if (!tax || rankindex < 0)
+		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
+		
+	return eco_findtaxonatrank(taxon,rankindex,tax);
+}
+
 ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 						ecotaxonomy_t *taxonomy)
 {