Change 1 : patch the help message to take into account option added and the new output format.

Change 2 : Change the used rules to define example and counter example taxon sets.
			By default all taxa are example taxa and no counterexample taxa are used.
			By using -r option (one or several time) you could restict example taxa to a subset of taxa
			In old version all taxa not in example set are in the counterexample set.
			Now restrict example set with -r option doesn't define the counter example set.
			You must use -i to define the conterexample set in a similar way or -r option for example taxa.  

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@234 60f365c0-8329-0410-b2a4-ec073aeeaa1d

.pydevproject

@@ -1,7 +1,7 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?eclipse-pydev version="1.0"?>
 
 <pydev_project>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python 2.6</pydev_property>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.6</pydev_property>
 </pydev_project>

src/ecoprimer.c

@@ -53,37 +53,50 @@ static void PrintHelp()
               PP      "        database radical without any extension. For example /ecoPrimerDB/fstvert\n\n");
               PP      "-e    : [E]rror : max error allowed by oligonucleotide (0 by default)\n\n");
               PP      "-h    : [H]elp - print <this> help\n\n");
-              PP      "-i    : [I]gnore the given taxonomy id.\n\n");
+              PP      "-i    : [I]gnore the given taxonomy id (define the counterexample taxon set).\n\n");
               PP      "-l    : minimum [L]ength : define the minimum amplication length. \n\n");
               PP      "-L    : maximum [L]ength : define the maximum amplicationlength. \n\n");
-              PP      "-r    : [R]estricts the search to the given taxonomic id.\n\n");
+              PP      "-r    : [R]estricts the search to the given taxonomic id (restrict the example taxon set).\n\n");
               PP      "-c    : Consider that the database sequences are [c]ircular\n\n");
-//              PP      "-3 	 : Three prime strict match\n\n");
+              PP      "-3 	 : Three prime strict match\n\n");
               PP      "-q    : Strict matching [q]uorum, percentage of the sequences in which strict primers are found. By default it is 70\n\n");
               PP      "-s    : [S]ensitivity quorum\n\n");
               PP      "-t    : required [t]axon level for results, by default the results are computed at species level\n\n");
               PP      "-x    : false positive quorum\n\n");
               PP      "-D    : set in [d]ouble strand mode\n\n");
+              PP      "-O    : set the primer length (default 18) \n\n");
               PP      "-S    : Set in [s]ingle strand mode\n\n");
+              PP      "-m    : Salt correction method for Tm computation (SANTALUCIA : 1 or OWCZARZY:2, default=1)\n\n");
+              PP      "-a    : Salt contentration in M for Tm computation (default 0.05 M)\n\n");
               PP      "-U    : No multi match\n\n");
+              PP      "-U    : Define the [R]eference sequence identifier (must be part of example set)\n\n");
+              PP      "-A    : Print the list of all identifier of sequences present in the database\n\n");
+              PP      "-f    : Remove data mining step during  strict primer identification\n\n");
+              PP      "-v    : Store statistic file about memory usage during strict primer identification\n\n");
               PP      "\n");
               PP      "------------------------------------------\n");
               PP      "Table result description : \n");
-              PP      "column 1 : serial number\n");
+              PP      "column  1 : serial number\n");
-              PP      "column 2 : primer1\n");
+              PP      "column  2 : primer1\n");
-              PP      "column 3 : primer2\n");
+              PP      "column  3 : primer2\n");
-              PP      "column 4 : good/bad\n");
+              PP      "column  4 : primer1 Tm without mismatch\n");
-              PP      "column 5 : in sequence count\n");
+              PP      "column  5 : primer1 lowest Tm against exemple sequences\n");
-              PP      "column 6 : out sequence count\n");
+              PP      "column  6 : primer2 Tm without mismatch\n");
-              PP      "column 7 : yule\n");
+              PP      "column  7 : primer2 lowest Tm against exemple sequences\n");
-              PP      "column 8 : in taxa count\n");
+              PP      "column  8 : primer1 G+C count\n");
-              PP      "column 9 : out taxa count\n");
+              PP      "column  9 : primer2 G+C count\n");
-              PP      "column 10 : coverage\n");
+              PP      "column 10 : good/bad\n");
-              PP      "column 11 : unambiguously identified taxa\n");
+              PP      "column 11 : amplified example sequence count\n");
-              PP      "column 12 : specificity\n");
+              PP      "column 12 : amplified counterexample sequence count\n");
-              PP      "column 13 : minimum amplified length\n");
+              PP      "column 13 : yule\n");
-              PP      "column 14 : maximum amplified length\n");
+              PP      "column 14 : amplified example taxa count\n");
-              PP      "column 15 : average amplified length\n");
+              PP      "column 15 : amplified counterexample taxa count\n");
+              PP      "column 16 : ratio of amplified example taxa versus all example taxa (Bc index)\n");
+              PP      "column 17 : unambiguously identified example taxa count\n");
+              PP      "column 18 : ratio of specificity unambiguously identified example taxa versus all example taxa (Bs index)\n");
+              PP      "column 19 : minimum amplified length\n");
+              PP      "column 20 : maximum amplified length\n");
+              PP      "column 21 : average amplified length\n");
               PP      "------------------------------------------\n");
               PP		" http://www.grenoble.prabi.fr/trac/ecoPrimer/\n");
               PP      "------------------------------------------\n\n");
@@ -690,7 +703,7 @@ int main(int argc, char **argv)
 
     fprintf(stderr,"Reading sequence database ...\n");
 
-    seqdb = readdnadb(options.prefix,&seqdbsize);
+    seqdb = readdnadb(options.prefix,taxonomy,&seqdbsize, &options);
 
 	if (options.printAC)
 	{

src/libecoprimer/ecoprimer.h

@@ -290,9 +290,11 @@ typedef ecoseq_t  **pecodnadb_t;
 void sortword(pword_t table,uint32_t N);
 
 
-pecodnadb_t readdnadb(const char *name, uint32_t *size);
+pecodnadb_t readdnadb(const char *name, ecotaxonomy_t *taxonomy, uint32_t *size,poptions_t options);
 
 int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options);
+int isExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options);
+int isCounterExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options);
 
 uint32_t ecoWordCount(uint32_t wordsize, uint32_t circular, ecoseq_t *seq);
 pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint32_t doublestrand, ecoseq_t *seq,uint32_t *size,int32_t *neededWords,uint32_t neededWordCount,

src/libecoprimer/goodtaxon.c

@@ -25,3 +25,31 @@ int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
 
 	return result;
 }
+
+int isExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
+{
+	int result;
+
+	result=( (options->r == 0) || (eco_is_taxid_included(taxonomy,
+			                            options->restricted_taxid,
+			                            options->r,
+			                            taxonomy->taxons->taxon[taxon].taxid)
+		   ));
+
+	return result;
+}
+
+
+int isCounterExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
+{
+	int result;
+
+	result=((options->g != 0) && (eco_is_taxid_included(taxonomy,
+								   options->ignored_taxid,
+								   options->g,
+								   taxonomy->taxons->taxon[taxon].taxid)
+           ));
+
+
+	return result;
+}

src/libecoprimer/readdnadb.c

@@ -7,7 +7,7 @@
 
 #include "ecoprimer.h"
 
-pecodnadb_t readdnadb(const char *name, uint32_t *size)
+pecodnadb_t readdnadb(const char *name, ecotaxonomy_t *taxonomy, uint32_t *size,poptions_t options)
 {
 	ecoseq_t      *seq;
 	uint32_t       buffsize=100;
@@ -18,15 +18,24 @@ pecodnadb_t readdnadb(const char *name, uint32_t *size)
 
 	for(seq=ecoseq_iterator(name), *size=0;
 	    seq;
-	    seq=ecoseq_iterator(NULL), (*size)++
+	    seq=ecoseq_iterator(NULL)
 	   )
 	{
-		if (*size==buffsize)
+	  if (isExampleTaxon(taxonomy,seq->taxid,options) ||
-		{
+		  isCounterExampleTaxon(taxonomy,seq->taxid,options))
-			buffsize*=2;
+	  {
-			db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
+			if (*size==buffsize)
-		}
+			{
-		db[*size]=seq;
+				buffsize*=2;
+				db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
+			}
+			db[*size]=seq;
+			(*size)++;
+	  }
+	  else
+	  {
+		  delete_ecoseq(seq);
+	  }
 	};
 
 	db = ECOREALLOC(db,(*size)*sizeof(ecoseq_t*),"I cannot allocate db memory");
@@ -47,4 +56,4 @@ void printSeqTest(pecodnadb_t seqdb,uint32_t seqdbsize)
 		fprintf (stderr, "seq %d = %s\n", i, ch);
 	}
 	exit (0);
-}
+}