diff --git a/.pydevproject b/.pydevproject
index 6725cde..ac30bc7 100644
--- a/.pydevproject
+++ b/.pydevproject
@@ -1,7 +1,7 @@
-
+
-Default
+Python 2.6
python 2.6
diff --git a/src/ecoprimer.c b/src/ecoprimer.c
index 2342318..c55dda3 100644
--- a/src/ecoprimer.c
+++ b/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 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 2 : primer1\n");
- PP "column 3 : primer2\n");
- PP "column 4 : good/bad\n");
- PP "column 5 : in sequence count\n");
- PP "column 6 : out sequence count\n");
- PP "column 7 : yule\n");
- PP "column 8 : in taxa count\n");
- PP "column 9 : out taxa count\n");
- PP "column 10 : coverage\n");
- PP "column 11 : unambiguously identified taxa\n");
- PP "column 12 : specificity\n");
- PP "column 13 : minimum amplified length\n");
- PP "column 14 : maximum amplified length\n");
- PP "column 15 : average amplified length\n");
+ PP "column 1 : serial number\n");
+ PP "column 2 : primer1\n");
+ PP "column 3 : primer2\n");
+ PP "column 4 : primer1 Tm without mismatch\n");
+ PP "column 5 : primer1 lowest Tm against exemple sequences\n");
+ PP "column 6 : primer2 Tm without mismatch\n");
+ PP "column 7 : primer2 lowest Tm against exemple sequences\n");
+ PP "column 8 : primer1 G+C count\n");
+ PP "column 9 : primer2 G+C count\n");
+ PP "column 10 : good/bad\n");
+ PP "column 11 : amplified example sequence count\n");
+ PP "column 12 : amplified counterexample sequence count\n");
+ PP "column 13 : yule\n");
+ PP "column 14 : amplified example taxa count\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)
{
diff --git a/src/libecoprimer/ecoprimer.h b/src/libecoprimer/ecoprimer.h
index a25c8ad..195ae57 100644
--- a/src/libecoprimer/ecoprimer.h
+++ b/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,
diff --git a/src/libecoprimer/goodtaxon.c b/src/libecoprimer/goodtaxon.c
index f4d7598..09b47ce 100644
--- a/src/libecoprimer/goodtaxon.c
+++ b/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;
+}
diff --git a/src/libecoprimer/readdnadb.c b/src/libecoprimer/readdnadb.c
index 98867dd..ced45c5 100644
--- a/src/libecoprimer/readdnadb.c
+++ b/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)
- {
- buffsize*=2;
- db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
- }
- db[*size]=seq;
+ if (isExampleTaxon(taxonomy,seq->taxid,options) ||
+ isCounterExampleTaxon(taxonomy,seq->taxid,options))
+ {
+ if (*size==buffsize)
+ {
+ 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);
-}
\ No newline at end of file
+}
diff --git a/src/libthermo/libthermo.a b/src/libthermo/libthermo.a
deleted file mode 100644
index be29e70..0000000
Binary files a/src/libthermo/libthermo.a and /dev/null differ