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

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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
This commit is contained in:
Eric Coissac
2009-10-12 13:31:41 +00:00
parent 088b5c09d0
commit 6f5f2a16f3
6 changed files with 83 additions and 31 deletions
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4
.pydevproject
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@ -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>

45
src/ecoprimer.c
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@ -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 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 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)
{

4
src/libecoprimer/ecoprimer.h
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@ -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,

28
src/libecoprimer/goodtaxon.c
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@ -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;
}

13
src/libecoprimer/readdnadb.c
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@ -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;
@ -18,8 +18,11 @@ 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 (isExampleTaxon(taxonomy,seq->taxid,options) ||
isCounterExampleTaxon(taxonomy,seq->taxid,options))
{
if (*size==buffsize)
{
@ -27,6 +30,12 @@ pecodnadb_t readdnadb(const char *name, uint32_t *size)
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");

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src/libthermo/libthermo.a
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