Compare commits
16 Commits
| Author | SHA1 | Date | |
|---|---|---|---|
| 68c4743303 | |||
| 035495b2a1 | |||
| 3c21789533 | |||
| 75a6dac09a | |||
| 6726294c78 | |||
| 584d3c406d | |||
| 0440b8d761 | |||
| db061fbb12 | |||
| ac52f3303d | |||
| 29820c1e26 | |||
| 5d212d5753 | |||
| 9908a40aaa | |||
| 665b22989f | |||
| d911d6bd20 | |||
| dffebd5826 | |||
| 2be5f2659b |
BIN
src/ecoPrimer
BIN
src/ecoPrimer
Binary file not shown.
253
src/ecoprimer.c
253
src/ecoprimer.c
@ -25,9 +25,59 @@
|
||||
|
||||
static void PrintHelp()
|
||||
{
|
||||
PP "------------------------------------------\n");
|
||||
PP " ecoPrimer Version %s\n", VERSION);
|
||||
PP "------------------------------------------\n");
|
||||
PP "------------------------------------------\n");
|
||||
PP " ecoPrimer Version %s\n", VERSION);
|
||||
PP "------------------------------------------\n");
|
||||
PP "synopsis : finding primers and measureing the quality of primers and barcode region\n");
|
||||
PP "usage: ./ecoPrimer [options] \n");
|
||||
PP "------------------------------------------\n");
|
||||
PP "options:\n");
|
||||
PP "-d : [D]atabase : to match the expected format, the database\n");
|
||||
PP " has to be formated first by the ecoPCRFormat.py program located.\n");
|
||||
PP " in the ecoPCR/tools directory.\n");
|
||||
PP " ecoPCRFormat.py creates three file types :\n");
|
||||
PP " .sdx : contains the sequences\n");
|
||||
PP " .tdx : contains information concerning the taxonomy\n");
|
||||
PP " .rdx : contains the taxonomy rank\n\n");
|
||||
PP " ecoPrimer needs all the file type. As a result, you have to write the\n");
|
||||
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 "-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 "-c : Consider that the database sequences are [c]ircular\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 "-S : Set in [s]ingle strand mode\n\n");
|
||||
PP "-U : No multi match\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 : specificity\n");
|
||||
PP "column 12 : minimum amplified length\n");
|
||||
PP "column 13 : maximum amplified length\n");
|
||||
PP "column 14 : average amplified length\n");
|
||||
PP "------------------------------------------\n");
|
||||
PP " http://www.grenoble.prabi.fr/trac/ecoPrimer/\n");
|
||||
PP "------------------------------------------\n\n");
|
||||
PP "\n");
|
||||
|
||||
}
|
||||
|
||||
static void ExitUsage(int stat)
|
||||
@ -56,7 +106,7 @@ void initoptions(poptions_t options)
|
||||
options->strict_exclude_quorum=0.1;
|
||||
options->sensitivity_quorum=0.9;
|
||||
options->false_positive_quorum=0.1;
|
||||
options->strict_three_prime=2;
|
||||
options->strict_three_prime=0;
|
||||
options->r=0;
|
||||
options->g=0;
|
||||
options->no_multi_match=FALSE;
|
||||
@ -75,7 +125,7 @@ void printcurrenttime ()
|
||||
/* Format and print the time, "ddd yyyy-mm-dd hh:mm:ss zzz" */
|
||||
ts = localtime(&now);
|
||||
strftime(buf, sizeof(buf), "%a %Y-%m-%d %H:%M:%S %Z", ts);
|
||||
fprintf(stderr,"#%d#, %s\n",now, buf);
|
||||
fprintf(stderr,"#%d#, %s\n",(int)now, buf);
|
||||
}
|
||||
|
||||
void printcurrenttimeinmilli()
|
||||
@ -90,7 +140,125 @@ void printcurrenttimeinmilli()
|
||||
}
|
||||
|
||||
/*TR: Added*/
|
||||
|
||||
void printapair(int32_t index,ppair_t pair, poptions_t options)
|
||||
{
|
||||
uint32_t wellidentifiedtaxa;
|
||||
|
||||
printf("%6d\t",index);
|
||||
if (pair->asdirect1)
|
||||
printf("%s\t",ecoUnhashWord(pair->p1->word,options->primer_length));
|
||||
else
|
||||
printf("%s\t",ecoUnhashWord(ecoComplementWord(pair->p1->word,
|
||||
options->primer_length),options->primer_length));
|
||||
|
||||
if (pair->asdirect2)
|
||||
printf("%s",ecoUnhashWord(pair->p2->word,options->primer_length));
|
||||
else
|
||||
printf("%s",ecoUnhashWord(ecoComplementWord(pair->p2->word,
|
||||
options->primer_length),options->primer_length));
|
||||
|
||||
printf("\t%c%c", "bG"[(int)pair->p1->good],"bG"[(int)pair->p2->good]);
|
||||
|
||||
|
||||
printf("\t%d", pair->inexample);
|
||||
printf("\t%d", pair->outexample);
|
||||
printf("\t%4.3f", pair->yule);
|
||||
|
||||
printf("\t%d", pair->intaxa);
|
||||
printf("\t%d", pair->outtaxa);
|
||||
printf("\t%4.3f", (float)pair->intaxa/options->intaxa);
|
||||
|
||||
wellidentifiedtaxa = (pair->intaxa + pair->outtaxa) - pair->notwellidentifiedtaxa;
|
||||
|
||||
//printf("\t%d", pair->notwellidentifiedtaxa);
|
||||
|
||||
//printf("\t%d", (pair->intaxa + pair->outtaxa));
|
||||
|
||||
|
||||
|
||||
printf("\t%4.3f", (float)wellidentifiedtaxa/(options->intaxa + options->outtaxa));
|
||||
|
||||
|
||||
printf("\t%d", pair->mind);
|
||||
printf("\t%d", pair->maxd);
|
||||
printf("\t%3.2f\n", (float)pair->sumd/pair->inexample);
|
||||
|
||||
}
|
||||
|
||||
uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t options)
|
||||
{
|
||||
uint32_t i,j;
|
||||
float q,qfp;
|
||||
|
||||
for (i=0,j=0;i < count;i++)
|
||||
{
|
||||
if (options->insamples)
|
||||
q = (float)sortedpairs[i]->inexample/options->insamples;
|
||||
else q=1.0;
|
||||
|
||||
if (options->outsamples)
|
||||
qfp = (float)sortedpairs[i]->outexample/options->outsamples;
|
||||
else qfp=0.0;
|
||||
|
||||
sortedpairs[i]->quorumin = q;
|
||||
sortedpairs[i]->quorumout = qfp;
|
||||
sortedpairs[i]->yule = q -qfp;
|
||||
|
||||
|
||||
sortedpairs[j]=sortedpairs[i];
|
||||
|
||||
|
||||
|
||||
if (q > options->sensitivity_quorum &&
|
||||
qfp < options->false_positive_quorum)
|
||||
{
|
||||
(void)taxonomycoverage(sortedpairs[j],options);
|
||||
taxonomyspecificity(sortedpairs[j]);
|
||||
j++;
|
||||
}
|
||||
}
|
||||
|
||||
return j;
|
||||
}
|
||||
|
||||
void printpairs (ppairtree_t pairs, poptions_t options)
|
||||
{
|
||||
ppair_t* sortedpairs;
|
||||
ppair_t* index;
|
||||
ppairlist_t pl;
|
||||
size_t i,j;
|
||||
int32_t count;
|
||||
|
||||
//printf("Index\tPrimer1\tPrimer2\tGB\tInexampleCount\tOutexampleCount\tYule\tIntaxaCount\tOuttaxaCount\tCoverage\tSpecificity\tMinAmplifiedLength\tMaxAmplifiedLength\tAvgAmplifiedLength\n");
|
||||
|
||||
fprintf(stderr,"Total pair count : %d\n",pairs->count);
|
||||
|
||||
sortedpairs = ECOMALLOC(pairs->count*sizeof(ppair_t),"Cannot Allocate ordered pairs");
|
||||
index=sortedpairs;
|
||||
pl=pairs->first;
|
||||
j=0;
|
||||
while(pl->next)
|
||||
{
|
||||
for (i=0;i<pl->paircount;i++,j++)
|
||||
sortedpairs[j]=pl->pairs+i;
|
||||
pl=pl->next;
|
||||
}
|
||||
|
||||
for (i=0;i<pl->paircount;i++,j++)
|
||||
sortedpairs[j]=pl->pairs+i;
|
||||
|
||||
count=filterandsortpairs(sortedpairs,pairs->count,options);
|
||||
|
||||
for (i=0;i < count;i++)
|
||||
printapair(i,sortedpairs[i],options);
|
||||
|
||||
}
|
||||
|
||||
|
||||
#ifdef MASKEDCODE
|
||||
void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize)
|
||||
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t wordsize = options->primer_length;
|
||||
@ -121,8 +289,11 @@ void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, ui
|
||||
}
|
||||
}
|
||||
|
||||
#endif /* MASKEDCODE */
|
||||
|
||||
/*updateseqparams: This function counts the insample and outsample sequences
|
||||
* and with each sequences adds a tag of the taxon to which the sequence beongs*/
|
||||
|
||||
void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
|
||||
poptions_t options, int32_t *insamples, int32_t *outsamples)
|
||||
{
|
||||
@ -168,47 +339,10 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
|
||||
}
|
||||
}
|
||||
/* to get db stats, totals of species, genus etc....*/
|
||||
int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
|
||||
poptions_t options)
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t j;
|
||||
uint32_t nameslots = 500;
|
||||
uint32_t namesindex = 0;
|
||||
int32_t *ranktaxonids = ECOMALLOC(nameslots * sizeof(int32_t), "Error in taxon rank allocation");
|
||||
int32_t taxid;
|
||||
|
||||
ecotx_t *tmptaxon;
|
||||
#ifdef MASKEDCODE
|
||||
|
||||
for (i=0;i<seqdbsize;i++)
|
||||
{
|
||||
taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid;
|
||||
tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);
|
||||
if (tmptaxon)
|
||||
tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx);
|
||||
if (tmptaxon)
|
||||
{
|
||||
for (j = 0; j < namesindex; j++)
|
||||
{
|
||||
if (tmptaxon->taxid == ranktaxonids[j]) break;
|
||||
}
|
||||
if (j < namesindex) continue; /* name is already in list, so no need to add it*/
|
||||
|
||||
if (namesindex == nameslots)
|
||||
{
|
||||
nameslots += 500;
|
||||
ranktaxonids = ECOREALLOC(ranktaxonids, nameslots * sizeof(int32_t), "Cannot allocate pair rank taxon table");
|
||||
}
|
||||
ranktaxonids[namesindex] = tmptaxon->taxid;
|
||||
namesindex++;
|
||||
}
|
||||
}
|
||||
ECOFREE(ranktaxonids, "free rank taxon table");
|
||||
|
||||
return namesindex;
|
||||
}
|
||||
|
||||
void setoktaxforspecificity (ppairscount_t pairs)
|
||||
void setoktaxforspecificity (ppairtree_t pairs)
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t j;
|
||||
@ -251,6 +385,8 @@ void setoktaxforspecificity (ppairscount_t pairs)
|
||||
}
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
pecodnadb_t seqdb; /* of type ecoseq_t */
|
||||
@ -265,9 +401,9 @@ int main(int argc, char **argv)
|
||||
int32_t outsamples=0;
|
||||
uint32_t i;
|
||||
|
||||
pwordcount_t words;
|
||||
pprimercount_t primers;
|
||||
pairscount_t pairs;
|
||||
pwordcount_t words;
|
||||
pprimercount_t primers;
|
||||
ppairtree_t pairs;
|
||||
|
||||
int32_t rankdbstats = 0;
|
||||
|
||||
@ -290,9 +426,9 @@ int main(int argc, char **argv)
|
||||
/* -------------------- */
|
||||
case 'h': /* help */
|
||||
/* -------------------- */
|
||||
PrintHelp();
|
||||
exit(0);
|
||||
break;
|
||||
PrintHelp();
|
||||
exit(0);
|
||||
break;
|
||||
|
||||
/* ------------------------- */
|
||||
case 'l': /* min amplification lenght */
|
||||
@ -407,11 +543,16 @@ int main(int argc, char **argv)
|
||||
fprintf(stderr,"Sequence read : %d\n",(int32_t)seqdbsize);
|
||||
|
||||
updateseqparams(seqdb, seqdbsize, taxonomy, &options, &insamples , &outsamples);
|
||||
options.dbsize=seqdbsize;
|
||||
options.insamples=insamples;
|
||||
options.outsamples=outsamples;
|
||||
|
||||
rankdbstats = getrankdbstats(seqdb, seqdbsize, taxonomy, &options);
|
||||
|
||||
fprintf(stderr,"Database is constituted of %5d examples\n",insamples);
|
||||
fprintf(stderr," and %5d counterexamples\n",outsamples);
|
||||
fprintf(stderr,"Database is constituted of %5d examples corresponding to %5d %s\n",insamples,
|
||||
options.intaxa,options.taxonrank);
|
||||
fprintf(stderr," and %5d counterexamples corresponding to %5d %s\n",outsamples,
|
||||
options.outtaxa,options.taxonrank);
|
||||
fprintf(stderr,"Total distinct %s count %d\n",options.taxonrank, rankdbstats);
|
||||
|
||||
fprintf(stderr,"\nIndexing words in sequences\n");
|
||||
@ -460,13 +601,15 @@ int main(int argc, char **argv)
|
||||
|
||||
/*TR: Added*/
|
||||
pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
|
||||
setoktaxforspecificity (&pairs);
|
||||
|
||||
printpairs (pairs, &options, rankdbstats, seqdbsize);
|
||||
|
||||
// setoktaxforspecificity (&pairs);
|
||||
|
||||
printpairs (pairs, &options);
|
||||
|
||||
|
||||
|
||||
ECOFREE(pairs.pairs,"Free pairs table");
|
||||
//ECOFREE(pairs.pairs,"Free pairs table");
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
15
src/libecoPCR/ecoError.P
Normal file
15
src/libecoPCR/ecoError.P
Normal file
@ -0,0 +1,15 @@
|
||||
ecoError.o ecoError.P : ecoError.c ecoPCR.h /usr/include/stdio.h \
|
||||
/usr/include/_types.h /usr/include/sys/_types.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h /usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h
|
||||
15
src/libecoPCR/ecoIOUtils.P
Normal file
15
src/libecoPCR/ecoIOUtils.P
Normal file
@ -0,0 +1,15 @@
|
||||
ecoIOUtils.o ecoIOUtils.P : ecoIOUtils.c ecoPCR.h /usr/include/stdio.h \
|
||||
/usr/include/_types.h /usr/include/sys/_types.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h /usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h
|
||||
15
src/libecoPCR/ecoMalloc.P
Normal file
15
src/libecoPCR/ecoMalloc.P
Normal file
@ -0,0 +1,15 @@
|
||||
ecoMalloc.o ecoMalloc.P : ecoMalloc.c ecoPCR.h /usr/include/stdio.h \
|
||||
/usr/include/_types.h /usr/include/sys/_types.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h /usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h
|
||||
5
src/libecoPCR/ecodna.P
Normal file
5
src/libecoPCR/ecodna.P
Normal file
@ -0,0 +1,5 @@
|
||||
ecodna.o ecodna.P : ecodna.c /usr/include/string.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h ecoPCR.h \
|
||||
/usr/include/stdio.h /usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h
|
||||
5
src/libecoPCR/ecofilter.P
Normal file
5
src/libecoPCR/ecofilter.P
Normal file
@ -0,0 +1,5 @@
|
||||
ecofilter.o ecofilter.P : ecofilter.c ecoPCR.h /usr/include/stdio.h \
|
||||
/usr/include/_types.h /usr/include/sys/_types.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h /usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h
|
||||
15
src/libecoPCR/econame.P
Normal file
15
src/libecoPCR/econame.P
Normal file
@ -0,0 +1,15 @@
|
||||
econame.o econame.P : econame.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/string.h /usr/include/stdlib.h /usr/include/available.h \
|
||||
/usr/include/sys/wait.h /usr/include/sys/signal.h \
|
||||
/usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
|
||||
/usr/include/i386/signal.h /usr/include/i386/_structs.h \
|
||||
/usr/include/sys/_structs.h /usr/include/machine/_structs.h \
|
||||
/usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
|
||||
/usr/include/machine/endian.h /usr/include/i386/endian.h \
|
||||
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h
|
||||
15
src/libecoPCR/ecorank.P
Normal file
15
src/libecoPCR/ecorank.P
Normal file
@ -0,0 +1,15 @@
|
||||
ecorank.o ecorank.P : ecorank.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/string.h /usr/include/stdlib.h /usr/include/available.h \
|
||||
/usr/include/sys/wait.h /usr/include/sys/signal.h \
|
||||
/usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
|
||||
/usr/include/i386/signal.h /usr/include/i386/_structs.h \
|
||||
/usr/include/sys/_structs.h /usr/include/machine/_structs.h \
|
||||
/usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
|
||||
/usr/include/machine/endian.h /usr/include/i386/endian.h \
|
||||
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h
|
||||
19
src/libecoPCR/ecoseq.P
Normal file
19
src/libecoPCR/ecoseq.P
Normal file
@ -0,0 +1,19 @@
|
||||
ecoseq.o ecoseq.P : ecoseq.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/string.h /usr/include/zlib.h /usr/include/zconf.h \
|
||||
/usr/include/sys/types.h /usr/include/unistd.h \
|
||||
/usr/include/sys/unistd.h /usr/include/sys/select.h \
|
||||
/usr/include/sys/_select.h
|
||||
15
src/libecoPCR/ecotax.P
Normal file
15
src/libecoPCR/ecotax.P
Normal file
@ -0,0 +1,15 @@
|
||||
ecotax.o ecotax.P : ecotax.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/string.h /usr/include/stdlib.h /usr/include/available.h \
|
||||
/usr/include/sys/wait.h /usr/include/sys/signal.h \
|
||||
/usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
|
||||
/usr/include/i386/signal.h /usr/include/i386/_structs.h \
|
||||
/usr/include/sys/_structs.h /usr/include/machine/_structs.h \
|
||||
/usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
|
||||
/usr/include/machine/endian.h /usr/include/i386/endian.h \
|
||||
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h
|
||||
@ -10,7 +10,9 @@ SOURCES = goodtaxon.c \
|
||||
queue.c \
|
||||
libstki.c \
|
||||
sortmatch.c \
|
||||
pairtree.c \
|
||||
pairs.c \
|
||||
taxstats.c \
|
||||
apat_search.c
|
||||
|
||||
SRCS=$(SOURCES)
|
||||
|
||||
131
src/libecoprimer/amplifiatree.c
Normal file
131
src/libecoprimer/amplifiatree.c
Normal file
@ -0,0 +1,131 @@
|
||||
/*
|
||||
* amplifiatree.c
|
||||
*
|
||||
* Created on: 7 mars 2009
|
||||
* Author: coissac
|
||||
*/
|
||||
|
||||
#include "ecoprimer.h"
|
||||
#include <search.h>
|
||||
|
||||
static void cleanamplifia(pamplifia_t amplifia);
|
||||
static void deleteamplifialist(pamplifialist_t list);
|
||||
static int cmpamplifia(const void* p1,const void*p2);
|
||||
|
||||
|
||||
static void cleanamplifiatlist(pamplifiacount_t list)
|
||||
{
|
||||
if (list->amplifias)
|
||||
ECOFREE(list->amplifias,
|
||||
"Free amplifia list");
|
||||
}
|
||||
|
||||
static void cleanamplifia(pamplifia_t amplifia)
|
||||
{
|
||||
cleanamplifiatlist(&(amplifia->pcr));
|
||||
}
|
||||
|
||||
static pamplifialist_t newamplifialist(pamplifialist_t parent, size_t size)
|
||||
{
|
||||
pamplifialist_t tmp;
|
||||
|
||||
tmp=ECOMALLOC(sizeof(amplifialist_t)+sizeof(amplifia_t)*(size-1),
|
||||
"Cannot allocate new amplifia list");
|
||||
|
||||
tmp->amplifiaslots=size;
|
||||
tmp->amplifiacount=0;
|
||||
tmp->next=NULL;
|
||||
|
||||
if (parent)
|
||||
parent->next=(void*)tmp;
|
||||
|
||||
return tmp;
|
||||
}
|
||||
|
||||
static void deleteamplifialist(pamplifialist_t list)
|
||||
{
|
||||
size_t i;
|
||||
|
||||
if (list)
|
||||
{
|
||||
if (list->next)
|
||||
{
|
||||
deleteamplifialist(list->next);
|
||||
list->next=NULL;
|
||||
}
|
||||
for (i=0; i < list->amplifiacount; i++)
|
||||
cleanamplifia((list->amplifias)+i);
|
||||
|
||||
ECOFREE(list,"Delete amplifia list");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
static int cmpamplifia(const void* p1,const void*p2)
|
||||
{
|
||||
pamplifia_t pr1,pr2;
|
||||
|
||||
pr1=(pamplifia_t)p1;
|
||||
pr2=(pamplifia_t)p2;
|
||||
|
||||
if (pr1->p1 < pr2->p1) return -1;
|
||||
if (pr1->p1 > pr2->p1) return 1;
|
||||
|
||||
if (pr1->asdirect1 < pr2->asdirect1) return -1;
|
||||
if (pr1->asdirect1 > pr2->asdirect1) return 1;
|
||||
|
||||
if (pr1->p2 < pr2->p2) return -1;
|
||||
if (pr1->p2 > pr2->p2) return 1;
|
||||
|
||||
if (pr1->asdirect2 < pr2->asdirect2) return -1;
|
||||
if (pr1->asdirect2 > pr2->asdirect2) return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
pamplifia_t amplifiaintree (amplifia_t key,
|
||||
pamplifiatree_t amplifialist)
|
||||
{
|
||||
if (!amplifialist->tree)
|
||||
return NULL;
|
||||
|
||||
return *((pamplifia_t*)tsearch((const void *)(&key),
|
||||
&(amplifialist->tree),
|
||||
cmpamplifia
|
||||
));
|
||||
}
|
||||
|
||||
pamplifia_t insertamplifia(amplifia_t key,
|
||||
pamplifiatree_t list)
|
||||
{
|
||||
pamplifia_t current;
|
||||
pamplifia_t found;
|
||||
|
||||
if (list->last->amplifiacount==list->last->amplifiaslots)
|
||||
{
|
||||
list->last->next=newamplifialist(list,100);
|
||||
list->last=list->last->next;
|
||||
}
|
||||
|
||||
current = list->last->amplifias + list->last->amplifiacount;
|
||||
*current=key;
|
||||
|
||||
found = *((pamplifia_t*)tsearch((const void *)current,
|
||||
&(list->tree),
|
||||
cmpamplifia));
|
||||
if (found==current)
|
||||
list->last->amplifiacount++;
|
||||
|
||||
return found;
|
||||
}
|
||||
|
||||
pamplifiatree_t initamplifiatree(pamplifiatree_t tree)
|
||||
{
|
||||
if (!tree)
|
||||
tree = ECOMALLOC(sizeof(amplifiatree_t),"Cannot allocate amplifia tree");
|
||||
|
||||
tree->first=newamplifialist(NULL,500);
|
||||
tree->last=tree->first;
|
||||
|
||||
tree->tree=NULL;
|
||||
}
|
||||
17
src/libecoprimer/apat_search.P
Normal file
17
src/libecoprimer/apat_search.P
Normal file
@ -0,0 +1,17 @@
|
||||
apat_search.o apat_search.P : apat_search.c /usr/include/stdio.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/string.h libstki.h ecotype.h apat.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
../libecoPCR/ecoPCR.h
|
||||
17
src/libecoprimer/aproxpattern.P
Normal file
17
src/libecoprimer/aproxpattern.P
Normal file
@ -0,0 +1,17 @@
|
||||
aproxpattern.o aproxpattern.P : aproxpattern.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h /usr/include/math.h /usr/include/architecture/i386/math.h
|
||||
@ -61,7 +61,7 @@ void encodeSequence(ecoseq_t *seq)
|
||||
|
||||
for (i=0;i<seq->SQ_length;i++,data++,cseq++)
|
||||
{
|
||||
*data = encoder[(IS_UPPER(*cseq) ? *cseq - 'A' : 'Z')];
|
||||
*data = encoder[(IS_UPPER(*cseq) ? *cseq : 'Z') - 'A'];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -79,28 +79,39 @@ typedef union {
|
||||
uint32_t value;
|
||||
} poslist_t, *ppostlist_t;
|
||||
|
||||
typedef struct {
|
||||
word_t word;
|
||||
uint32_t *directCount;
|
||||
ppostlist_t directPos;
|
||||
/**
|
||||
* primer_t structure store fuzzy match positions for a primer
|
||||
* on all sequences
|
||||
*/
|
||||
|
||||
uint32_t *reverseCount;
|
||||
ppostlist_t reversePos;
|
||||
bool_t good;
|
||||
uint32_t inexample;
|
||||
uint32_t outexample;
|
||||
typedef struct {
|
||||
word_t word; //< code for the primer
|
||||
uint32_t *directCount; //< Occurrence count on direct strand
|
||||
ppostlist_t directPos; //< list of position list on direct strand
|
||||
|
||||
uint32_t *reverseCount; //< Occurrence count on reverse strand
|
||||
ppostlist_t reversePos; //< list of position list on reverse strand
|
||||
|
||||
bool_t good; //< primer match more than quorum example and no
|
||||
// more counterexample quorum.
|
||||
|
||||
uint32_t inexample; //< count of example sequences matching primer
|
||||
uint32_t outexample; //< count of counterexample sequences matching primer
|
||||
} primer_t, *pprimer_t;
|
||||
|
||||
/**
|
||||
* primercount_t structure store fuzzy match positions for all primers
|
||||
* on all sequences as a list of primer_t
|
||||
*/
|
||||
typedef struct {
|
||||
pprimer_t primers;
|
||||
uint32_t size;
|
||||
} primercount_t, *pprimercount_t;
|
||||
|
||||
typedef struct {
|
||||
word_t word;
|
||||
pprimer_t primer;
|
||||
uint32_t position;
|
||||
bool_t strand;
|
||||
bool_t good; /*TR: Added*/
|
||||
} primermatch_t, *pprimermatch_t;
|
||||
|
||||
/*TR: Added*/
|
||||
@ -109,6 +120,19 @@ typedef struct {
|
||||
uint32_t matchcount;
|
||||
} primermatchcount_t, *pprimermatchcount_t;
|
||||
|
||||
typedef struct {
|
||||
pecoseq_t sequence;
|
||||
bool_t strand;
|
||||
const char *amplifia;
|
||||
int32_t length;
|
||||
} amplifia_t, *pamplifia_t;
|
||||
|
||||
typedef struct {
|
||||
pamplifia_t amplifias;
|
||||
uint32_t ampcount;
|
||||
uint32_t ampslot;
|
||||
} amplifiacount_t, *pamplifiacount_t;
|
||||
|
||||
typedef struct {
|
||||
char *amplifia;
|
||||
int32_t *taxonids;
|
||||
@ -124,30 +148,52 @@ typedef struct {
|
||||
} taxampset_t, *ptaxampset_t;
|
||||
|
||||
typedef struct {
|
||||
word_t w1;
|
||||
word_t w2;
|
||||
uint32_t inexample; /*inexample count*/
|
||||
uint32_t outexample; /*outexample count*/
|
||||
pprimer_t p1;
|
||||
bool_t asdirect1;
|
||||
pprimer_t p2;
|
||||
bool_t asdirect2;
|
||||
|
||||
uint32_t mind;
|
||||
uint32_t maxd;
|
||||
amplifiacount_t pcr;
|
||||
|
||||
uint32_t ampsetcount;
|
||||
uint32_t ampsetindex;
|
||||
pampseqset_t ampset;
|
||||
uint32_t inexample; //< example sequence count
|
||||
uint32_t outexample; //< counterexample sequence count
|
||||
uint32_t intaxa; //< example taxa count
|
||||
uint32_t outtaxa; //< counterexample taxa count
|
||||
uint32_t notwellidentifiedtaxa;
|
||||
|
||||
uint32_t taxsetcount;
|
||||
uint32_t taxsetindex;
|
||||
ptaxampset_t taxset;
|
||||
|
||||
uint32_t oktaxoncount;
|
||||
} pairs_t, *ppairs_t;
|
||||
// these statistics are relative to inexample sequences
|
||||
|
||||
uint32_t mind; //< minimum distance between primers
|
||||
uint32_t maxd; //< maximum distance between primers
|
||||
uint32_t sumd; //< distance sum
|
||||
float yule;
|
||||
float quorumin;
|
||||
float quorumout;
|
||||
//
|
||||
// uint32_t taxsetcount;
|
||||
// uint32_t taxsetindex;
|
||||
// ptaxampset_t taxset;
|
||||
//
|
||||
// uint32_t oktaxoncount;
|
||||
|
||||
} pair_t, *ppair_t;
|
||||
|
||||
/*TR: Added*/
|
||||
|
||||
typedef struct {
|
||||
ppairs_t pairs;
|
||||
uint32_t paircount;
|
||||
}pairscount_t, *ppairscount_t;
|
||||
size_t paircount;
|
||||
size_t pairslots;
|
||||
void* next;
|
||||
pair_t pairs[1];
|
||||
} pairlist_t, *ppairlist_t;
|
||||
|
||||
typedef struct {
|
||||
ppairlist_t first;
|
||||
ppairlist_t last;
|
||||
void *tree;
|
||||
int32_t count;
|
||||
} pairtree_t, *ppairtree_t;
|
||||
|
||||
typedef struct {
|
||||
pword_t words;
|
||||
@ -168,6 +214,18 @@ typedef struct {
|
||||
uint32_t size;
|
||||
} merge_t, *pmerge_t;
|
||||
|
||||
typedef struct {
|
||||
const char *amplifia;
|
||||
bool_t strand;
|
||||
int32_t length;
|
||||
int32_t taxoncount;
|
||||
void *taxontree;
|
||||
}amptotaxon_t, *pamptotaxon_t;
|
||||
|
||||
typedef struct {
|
||||
int32_t taxid;
|
||||
void *amptree;
|
||||
}taxontoamp_t, *ptaxontoamp_t;
|
||||
|
||||
typedef struct {
|
||||
uint32_t lmin; //**< Amplifia minimal length
|
||||
@ -189,6 +247,14 @@ typedef struct {
|
||||
bool_t no_multi_match;
|
||||
char taxonrank[20]; //TR to count ranks against a pair
|
||||
int32_t taxonrankidx; //TR to count ranks against a pair
|
||||
|
||||
// Some statistics useful for options filters
|
||||
|
||||
int32_t dbsize;
|
||||
int32_t insamples;
|
||||
int32_t outsamples;
|
||||
int32_t intaxa;
|
||||
int32_t outtaxa;
|
||||
} options_t, *poptions_t;
|
||||
|
||||
typedef ecoseq_t **pecodnadb_t;
|
||||
@ -232,7 +298,21 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
|
||||
|
||||
void sortmatch(pprimermatch_t table,uint32_t N);
|
||||
|
||||
ppairtree_t initpairtree(ppairtree_t tree);
|
||||
ppair_t pairintree (pair_t key,ppairtree_t pairlist);
|
||||
ppair_t insertpair(pair_t key,ppairtree_t list);
|
||||
|
||||
|
||||
/*TR: Added*/
|
||||
pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
|
||||
ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
|
||||
|
||||
int32_t counttaxon(int32_t taxid);
|
||||
int32_t getrankdbstats(pecodnadb_t seqdb,
|
||||
uint32_t seqdbsize,
|
||||
ecotaxonomy_t *taxonomy,
|
||||
poptions_t options);
|
||||
float taxonomycoverage(ppair_t pair, poptions_t options);
|
||||
char ecoComplementChar(char base);
|
||||
void taxonomyspecificity (ppair_t pair);
|
||||
|
||||
#endif /* EPSORT_H_ */
|
||||
|
||||
17
src/libecoprimer/goodtaxon.P
Normal file
17
src/libecoprimer/goodtaxon.P
Normal file
@ -0,0 +1,17 @@
|
||||
goodtaxon.o goodtaxon.P : goodtaxon.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h
|
||||
17
src/libecoprimer/hashsequence.P
Normal file
17
src/libecoprimer/hashsequence.P
Normal file
@ -0,0 +1,17 @@
|
||||
hashsequence.o hashsequence.P : hashsequence.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h
|
||||
@ -201,3 +201,8 @@ uint32_t ecoFindWord(pwordcount_t table,word_t word)
|
||||
return ~0;
|
||||
}
|
||||
|
||||
char ecoComplementChar(char base)
|
||||
{
|
||||
return (base < 4)? !base & 3: 4;
|
||||
}
|
||||
|
||||
|
||||
17
src/libecoprimer/libstki.P
Normal file
17
src/libecoprimer/libstki.P
Normal file
@ -0,0 +1,17 @@
|
||||
libstki.o libstki.P : libstki.c /usr/include/stdio.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/string.h libstki.h ecotype.h ecoprimer.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
../libecoPCR/ecoPCR.h apat.h debug.h
|
||||
17
src/libecoprimer/merge.P
Normal file
17
src/libecoprimer/merge.P
Normal file
@ -0,0 +1,17 @@
|
||||
merge.o merge.P : merge.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h
|
||||
17
src/libecoprimer/pairs.P
Normal file
17
src/libecoprimer/pairs.P
Normal file
@ -0,0 +1,17 @@
|
||||
pairs.o pairs.P : pairs.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h /usr/include/string.h
|
||||
@ -7,22 +7,28 @@
|
||||
|
||||
#include "ecoprimer.h"
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t primers,poptions_t options);
|
||||
static void buildPrimerPairsForOneSeq(uint32_t seqid,
|
||||
pecodnadb_t seqdb,
|
||||
pprimercount_t primers,
|
||||
ppairtree_t pairs,
|
||||
poptions_t options);
|
||||
|
||||
int32_t pairinlist (ppairs_t pairlist, word_t w1, word_t w2, uint32_t size)
|
||||
{
|
||||
uint32_t i;
|
||||
|
||||
for (i = 0; i < size; i++)
|
||||
{
|
||||
if (w1 == pairlist[i].w1 && w2 == pairlist[i].w2) return i;
|
||||
if (w1 == pairlist[i].w2 && w2 == pairlist[i].w1) return i;
|
||||
}
|
||||
return -1;
|
||||
}
|
||||
|
||||
char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
|
||||
|
||||
|
||||
|
||||
/*************************************
|
||||
*
|
||||
* pair collection management
|
||||
*
|
||||
*************************************/
|
||||
|
||||
#ifdef MASKEDCODE
|
||||
|
||||
char *addamplifiasetelem (ppair_t pair, char* amplifia, int32_t taxid)
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t j;
|
||||
@ -79,7 +85,7 @@ char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
|
||||
return ampused;
|
||||
}
|
||||
|
||||
void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
|
||||
void addtaxampsetelem (ppair_t pair, int32_t taxid, char *amplifia)
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t j;
|
||||
@ -135,6 +141,7 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
|
||||
|
||||
char *getamplifia (pecoseq_t seq, uint32_t start, uint32_t len)
|
||||
{
|
||||
fprintf(stderr,"start : %d length : %d\n",start,len);
|
||||
char *amplifia = ECOMALLOC((len + 1) * sizeof(char),"Cannot allocate amplifia");
|
||||
char *seqc = &seq->SQ[start];
|
||||
|
||||
@ -142,125 +149,44 @@ char *getamplifia (pecoseq_t seq, uint32_t start, uint32_t len)
|
||||
return amplifia;
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
/*TR: Added*/
|
||||
pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options)
|
||||
ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options)
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t j;
|
||||
uint32_t k;
|
||||
uint32_t d;
|
||||
uint32_t strt;
|
||||
uint32_t end;
|
||||
uint32_t paircount = 0;
|
||||
uint32_t pairslots = 500;
|
||||
int32_t foundindex;
|
||||
ppairs_t pairs;
|
||||
pairscount_t primerpairs;
|
||||
primermatchcount_t seqmatchcount;
|
||||
word_t w1;
|
||||
word_t w2;
|
||||
char *amplifia;
|
||||
char *oldamp;
|
||||
ppairtree_t primerpairs;
|
||||
|
||||
|
||||
pairs = ECOMALLOC(pairslots * sizeof(pairs_t),"Cannot allocate pairs table");
|
||||
primerpairs = initpairtree(NULL);
|
||||
|
||||
for (i=0; i < seqdbsize; i++)
|
||||
{
|
||||
seqmatchcount = buildPrimerPairsForOneSeq(i, primers, options);
|
||||
if (seqmatchcount.matchcount == 0) continue;
|
||||
|
||||
for (j=0; j < seqmatchcount.matchcount; j++)
|
||||
{
|
||||
strt = 0;
|
||||
w1 = seqmatchcount.matches[j].word;
|
||||
/*first word should b on direct strand*/
|
||||
if (!seqmatchcount.matches[j].strand)
|
||||
w1 = ecoComplementWord(w1, options->primer_length);
|
||||
else
|
||||
strt = options->primer_length;
|
||||
|
||||
for (k=j+1; k < seqmatchcount.matchcount; k++)
|
||||
{
|
||||
end = 0;
|
||||
w2 = seqmatchcount.matches[k].word;
|
||||
/*second word should be on reverse strand*/
|
||||
if (seqmatchcount.matches[k].strand)
|
||||
w2 = ecoComplementWord(w2, options->primer_length);
|
||||
else
|
||||
end = options->primer_length;
|
||||
|
||||
if (!(seqmatchcount.matches[j].good || seqmatchcount.matches[k].good)) continue;
|
||||
if (w1 == w2) continue;
|
||||
|
||||
d = seqmatchcount.matches[k].position - seqmatchcount.matches[j].position;
|
||||
if (d >= options->lmin && d <= options->lmax)
|
||||
{
|
||||
/*get amplified string*/
|
||||
amplifia = getamplifia (seqdb[i], seqmatchcount.matches[j].position + strt, d - strt - end);
|
||||
|
||||
foundindex = pairinlist(pairs, w1, w2, paircount);
|
||||
if (foundindex != -1) /*pair is found*/
|
||||
{
|
||||
if (seqdb[i]->isexample)
|
||||
pairs[foundindex].inexample++;
|
||||
else
|
||||
pairs[foundindex].outexample++;
|
||||
|
||||
if (pairs[foundindex].mind > d) pairs[foundindex].mind = d;
|
||||
else if (pairs[foundindex].maxd < d) pairs[foundindex].maxd = d;
|
||||
|
||||
oldamp = addamplifiasetelem (&pairs[foundindex], amplifia, seqdb[i]->ranktaxonid);
|
||||
/*if exact same string is already in amplifia set then use that for taxon set, it will help for
|
||||
* calculating the fully identified taxons i.e specificity, we will compare pointrs instead of strings
|
||||
* because same string means same pointer*/
|
||||
if (oldamp)
|
||||
{
|
||||
ECOFREE (amplifia, "free amplifia");
|
||||
amplifia = oldamp;
|
||||
}
|
||||
addtaxampsetelem (&pairs[foundindex], seqdb[i]->ranktaxonid, amplifia);
|
||||
|
||||
continue;
|
||||
}
|
||||
|
||||
if (paircount == pairslots)
|
||||
{
|
||||
pairslots += 500;
|
||||
pairs = ECOREALLOC(pairs, pairslots * sizeof(pairs_t), "Cannot allocate pairs table");
|
||||
}
|
||||
pairs[paircount].w1 = w1;
|
||||
pairs[paircount].w2 = w2;
|
||||
if (seqdb[i]->isexample) pairs[paircount].inexample = 1;
|
||||
else pairs[paircount].outexample = 1;
|
||||
pairs[paircount].mind = d;
|
||||
pairs[paircount].maxd = d;
|
||||
oldamp = addamplifiasetelem (&pairs[paircount], amplifia, seqdb[i]->ranktaxonid);
|
||||
addtaxampsetelem (&pairs[paircount], seqdb[i]->ranktaxonid, amplifia);
|
||||
|
||||
paircount++;
|
||||
}
|
||||
else if (d > options->lmax)
|
||||
break; /*once if the distance is greater than lmax then it will keep on increasing*/
|
||||
}
|
||||
}
|
||||
ECOFREE(seqmatchcount.matches, "Cannot free matches table");
|
||||
buildPrimerPairsForOneSeq(i, seqdb, primers, primerpairs, options);
|
||||
}
|
||||
primerpairs.pairs = ECOREALLOC(pairs, paircount * sizeof(pairs_t), "Cannot allocate pairs table");
|
||||
primerpairs.paircount = paircount;
|
||||
|
||||
return primerpairs;
|
||||
|
||||
}
|
||||
|
||||
primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t primers,poptions_t options)
|
||||
{
|
||||
uint32_t i,j,k;
|
||||
uint32_t matchcount=0;
|
||||
pprimermatch_t matches = NULL;
|
||||
primermatchcount_t seqmatchcount;
|
||||
#define DMAX (2000000000)
|
||||
|
||||
seqmatchcount.matchcount = 0;
|
||||
seqmatchcount.matches = NULL;
|
||||
static void buildPrimerPairsForOneSeq(uint32_t seqid,
|
||||
pecodnadb_t seqdb,
|
||||
pprimercount_t primers,
|
||||
ppairtree_t pairs,
|
||||
poptions_t options)
|
||||
{
|
||||
static uint32_t paircount=0;
|
||||
uint32_t i,j,k;
|
||||
uint32_t matchcount=0;
|
||||
pprimermatch_t matches = NULL;
|
||||
primermatchcount_t seqmatchcount;
|
||||
ppair_t pcurrent;
|
||||
pair_t current;
|
||||
pprimer_t wswp;
|
||||
bool_t bswp;
|
||||
size_t distance;
|
||||
bool_t strand;
|
||||
|
||||
for (i=0;i < primers->size; i++)
|
||||
{
|
||||
@ -268,7 +194,9 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
|
||||
matchcount+=primers->primers[i].reverseCount[seqid];
|
||||
}
|
||||
|
||||
if (matchcount <= 0) return seqmatchcount;
|
||||
if (matchcount <= 0)
|
||||
return;
|
||||
|
||||
matches = ECOMALLOC(matchcount * sizeof(primermatch_t),"Cannot allocate primers match table");
|
||||
|
||||
for (i=0,j=0;i < primers->size; i++)
|
||||
@ -277,17 +205,15 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
|
||||
{
|
||||
if (primers->primers[i].directCount[seqid]==1)
|
||||
{
|
||||
matches[j].word = primers->primers[i].word;
|
||||
matches[j].primer = primers->primers+i;
|
||||
matches[j].strand=TRUE;
|
||||
matches[j].good=primers->primers[i].good;/*TR: Added*/
|
||||
matches[j].position=primers->primers[i].directPos[seqid].value;
|
||||
j++;
|
||||
}
|
||||
else for (k=0; k < primers->primers[i].directCount[seqid]; k++,j++)
|
||||
{
|
||||
matches[j].word = primers->primers[i].word;
|
||||
matches[j].primer = primers->primers+i;
|
||||
matches[j].strand=TRUE;
|
||||
matches[j].good=primers->primers[i].good;/*TR: Added*/
|
||||
matches[j].position=primers->primers[i].directPos[seqid].pointer[k];
|
||||
}
|
||||
}
|
||||
@ -296,26 +222,144 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
|
||||
{
|
||||
if (primers->primers[i].reverseCount[seqid]==1)
|
||||
{
|
||||
matches[j].word = primers->primers[i].word;
|
||||
matches[j].primer = primers->primers+i;
|
||||
matches[j].strand=FALSE;
|
||||
matches[j].good=primers->primers[i].good;/*TR: Added*/
|
||||
matches[j].position=primers->primers[i].reversePos[seqid].value;
|
||||
j++;
|
||||
}
|
||||
else for (k=0; k < primers->primers[i].reverseCount[seqid]; k++,j++)
|
||||
{
|
||||
matches[j].word = primers->primers[i].word;
|
||||
matches[j].primer = primers->primers+i;
|
||||
matches[j].strand=FALSE;
|
||||
matches[j].good=primers->primers[i].good;/*TR: Added*/
|
||||
matches[j].position=primers->primers[i].reversePos[seqid].pointer[k];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
sortmatch(matches,matchcount); // sort in asscending order by position
|
||||
if (matchcount>1)
|
||||
{
|
||||
// fprintf(stderr,"\n====================================\n");
|
||||
|
||||
sortmatch(matches,matchcount); // sort in ascending order by position
|
||||
|
||||
for (i=0; i < matchcount;i++)
|
||||
{
|
||||
// For all primers matching the sequence
|
||||
|
||||
for(j=i+1;
|
||||
(j<matchcount)
|
||||
&& ((distance=matches[j].position - matches[i].position - options->primer_length) < options->lmax);
|
||||
j++
|
||||
)
|
||||
|
||||
// For all not too far primers
|
||||
|
||||
if ( (matches[i].primer->good || matches[j].primer->good)
|
||||
&& (distance > options->lmin)
|
||||
)
|
||||
{
|
||||
|
||||
// If possible primer pair
|
||||
|
||||
current.p1 = matches[i].primer;
|
||||
current.asdirect1=matches[i].strand;
|
||||
current.p2 = matches[j].primer;
|
||||
current.asdirect2= !matches[j].strand;
|
||||
current.maxd=DMAX;
|
||||
current.mind=DMAX;
|
||||
current.sumd=0;
|
||||
current.inexample=0;
|
||||
current.outexample=0;
|
||||
|
||||
|
||||
// Standardize the pair
|
||||
|
||||
strand = current.p2->word > current.p1->word;
|
||||
if (!strand)
|
||||
{
|
||||
wswp = current.p1;
|
||||
current.p1=current.p2;
|
||||
current.p2=wswp;
|
||||
|
||||
bswp = current.asdirect1;
|
||||
current.asdirect1=current.asdirect2;
|
||||
current.asdirect2=bswp;
|
||||
}
|
||||
|
||||
|
||||
// Look for the new pair in already seen pairs
|
||||
|
||||
pcurrent = insertpair(current,pairs);
|
||||
|
||||
|
||||
if (seqdb[seqid]->isexample)
|
||||
|
||||
{
|
||||
pcurrent->inexample++;
|
||||
pcurrent->sumd+=distance;
|
||||
|
||||
if ((pcurrent->maxd==DMAX) || (distance > pcurrent->maxd))
|
||||
pcurrent->maxd = distance;
|
||||
|
||||
if (distance < pcurrent->mind)
|
||||
pcurrent->mind = distance;
|
||||
}
|
||||
else
|
||||
pcurrent->outexample++;
|
||||
|
||||
if ((pcurrent->outexample+pcurrent->inexample)==1)
|
||||
{
|
||||
paircount++;
|
||||
pcurrent->pcr.ampslot=200;
|
||||
pcurrent->pcr.ampcount=0;
|
||||
pcurrent->pcr.amplifias = ECOMALLOC(sizeof(amplifia_t)*pcurrent->pcr.ampslot,
|
||||
"Cannot allocate amplifia table");
|
||||
}
|
||||
else
|
||||
{
|
||||
if (pcurrent->pcr.ampslot==pcurrent->pcr.ampcount)
|
||||
{
|
||||
pcurrent->pcr.ampslot+=200;
|
||||
pcurrent->pcr.amplifias = ECOREALLOC(pcurrent->pcr.amplifias,
|
||||
sizeof(amplifia_t)*pcurrent->pcr.ampslot,
|
||||
"Cannot allocate amplifia table");
|
||||
}
|
||||
}
|
||||
|
||||
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].length=distance;
|
||||
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].sequence=seqdb[seqid];
|
||||
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].strand=strand;
|
||||
|
||||
if (strand)
|
||||
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia= seqdb[seqid]->SQ + matches[i].position + options->primer_length;
|
||||
else
|
||||
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia= seqdb[seqid]->SQ + matches[j].position - 1 ;
|
||||
|
||||
pcurrent->pcr.ampcount++;
|
||||
// fprintf(stderr,"%c%c W1 : %s direct : %c",
|
||||
// "bG"[(int)pcurrent->p1->good],
|
||||
// "bG"[(int)pcurrent->p2->good],
|
||||
// ecoUnhashWord(pcurrent->p1->word, options->primer_length),
|
||||
// "><"[(int)pcurrent->asdirect1]
|
||||
// );
|
||||
//
|
||||
// fprintf(stderr," W2 : %s direct : %c distance : %d (min/max/avg : %d/%d/%f) in/out: %d/%d %c (%d pairs)\n",
|
||||
// ecoUnhashWord(pcurrent->p2->word, options->primer_length),
|
||||
// "><"[(int)pcurrent->asdirect2],
|
||||
// distance,
|
||||
// pcurrent->mind,pcurrent->maxd,
|
||||
// (pcurrent->inexample) ? (float)pcurrent->sumd/pcurrent->inexample:0.0,
|
||||
// pcurrent->inexample,pcurrent->outexample,
|
||||
// " N"[(pcurrent->outexample+pcurrent->inexample)==1],
|
||||
// paircount
|
||||
//
|
||||
// );
|
||||
//
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
pairs->count=paircount;
|
||||
|
||||
/*TR: Added*/
|
||||
seqmatchcount.matches = matches;
|
||||
seqmatchcount.matchcount = matchcount;
|
||||
return seqmatchcount;
|
||||
}
|
||||
|
||||
17
src/libecoprimer/pairtree.P
Normal file
17
src/libecoprimer/pairtree.P
Normal file
@ -0,0 +1,17 @@
|
||||
pairtree.o pairtree.P : pairtree.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h /usr/include/search.h
|
||||
136
src/libecoprimer/pairtree.c
Normal file
136
src/libecoprimer/pairtree.c
Normal file
@ -0,0 +1,136 @@
|
||||
/*
|
||||
* pairtree.c
|
||||
*
|
||||
* Created on: 7 mars 2009
|
||||
* Author: coissac
|
||||
*/
|
||||
|
||||
#include "ecoprimer.h"
|
||||
#include <search.h>
|
||||
|
||||
static void cleanpair(ppair_t pair);
|
||||
static void deletepairlist(ppairlist_t list);
|
||||
static int cmppair(const void* p1,const void*p2);
|
||||
|
||||
|
||||
static void cleanamplifiatlist(pamplifiacount_t list)
|
||||
{
|
||||
if (list->amplifias)
|
||||
ECOFREE(list->amplifias,
|
||||
"Free amplifia list");
|
||||
}
|
||||
|
||||
static void cleanpair(ppair_t pair)
|
||||
{
|
||||
cleanamplifiatlist(&(pair->pcr));
|
||||
}
|
||||
|
||||
static ppairlist_t newpairlist(ppairlist_t parent, size_t size)
|
||||
{
|
||||
ppairlist_t tmp;
|
||||
|
||||
tmp=ECOMALLOC(sizeof(pairlist_t)+sizeof(pair_t)*(size-1),
|
||||
"Cannot allocate new pair list");
|
||||
|
||||
tmp->pairslots=size;
|
||||
tmp->paircount=0;
|
||||
tmp->next=NULL;
|
||||
|
||||
if (parent)
|
||||
parent->next=(void*)tmp;
|
||||
|
||||
|
||||
return tmp;
|
||||
}
|
||||
|
||||
static void deletepairlist(ppairlist_t list)
|
||||
{
|
||||
size_t i;
|
||||
|
||||
if (list)
|
||||
{
|
||||
if (list->next)
|
||||
{
|
||||
deletepairlist(list->next);
|
||||
list->next=NULL;
|
||||
}
|
||||
for (i=0; i < list->paircount; i++)
|
||||
cleanpair((list->pairs)+i);
|
||||
|
||||
ECOFREE(list,"Delete pair list");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
static int cmppair(const void* p1,const void*p2)
|
||||
{
|
||||
ppair_t pr1,pr2;
|
||||
|
||||
pr1=(ppair_t)p1;
|
||||
pr2=(ppair_t)p2;
|
||||
|
||||
if (pr1->p1 < pr2->p1) return -1;
|
||||
if (pr1->p1 > pr2->p1) return 1;
|
||||
|
||||
if (pr1->asdirect1 < pr2->asdirect1) return -1;
|
||||
if (pr1->asdirect1 > pr2->asdirect1) return 1;
|
||||
|
||||
if (pr1->p2 < pr2->p2) return -1;
|
||||
if (pr1->p2 > pr2->p2) return 1;
|
||||
|
||||
if (pr1->asdirect2 < pr2->asdirect2) return -1;
|
||||
if (pr1->asdirect2 > pr2->asdirect2) return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
ppair_t pairintree (pair_t key,
|
||||
ppairtree_t pairlist)
|
||||
{
|
||||
if (!pairlist->tree)
|
||||
return NULL;
|
||||
|
||||
return *((ppair_t*)tsearch((const void *)(&key),
|
||||
&(pairlist->tree),
|
||||
cmppair
|
||||
));
|
||||
}
|
||||
|
||||
ppair_t insertpair(pair_t key,
|
||||
ppairtree_t list)
|
||||
{
|
||||
ppair_t current;
|
||||
ppair_t found;
|
||||
|
||||
if (list->last->paircount==list->last->pairslots)
|
||||
{
|
||||
list->last->next=newpairlist(list->last,100);
|
||||
list->last=list->last->next;
|
||||
}
|
||||
|
||||
current = list->last->pairs + list->last->paircount;
|
||||
*current=key;
|
||||
|
||||
found = *((ppair_t*)tsearch((const void *)current,
|
||||
&(list->tree),
|
||||
cmppair));
|
||||
if (found==current)
|
||||
list->last->paircount++;
|
||||
|
||||
return found;
|
||||
}
|
||||
|
||||
ppairtree_t initpairtree(ppairtree_t tree)
|
||||
{
|
||||
|
||||
if (!tree)
|
||||
tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree");
|
||||
|
||||
tree->first=newpairlist(NULL,300);
|
||||
tree->last=tree->first;
|
||||
|
||||
tree->tree=NULL;
|
||||
tree->count=0;
|
||||
|
||||
return tree;
|
||||
}
|
||||
17
src/libecoprimer/queue.P
Normal file
17
src/libecoprimer/queue.P
Normal file
@ -0,0 +1,17 @@
|
||||
queue.o queue.P : queue.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h
|
||||
17
src/libecoprimer/readdnadb.P
Normal file
17
src/libecoprimer/readdnadb.P
Normal file
@ -0,0 +1,17 @@
|
||||
readdnadb.o readdnadb.P : readdnadb.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h
|
||||
10
src/libecoprimer/smothsort.P
Normal file
10
src/libecoprimer/smothsort.P
Normal file
@ -0,0 +1,10 @@
|
||||
smothsort.o smothsort.P : smothsort.c /usr/include/assert.h /usr/include/sys/cdefs.h \
|
||||
/usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
|
||||
/usr/include/machine/_types.h /usr/include/i386/_types.h \
|
||||
/usr/include/sys/types.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/machine/endian.h /usr/include/i386/endian.h \
|
||||
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
|
||||
/usr/include/inttypes.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h
|
||||
17
src/libecoprimer/sortmatch.P
Normal file
17
src/libecoprimer/sortmatch.P
Normal file
@ -0,0 +1,17 @@
|
||||
sortmatch.o sortmatch.P : sortmatch.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h /usr/include/math.h /usr/include/architecture/i386/math.h
|
||||
17
src/libecoprimer/sortword.P
Normal file
17
src/libecoprimer/sortword.P
Normal file
@ -0,0 +1,17 @@
|
||||
sortword.o sortword.P : sortword.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h /usr/include/math.h /usr/include/architecture/i386/math.h
|
||||
18
src/libecoprimer/strictprimers.P
Normal file
18
src/libecoprimer/strictprimers.P
Normal file
@ -0,0 +1,18 @@
|
||||
strictprimers.o strictprimers.P : strictprimers.c ecoprimer.h /usr/include/inttypes.h \
|
||||
/usr/include/sys/cdefs.h /usr/include/_types.h \
|
||||
/usr/include/sys/_types.h /usr/include/machine/_types.h \
|
||||
/usr/include/i386/_types.h \
|
||||
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
|
||||
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
|
||||
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
|
||||
/usr/include/machine/signal.h /usr/include/i386/signal.h \
|
||||
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
|
||||
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
|
||||
/usr/include/sys/resource.h /usr/include/machine/endian.h \
|
||||
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
|
||||
/usr/include/libkern/_OSByteOrder.h \
|
||||
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
|
||||
/usr/include/machine/types.h /usr/include/i386/types.h \
|
||||
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
|
||||
debug.h /usr/include/string.h /usr/include/math.h \
|
||||
/usr/include/architecture/i386/math.h
|
||||
224
src/libecoprimer/taxstats.c
Normal file
224
src/libecoprimer/taxstats.c
Normal file
@ -0,0 +1,224 @@
|
||||
/*
|
||||
* taxstats.c
|
||||
*
|
||||
* Created on: 12 mars 2009
|
||||
* Author: coissac
|
||||
*/
|
||||
|
||||
#include <search.h>
|
||||
#include "ecoprimer.h"
|
||||
|
||||
static int cmptaxon(const void *t1, const void* t2);
|
||||
|
||||
static int cmptaxon(const void *t1, const void* t2)
|
||||
{
|
||||
const size_t taxid1=(size_t)t1;
|
||||
const size_t taxid2=(size_t)t2;
|
||||
|
||||
// fprintf(stderr,"==> counted taxid1 : %d\n",taxid1);
|
||||
// fprintf(stderr,"==> counted taxid2 : %d\n",taxid2);
|
||||
|
||||
if (taxid1 < taxid2)
|
||||
return -1;
|
||||
if (taxid1 > taxid2)
|
||||
return +1;
|
||||
return 0;
|
||||
}
|
||||
|
||||
int32_t counttaxon(int32_t taxid)
|
||||
{
|
||||
static void* taxontree=NULL;
|
||||
static int32_t taxoncount=0;
|
||||
|
||||
// fprintf(stderr,"counted taxid : %d taxontree %p\n",taxid,taxontree);
|
||||
|
||||
if (taxid==-1)
|
||||
{
|
||||
if (taxontree)
|
||||
ECOFREE(taxontree,"Free taxon tree");
|
||||
taxontree=NULL;
|
||||
taxoncount=0;
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
if ((taxid > 0) && ((!taxontree) || (!tfind((void*)((size_t)taxid),&taxontree,cmptaxon))))
|
||||
{
|
||||
tsearch((void*)((size_t)taxid),&taxontree,cmptaxon);
|
||||
taxoncount++;
|
||||
}
|
||||
|
||||
return taxoncount;
|
||||
}
|
||||
|
||||
int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
|
||||
poptions_t options)
|
||||
{
|
||||
|
||||
uint32_t i;
|
||||
ecotx_t *taxon;
|
||||
ecotx_t *tmptaxon;
|
||||
|
||||
counttaxon(-1);
|
||||
|
||||
for (i=0;i<seqdbsize;i++)
|
||||
{
|
||||
taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]);
|
||||
seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
|
||||
|
||||
tmptaxon = eco_findtaxonatrank(taxon,
|
||||
options->taxonrankidx);
|
||||
|
||||
// fprintf(stderr,"Taxid : %d %p\n",taxon->taxid,tmptaxon);
|
||||
|
||||
if (tmptaxon)
|
||||
{
|
||||
// fprintf(stderr,"orig : %d trans : %d\n",taxon->taxid,
|
||||
// tmptaxon->taxid);
|
||||
|
||||
seqdb[i]->ranktaxonid=tmptaxon->taxid;
|
||||
if (seqdb[i]->isexample)
|
||||
options->intaxa = counttaxon(tmptaxon->taxid);
|
||||
}
|
||||
else
|
||||
seqdb[i]->ranktaxonid=-1;
|
||||
}
|
||||
|
||||
counttaxon(-1);
|
||||
|
||||
for (i=0;i<seqdbsize;i++)
|
||||
{
|
||||
if (seqdb[i]->ranktaxonid>=0 && !seqdb[i]->isexample)
|
||||
options->outtaxa = counttaxon(seqdb[i]->ranktaxonid);
|
||||
}
|
||||
|
||||
return options->outtaxa + options->intaxa;
|
||||
}
|
||||
|
||||
|
||||
float taxonomycoverage(ppair_t pair, poptions_t options)
|
||||
{
|
||||
int32_t seqcount;
|
||||
int32_t i;
|
||||
int32_t incount=0;
|
||||
int32_t outcount=0;
|
||||
|
||||
|
||||
seqcount=pair->pcr.ampcount;
|
||||
|
||||
counttaxon(-1);
|
||||
for (i=0; i < seqcount; i++)
|
||||
if (pair->pcr.amplifias[i].sequence->isexample)
|
||||
incount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
|
||||
|
||||
counttaxon(-1);
|
||||
for (i=0; i < seqcount; i++)
|
||||
if (!pair->pcr.amplifias[i].sequence->isexample)
|
||||
outcount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
|
||||
|
||||
|
||||
pair->intaxa=incount;
|
||||
pair->outtaxa=outcount;
|
||||
return (float)incount/options->intaxa;
|
||||
}
|
||||
|
||||
|
||||
static int cmpamp(const void *ampf1, const void* ampf2)
|
||||
{
|
||||
int i;
|
||||
int j = 0;
|
||||
int incr = 1;
|
||||
char cd1;
|
||||
char cd2;
|
||||
int chd = 0;
|
||||
int len = 0;
|
||||
|
||||
pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
|
||||
pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
|
||||
|
||||
|
||||
if (pampf1->strand != pampf2->strand)
|
||||
{
|
||||
incr = -1;
|
||||
j = pampf1->length - 1;
|
||||
if (pampf2->strand)
|
||||
{
|
||||
pampf1 = (pamptotaxon_t) ampf2;
|
||||
pampf2 = (pamptotaxon_t) ampf1;
|
||||
chd = 1;
|
||||
}
|
||||
}
|
||||
|
||||
len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
|
||||
|
||||
for (i = 0; i < len; i++, j += incr)
|
||||
{
|
||||
cd1 = pampf1->amplifia[i];
|
||||
if (incr == -1)
|
||||
cd2 = ecoComplementChar(pampf2->amplifia[j]);
|
||||
else
|
||||
cd2 = pampf2->amplifia[j];
|
||||
|
||||
if (cd1 < cd2) return chd ? 1: -1;
|
||||
if (cd2 < cd1) return chd ? -1: 1;
|
||||
}
|
||||
|
||||
if (pampf1->length > pampf2->length) return chd ? -1: 1;
|
||||
if (pampf2->length > pampf1->length) return chd ? 1: -1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
void twalkaction (const void *node, VISIT order, int level)
|
||||
{
|
||||
const size_t taxid=(size_t)node;
|
||||
counttaxon(taxid);
|
||||
}
|
||||
|
||||
void taxonomyspecificity (ppair_t pair)
|
||||
{
|
||||
uint32_t i;
|
||||
uint32_t ampfindex = 0;
|
||||
int32_t taxid;
|
||||
void *ampftree = NULL;
|
||||
pamptotaxon_t pcurrentampf;
|
||||
pamptotaxon_t *ptmp;
|
||||
|
||||
pamptotaxon_t ampfwithtaxtree = ECOMALLOC(sizeof(amptotaxon_t) * pair->pcr.ampcount,"Cannot allocate amplifia tree");
|
||||
|
||||
for (i = 0; i < pair->pcr.ampcount; i++)
|
||||
{
|
||||
/*populate taxon ids tree against each unique amplifia
|
||||
i.e set of taxon ids for each amplifia*/
|
||||
ampfwithtaxtree[ampfindex].amplifia = pair->pcr.amplifias[i].amplifia;
|
||||
ampfwithtaxtree[ampfindex].strand = pair->pcr.amplifias[i].strand;
|
||||
ampfwithtaxtree[ampfindex].length = pair->pcr.amplifias[i].length;
|
||||
pcurrentampf = &fwithtaxtree[ampfindex];
|
||||
taxid = pair->pcr.amplifias[i].sequence->ranktaxonid;
|
||||
ptmp = tfind((const void*)pcurrentampf, &ftree, cmpamp);
|
||||
if (ptmp == NULL)
|
||||
{
|
||||
pcurrentampf = &fwithtaxtree[ampfindex];
|
||||
tsearch((void*)pcurrentampf,&ftree,cmpamp);
|
||||
ampfindex++;
|
||||
}
|
||||
else
|
||||
pcurrentampf = *ptmp;
|
||||
|
||||
if (tfind((void*)((size_t)taxid), &(pcurrentampf->taxontree), cmptaxon) == NULL)
|
||||
{
|
||||
pcurrentampf->taxoncount++;
|
||||
tsearch((void*)((size_t)taxid),&(pcurrentampf->taxontree),cmptaxon);
|
||||
}
|
||||
}
|
||||
|
||||
counttaxon(-1);
|
||||
for (i = 0; i < ampfindex; i++)
|
||||
{
|
||||
if (ampfwithtaxtree[i].taxoncount > 1)
|
||||
twalk(ampfwithtaxtree[i].taxontree, twalkaction);
|
||||
}
|
||||
|
||||
pair->notwellidentifiedtaxa = counttaxon(-2);
|
||||
ECOFREE (ampfwithtaxtree, "Free amplifia table");
|
||||
}
|
||||
Reference in New Issue
Block a user