diff --git a/src/ecoPrimer b/src/ecoPrimer index 13716c1..c3e5c3e 100755 Binary files a/src/ecoPrimer and b/src/ecoPrimer differ diff --git a/src/ecoprimer.c b/src/ecoprimer.c index b54ef97..fb6b9fb 100644 --- a/src/ecoprimer.c +++ b/src/ecoprimer.c @@ -75,7 +75,7 @@ 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() @@ -90,6 +90,9 @@ void printcurrenttimeinmilli() } /*TR: Added*/ + +#ifdef MASKEDCODE + void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize) { uint32_t i; @@ -98,9 +101,9 @@ void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, ui double sens; double speci; float avg; - + quorumseqs = seqdbsize * 70 / 100; - + printf("primer_1\tseq_1\tPrimer_2\tseq_2\tamplifia_count\t%s_snes\t%s_spe\tmin_l\tmax_l\tavr_l\n", options->taxonrank, options->taxonrank); for (i=0; i < pairs.paircount; i++) @@ -121,9 +124,12 @@ 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, + +void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy, poptions_t options, int32_t *insamples, int32_t *outsamples) { uint32_t i; @@ -131,7 +137,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo ecotx_t *tmptaxon; for (i=0;iisexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options); if (seqdb[i]->isexample) (*insamples)++; @@ -139,7 +145,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo (*outsamples)++; taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid; - tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid); + tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid); if (tmptaxon) tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx); if (tmptaxon) @@ -154,7 +160,7 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options) /*set taxon rank for which result is to be given*/ for (i = 0; i < taxonomy->ranks->count; i++) { - if (strcmp(taxonomy->ranks->label[i], options->taxonrank) == 0) + if (strcmp(taxonomy->ranks->label[i], options->taxonrank) == 0) { options->taxonrankidx = i; break; @@ -168,7 +174,7 @@ 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, +int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy, poptions_t options) { uint32_t i; @@ -177,7 +183,7 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax uint32_t namesindex = 0; int32_t *ranktaxonids = ECOMALLOC(nameslots * sizeof(int32_t), "Error in taxon rank allocation"); int32_t taxid; - + ecotx_t *tmptaxon; for (i=0;itaxid == ranktaxonids[j]) break; } if (j < namesindex) continue; /* name is already in list, so no need to add it*/ - + if (namesindex == nameslots) { nameslots += 500; @@ -204,11 +210,13 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax } } ECOFREE(ranktaxonids, "free rank taxon table"); - + return namesindex; } -void setoktaxforspecificity (ppairscount_t pairs) +#ifdef MASKEDCODE + +void setoktaxforspecificity (ppairtree_t pairs) { uint32_t i; uint32_t j; @@ -216,7 +224,7 @@ void setoktaxforspecificity (ppairscount_t pairs) uint32_t l; int taxcount; int32_t taxid; - + for (i = 0; i < pairs->paircount; i++) { for (j = 0; j < pairs->pairs[i].taxsetindex; j++) @@ -235,13 +243,13 @@ void setoktaxforspecificity (ppairscount_t pairs) taxcount += pairs->pairs[i].ampset[l].seqidindex; break; } - + if (taxid != pairs->pairs[i].ampset[l].taxonids[0]) { if (!taxid) taxid = pairs->pairs[i].ampset[l].taxonids[0]; - taxcount++; + taxcount++; } - + if (taxcount > 1) break; } } @@ -251,6 +259,8 @@ void setoktaxforspecificity (ppairscount_t pairs) } } +#endif + int main(int argc, char **argv) { pecodnadb_t seqdb; /* of type ecoseq_t */ @@ -264,11 +274,11 @@ int main(int argc, char **argv) int32_t insamples=0; 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; //printcurrenttime(); @@ -337,7 +347,7 @@ int main(int argc, char **argv) strncpy(options.taxonrank, optarg, 19); options.taxonrank[19] = 0; break; - + /* -------------------- */ case 'x': /* strict matching quorum */ /* -------------------- */ @@ -396,16 +406,16 @@ int main(int argc, char **argv) fprintf(stderr,"Reading taxonomy database ..."); taxonomy = read_taxonomy(options.prefix,0); fprintf(stderr,"Ok\n"); - + setresulttaxonrank(taxonomy, &options); /*TR: set rank level for statistics*/ - + fprintf(stderr,"Reading sequence database ...\n"); seqdb = readdnadb(options.prefix,&seqdbsize); fprintf(stderr,"Ok\n"); fprintf(stderr,"Sequence read : %d\n",(int32_t)seqdbsize); - + updateseqparams(seqdb, seqdbsize, taxonomy, &options, &insamples , &outsamples); rankdbstats = getrankdbstats(seqdb, seqdbsize, taxonomy, &options); @@ -419,7 +429,7 @@ int main(int argc, char **argv) printcurrenttimeinmilli(); words = lookforStrictPrimer(seqdb,seqdbsize,insamples,&options); printcurrenttimeinmilli(); - + fprintf(stderr,"\n Strict primer count : %d\n",words->size); if (options.no_multi_match) @@ -460,13 +470,14 @@ int main(int argc, char **argv) /*TR: Added*/ pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options); - setoktaxforspecificity (&pairs); - - printpairs (pairs, &options, rankdbstats, seqdbsize); - - - - ECOFREE(pairs.pairs,"Free pairs table"); + + // setoktaxforspecificity (&pairs); + + // printpairs (pairs, &options, rankdbstats, seqdbsize); + + + + //ECOFREE(pairs.pairs,"Free pairs table"); return 0; } diff --git a/src/global.mk b/src/global.mk index 94cf61d..7135690 100644 --- a/src/global.mk +++ b/src/global.mk @@ -3,7 +3,7 @@ LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $< CC=gcc -CFLAGS= -W -Wall -O5 -m64 -fast -g +CFLAGS= -W -Wall -O3 -m64 -fast -g #CFLAGS= -W -Wall -O0 -m64 -g #CFLAGS= -W -Wall -O5 -fast -g diff --git a/src/libecoPCR/ecoError.P b/src/libecoPCR/ecoError.P new file mode 100644 index 0000000..7c7ae71 --- /dev/null +++ b/src/libecoPCR/ecoError.P @@ -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 diff --git a/src/libecoPCR/ecoIOUtils.P b/src/libecoPCR/ecoIOUtils.P new file mode 100644 index 0000000..fc34a70 --- /dev/null +++ b/src/libecoPCR/ecoIOUtils.P @@ -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 diff --git a/src/libecoPCR/ecoMalloc.P b/src/libecoPCR/ecoMalloc.P new file mode 100644 index 0000000..ea3767b --- /dev/null +++ b/src/libecoPCR/ecoMalloc.P @@ -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 diff --git a/src/libecoPCR/ecodna.P b/src/libecoPCR/ecodna.P new file mode 100644 index 0000000..b9a71b9 --- /dev/null +++ b/src/libecoPCR/ecodna.P @@ -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 diff --git a/src/libecoPCR/ecofilter.P b/src/libecoPCR/ecofilter.P new file mode 100644 index 0000000..d46d3e0 --- /dev/null +++ b/src/libecoPCR/ecofilter.P @@ -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 diff --git a/src/libecoPCR/econame.P b/src/libecoPCR/econame.P new file mode 100644 index 0000000..4c9946c --- /dev/null +++ b/src/libecoPCR/econame.P @@ -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 diff --git a/src/libecoPCR/ecorank.P b/src/libecoPCR/ecorank.P new file mode 100644 index 0000000..75e09b9 --- /dev/null +++ b/src/libecoPCR/ecorank.P @@ -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 diff --git a/src/libecoPCR/ecoseq.P b/src/libecoPCR/ecoseq.P new file mode 100644 index 0000000..6222690 --- /dev/null +++ b/src/libecoPCR/ecoseq.P @@ -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 diff --git a/src/libecoPCR/ecotax.P b/src/libecoPCR/ecotax.P new file mode 100644 index 0000000..489fc97 --- /dev/null +++ b/src/libecoPCR/ecotax.P @@ -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 diff --git a/src/libecoprimer/Makefile b/src/libecoprimer/Makefile index d68202b..b4ae709 100644 --- a/src/libecoprimer/Makefile +++ b/src/libecoprimer/Makefile @@ -10,6 +10,7 @@ SOURCES = goodtaxon.c \ queue.c \ libstki.c \ sortmatch.c \ + pairtree.c \ pairs.c \ apat_search.c diff --git a/src/libecoprimer/amplifiatree.c b/src/libecoprimer/amplifiatree.c new file mode 100644 index 0000000..3698dea --- /dev/null +++ b/src/libecoprimer/amplifiatree.c @@ -0,0 +1,131 @@ +/* + * amplifiatree.c + * + * Created on: 7 mars 2009 + * Author: coissac + */ + +#include "ecoprimer.h" +#include + +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; +} diff --git a/src/libecoprimer/apat_search.P b/src/libecoprimer/apat_search.P new file mode 100644 index 0000000..bfc181f --- /dev/null +++ b/src/libecoprimer/apat_search.P @@ -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 diff --git a/src/libecoprimer/aproxpattern.P b/src/libecoprimer/aproxpattern.P new file mode 100644 index 0000000..1b3ebf8 --- /dev/null +++ b/src/libecoprimer/aproxpattern.P @@ -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 diff --git a/src/libecoprimer/ecoprimer.h b/src/libecoprimer/ecoprimer.h index 5d26573..0feb6cb 100644 --- a/src/libecoprimer/ecoprimer.h +++ b/src/libecoprimer/ecoprimer.h @@ -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 +148,51 @@ typedef struct { } taxampset_t, *ptaxampset_t; typedef struct { - word_t w1; - word_t w2; - uint32_t inexample; /*inexample count*/ - uint32_t outexample; /*outexample count*/ - - uint32_t mind; - uint32_t maxd; - - uint32_t ampsetcount; - uint32_t ampsetindex; - pampseqset_t ampset; - - uint32_t taxsetcount; - uint32_t taxsetindex; - ptaxampset_t taxset; - - uint32_t oktaxoncount; -} pairs_t, *ppairs_t; + pprimer_t p1; + bool_t asdirect1; + pprimer_t p2; + bool_t asdirect2; + + amplifiacount_t pcr; + + uint32_t inexample; //< example sequence count + uint32_t outexample; //< counterexample sequence count + + + + // 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 + +// +// uint32_t ampsetcount; +// uint32_t ampsetindex; +// pampseqset_t ampset; +// +// 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; +} pairtree_t, *ppairtree_t; typedef struct { pword_t words; @@ -232,7 +277,12 @@ 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); #endif /* EPSORT_H_ */ diff --git a/src/libecoprimer/goodtaxon.P b/src/libecoprimer/goodtaxon.P new file mode 100644 index 0000000..a990580 --- /dev/null +++ b/src/libecoprimer/goodtaxon.P @@ -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 diff --git a/src/libecoprimer/hashsequence.P b/src/libecoprimer/hashsequence.P new file mode 100644 index 0000000..d4be603 --- /dev/null +++ b/src/libecoprimer/hashsequence.P @@ -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 diff --git a/src/libecoprimer/libstki.P b/src/libecoprimer/libstki.P new file mode 100644 index 0000000..3b125ef --- /dev/null +++ b/src/libecoprimer/libstki.P @@ -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 diff --git a/src/libecoprimer/merge.P b/src/libecoprimer/merge.P new file mode 100644 index 0000000..fdb5796 --- /dev/null +++ b/src/libecoprimer/merge.P @@ -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 diff --git a/src/libecoprimer/pairs.P b/src/libecoprimer/pairs.P new file mode 100644 index 0000000..61a7976 --- /dev/null +++ b/src/libecoprimer/pairs.P @@ -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 diff --git a/src/libecoprimer/pairs.c b/src/libecoprimer/pairs.c index a5308a6..f01da82 100644 --- a/src/libecoprimer/pairs.c +++ b/src/libecoprimer/pairs.c @@ -7,34 +7,40 @@ #include "ecoprimer.h" #include +#include -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; char *ampused = NULL; - + if(pair->ampsetcount == 0) { pair->ampsetcount = 500; pair->ampsetindex = 0; pair->ampset = ECOMALLOC(pair->ampsetcount * sizeof(ampseqset_t),"Cannot allocate amplifia set"); } - + for (i = 0; i < pair->ampsetindex; i++) { if (strcmp (pair->ampset[i].amplifia, amplifia) == 0) @@ -43,43 +49,43 @@ char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid) break; } } - + if (i == 0) { pair->ampset[i].seqidcount = 100; pair->ampset[i].seqidindex = 0; pair->ampset[i].taxonids = ECOMALLOC(pair->ampset[i].seqidcount * sizeof(uint32_t),"Cannot allocate amplifia sequence table"); } - + if (pair->ampsetindex == pair->ampsetcount) { pair->ampsetcount += 500; pair->ampset = ECOREALLOC(pair->ampset, pair->ampsetcount * sizeof(ampseqset_t), "Cannot allocate amplifia set"); } - + if (pair->ampset[i].seqidindex == pair->ampset[i].seqidcount) { pair->ampset[i].seqidcount += 100; pair->ampset[i].taxonids = ECOREALLOC(pair->ampset[i].taxonids, pair->ampset[i].seqidcount * sizeof(int32_t), "Cannot allocate amplifia sequence table"); } - + if (pair->ampset[i].amplifia == NULL) { pair->ampset[i].amplifia = amplifia; pair->ampsetindex++; } - + for (j = 0; j < pair->ampset[i].seqidindex; j++) { if (pair->ampset[i].taxonids[j] == taxid) break; } - + if (j == pair->ampset[i].seqidindex) pair->ampset[i].taxonids[pair->ampset[i].seqidindex++] = 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; @@ -90,42 +96,42 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia) pair->taxsetindex = 0; pair->taxset = ECOMALLOC(pair->taxsetcount * sizeof(taxampset_t),"Cannot allocate taxon set"); } - + for (i = 0; i < pair->taxsetindex; i++) { if (pair->taxset[i].taxonid == taxid) break; } - + if (i == 0) { pair->taxset[i].amplifiacount = 100; pair->taxset[i].amplifiaindex = 0; pair->taxset[i].amplifia = ECOMALLOC(pair->taxset[i].amplifiacount * sizeof(char *),"Cannot allocate amplifia table"); } - + if (pair->taxsetindex == pair->taxsetcount) { pair->taxsetcount += 500; pair->taxset = ECOREALLOC(pair->taxset, pair->taxsetcount * sizeof(taxampset_t), "Cannot allocate taxon set"); } - + if (pair->taxset[i].amplifiaindex == pair->taxset[i].amplifiacount) { pair->taxset[i].amplifiacount += 100; pair->taxset[i].amplifia = ECOREALLOC(pair->taxset[i].amplifia, pair->taxset[i].amplifiacount * sizeof(char *), "Cannot allocate amplifia table"); } - + if (pair->taxset[i].taxonid == 0) { pair->taxset[i].taxonid = taxid; pair->taxsetindex++; } - + for (j = 0; j < pair->taxset[i].amplifiaindex; j++) { if (strcmp(pair->taxset[i].amplifia[j], amplifia) == 0) break; } - + if (j == pair->taxset[i].amplifiaindex) { pair->taxset[i].amplifia[j] = amplifia; @@ -135,16 +141,18 @@ 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]; - + strncpy(amplifia, seqc, 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; @@ -152,123 +160,131 @@ pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_ 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; + ppairtree_t primerpairs; primermatchcount_t seqmatchcount; word_t w1; word_t w2; char *amplifia; char *oldamp; - - 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; +// 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"); +// } +// 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) + +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; - seqmatchcount.matchcount = 0; - seqmatchcount.matches = NULL; - for (i=0;i < primers->size; i++) { matchcount+=primers->primers[i].directCount[seqid]; 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 +293,15 @@ 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 +310,139 @@ 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 - - /*TR: Added*/ - seqmatchcount.matches = matches; - seqmatchcount.matchcount = matchcount; - return seqmatchcount; + 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; + (jprimer_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 + + if (current.p2->word < current.p1->word) + { + 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[pcr.ampcount].length=distance; + pcurrent->pcr.amplifias[pcr.ampcount].sequence=*(seqdb[seqid]); + // pcurrent->pcr.amplifias[pcr.ampcount].strand= ; + // pcurrent->pcr.amplifias[pcr.ampcount].amplifia= ; + + 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 + + ); + + + } + } + } + + + } diff --git a/src/libecoprimer/pairtree.P b/src/libecoprimer/pairtree.P new file mode 100644 index 0000000..e38e995 --- /dev/null +++ b/src/libecoprimer/pairtree.P @@ -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 diff --git a/src/libecoprimer/pairtree.c b/src/libecoprimer/pairtree.c new file mode 100644 index 0000000..53a38c3 --- /dev/null +++ b/src/libecoprimer/pairtree.c @@ -0,0 +1,133 @@ +/* + * pairtree.c + * + * Created on: 7 mars 2009 + * Author: coissac + */ + +#include "ecoprimer.h" +#include + +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,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) +{ + fprintf(stderr,"coucou from initpairtree\n"); + + if (!tree) + tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree"); + + tree->first=newpairlist(NULL,500); + tree->last=tree->first; + + tree->tree=NULL; +} diff --git a/src/libecoprimer/queue.P b/src/libecoprimer/queue.P new file mode 100644 index 0000000..e7a6bc9 --- /dev/null +++ b/src/libecoprimer/queue.P @@ -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 diff --git a/src/libecoprimer/readdnadb.P b/src/libecoprimer/readdnadb.P new file mode 100644 index 0000000..9d16e11 --- /dev/null +++ b/src/libecoprimer/readdnadb.P @@ -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 diff --git a/src/libecoprimer/smothsort.P b/src/libecoprimer/smothsort.P new file mode 100644 index 0000000..2441cad --- /dev/null +++ b/src/libecoprimer/smothsort.P @@ -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 diff --git a/src/libecoprimer/sortmatch.P b/src/libecoprimer/sortmatch.P new file mode 100644 index 0000000..721cd46 --- /dev/null +++ b/src/libecoprimer/sortmatch.P @@ -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 diff --git a/src/libecoprimer/sortword.P b/src/libecoprimer/sortword.P new file mode 100644 index 0000000..57df213 --- /dev/null +++ b/src/libecoprimer/sortword.P @@ -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 diff --git a/src/libecoprimer/strictprimers.P b/src/libecoprimer/strictprimers.P new file mode 100644 index 0000000..cd887aa --- /dev/null +++ b/src/libecoprimer/strictprimers.P @@ -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