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first version with preliminary print function

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@186 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-03-12 09:55:01 +00:00
parent d911d6bd20
commit 665b22989f
6 changed files with 174 additions and 105 deletions
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8
src/libecoprimer/ecoprimer.h
View File

@@ -165,7 +165,9 @@ typedef struct {
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 ampsetcount;
// uint32_t ampsetindex;
@@ -192,6 +194,7 @@ typedef struct {
ppairlist_t first;
ppairlist_t last;
void *tree;
int32_t count;
} pairtree_t, *ppairtree_t;
typedef struct {
@@ -234,6 +237,9 @@ 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
int32_t dbsize;
int32_t insamples;
int32_t outsamples;
} options_t, *poptions_t;
typedef ecoseq_t **pecodnadb_t;

126
src/libecoprimer/pairs.c
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@@ -174,87 +174,9 @@ ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t
{
buildPrimerPairsForOneSeq(i, seqdb, primers, primerpairs, 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");
// }
// primerpairs.pairs = ECOREALLOC(pairs, paircount * sizeof(pairs_t), "Cannot allocate pairs table");
// primerpairs.paircount = paircount;
// return primerpairs;
return primerpairs;
}
#define DMAX (2000000000)
@@ -327,7 +249,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
if (matchcount>1)
{
fprintf(stderr,"\n====================================\n");
// fprintf(stderr,"\n====================================\n");
sortmatch(matches,matchcount); // sort in ascending order by position
@@ -425,30 +347,30 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
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
);
// 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;
}

2
src/libecoprimer/pairtree.c
View File

@@ -130,5 +130,7 @@ ppairtree_t initpairtree(ppairtree_t tree)
tree->last=tree->first;
tree->tree=NULL;
tree->count=0;
return tree;
}

46
src/libecoprimer/taxstats.c Normal file
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@@ -0,0 +1,46 @@
/*
* taxstats.c
*
* Created on: 12 mars 2009
* Author: coissac
*/
#include <search.h>
static int cmptaxon(void *t1, void* t2);
static int cmptaxon(void *t1, void* t2)
{
if (*t1 < *t2)
return -1;
if (*t1 > *t2)
return +1;
return 0;
}
float taxonomycoverage(ppair_t pair, poptions_t options)
{
int32_t seqcount;
int32_t *taxon;
int32_t i;
void **taxontree;
ppair_t *inserted;
int32_t taxoncount;
seqcount=pair->pcr.ampcount;
taxon = ECOMALLOC(seqcount * sizeof(int32_t));
taxoncount=0;
taxontree=NULL;
for (i=0; i < seqcount; i++)
if (pair->pcr.amplifias[i].sequence->isexample)
{
inserted = tsearch(pair->pcr.amplifias[i].sequence->ranktaxonid,
taxontree,
cmptaxon);
}
}