From 665b22989f606961a056030d9d7a7691132df105 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 12 Mar 2009 09:55:01 +0000
Subject: [PATCH] first version with preliminary print function

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@186 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecoPrimer                | Bin 58176 -> 62632 bytes
 src/ecoprimer.c              |  97 ++++++++++++++++++++++++++-
 src/libecoprimer/ecoprimer.h |   8 ++-
 src/libecoprimer/pairs.c     | 126 +++++++----------------------------
 src/libecoprimer/pairtree.c  |   2 +
 src/libecoprimer/taxstats.c  |  46 +++++++++++++
 6 files changed, 174 insertions(+), 105 deletions(-)
 create mode 100644 src/libecoprimer/taxstats.c

diff --git a/src/ecoPrimer b/src/ecoPrimer
index 96477a6a365c7c9b2a4801c5dda621252d32b3f3..2976f923f12a332d38b21cc689399e9b1dd26bf3 100755
GIT binary patch
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diff --git a/src/ecoprimer.c b/src/ecoprimer.c
index fb6b9fb..36cb480 100644
--- a/src/ecoprimer.c
+++ b/src/ecoprimer.c
@@ -91,9 +91,99 @@ void printcurrenttimeinmilli()
 
 /*TR: Added*/
 
-#ifdef MASKEDCODE
+void printapair(int32_t index,ppair_t pair, poptions_t options)
+{
+	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(ecoComplementWord(pair->p2->word,
+				                                    options->primer_length),options->primer_length));
+	else
+		printf("%s",ecoUnhashWord(pair->p2->word,options->primer_length));
+
+	printf("\t%d", pair->inexample);
+	printf("\t%d", pair->outexample);
+
+	printf("\t%d", pair->mind);
+	printf("\t%d", pair->maxd);
+	printf("\t%3.2f\t", (float)pair->sumd/pair->inexample);
+	printf("\t%4.3f\n", pair->yule);
+
+}
+
+uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t options)
+{
+	uint32_t i,j;
+	float q,qfp;
+	float y1,y2;
+
+	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)
+			j++;
+	}
+
+	return j;
+}
+
+void printpairs (ppairtree_t pairs, poptions_t options)
+{
+   ppair_t* sortedpairs;
+   ppair_t* index;
+   ppairlist_t pl;
+   int32_t i,j;
+   int32_t count;
+
+   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;
@@ -417,6 +507,9 @@ 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);
 
@@ -473,7 +566,7 @@ int main(int argc, char **argv)
 
   //  setoktaxforspecificity (&pairs);
 
-  //  printpairs (pairs, &options, rankdbstats, seqdbsize);
+     printpairs (pairs, &options);
 
 
 
diff --git a/src/libecoprimer/ecoprimer.h b/src/libecoprimer/ecoprimer.h
index 0feb6cb..cfbdcc7 100644
--- a/src/libecoprimer/ecoprimer.h
+++ b/src/libecoprimer/ecoprimer.h
@@ -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;
diff --git a/src/libecoprimer/pairs.c b/src/libecoprimer/pairs.c
index 0af6825..838bbc7 100644
--- a/src/libecoprimer/pairs.c
+++ b/src/libecoprimer/pairs.c
@@ -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;
 
 }
diff --git a/src/libecoprimer/pairtree.c b/src/libecoprimer/pairtree.c
index d1c0895..7155104 100644
--- a/src/libecoprimer/pairtree.c
+++ b/src/libecoprimer/pairtree.c
@@ -130,5 +130,7 @@ ppairtree_t initpairtree(ppairtree_t tree)
 	tree->last=tree->first;
 
 	tree->tree=NULL;
+	tree->count=0;
+
 	return tree;
 }
diff --git a/src/libecoprimer/taxstats.c b/src/libecoprimer/taxstats.c
new file mode 100644
index 0000000..b08d783
--- /dev/null
+++ b/src/libecoprimer/taxstats.c
@@ -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);
+		}
+
+}