Actualiser src/libecoPCR/ecorank.c

the -c option was present or not.

.gitignore

@@ -1,8 +1,12 @@
+/.gitignore
+/.cproject
+/.project
 
 # /src/
 /src/ecoPCR
 /src/ecofind
 /src/*.P
+/src/*.o
 /src/ecogrep
 
 # /src/libapat/
@@ -14,3 +18,4 @@
 
 # /src/libthermo/
 /src/libthermo/*.P
+

VERSION

@@ -1 +1 @@
-0.6.0
+1.0.0

src/ecopcr.c

@@ -6,7 +6,7 @@
 #include <getopt.h>
 
 
-#define VERSION "0.6.0"
+#define VERSION "1.0.1"
 
 
 /* ----------------------------------------------- */
@@ -26,7 +26,7 @@ static void PrintHelp()
         PP      "-a    : Salt concentration in M for Tm computation (default 0.05 M)\n\n");
         PP      "-c    : Consider that the database sequences are [c]ircular\n\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      "        has to be formatted first by the ecoPCRFormat.py program located.\n");
         PP      "        in the tools directory.\n");
         PP      "        ecoPCRFormat.py creates three file types :\n");
         PP      "            .sdx : contains the sequences\n");
@@ -80,7 +80,7 @@ static void PrintHelp()
         PP      "column 21 : sequence\n");
         PP      "column 22 : definition\n");
         PP      "------------------------------------------\n");
-        PP		" http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
+        PP		" https://git.metabarcoding.org/obitools/ecopcr/wikis/home\n");
         PP      "------------------------------------------\n\n");        
         PP      "\n");
 
@@ -566,11 +566,11 @@ int main(int argc, char **argv)
 		        )
 		     {
 		
-				scname = taxonomy->taxons->taxon[seq->taxid].name;
-				strncpy(head,seq->SQ,10);
-				head[10]=0;
-				strncpy(tail,seq->SQ+seq->SQ_length-10,10);
-				tail[10]=0;
+				//scname = taxonomy->taxons->taxon[seq->taxid].name;
+				//strncpy(head,seq->SQ,10);
+				//head[10]=0;
+				//strncpy(tail,seq->SQ+seq->SQ_length-10,10);
+				//tail[10]=0;
 		
 				apatseq=ecoseq2apatseq(seq,apatseq,circular);
 				
@@ -614,14 +614,17 @@ int main(int argc, char **argv)
 										length = 0;
 										if (posj > posi)
 											length = posj - posi - o1->patlen - o2->patlen;
-										if (posj < posi)
+										else {
+											if (circular > 0)
 												length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
-										if (length &&
+										}
+										if ((length>0) &&	// For when primers touch or overlap
 											(!lmin || (length >= lmin)) &&
 											(!lmax || (length <= lmax)))
+										{
 										    printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
 											//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
-	
+										}
 									}
 								}
 							}
@@ -647,7 +650,7 @@ int main(int argc, char **argv)
 					}	
 
 					o1cHits = ManberAll(apatseq,o1c,3,begin,length);
-					
+					// printf("circular=  %d\n",circular);
 					if (o1cHits)
 						for (i=0; i < o2Hits;i++)
 						{
@@ -666,13 +669,16 @@ int main(int argc, char **argv)
 
 										length = 0;
 										if (posj > posi)
-											length=posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : suppress by <EC> */
-										if (posj < posi)
+											length = posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
+										else {
+										if (circular > 0)
 											length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										}
 
-										if (length &&
+										if ((length>0) &&	// For when primers touch or overlap
 											(!lmin || (length >= lmin)) &&
 											(!lmax || (length <= lmax)))
+										{
 										    printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
 											//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);
 										}
@@ -680,6 +686,7 @@ int main(int argc, char **argv)
 								}
 							}
 						}
+				}	
 				
 		} /* End of taxonomic selection */
 		

src/global.mk

@@ -1,14 +1,13 @@
-MACHINE=MAC_OS_X
 LIBPATH= -Llibapat -LlibecoPCR -Llibthermo
-MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
+MAKEDEPEND = gcc -M $(CPPFLAGS) -o $*.d $<
 
 CC=gcc
-CFLAGS= -W -Wall -O2 -g
+CFLAGS= -O3 -w
 
 default: all
 
 %.o: %.c
-	$(CC) -D$(MACHINE) $(CFLAGS) -c -o $@ $<
+	$(CC) $(CFLAGS) -c -o $@ $<
 
 %.P : %.c
 	$(MAKEDEPEND)

src/libapat/Gtypes.h

@@ -27,13 +27,9 @@
 #define PROTO   1                       /* prototypes flag              */
 #endif
 
-#ifdef MAC_OS_C
-#define Vrai    true                    /* TC boolean values            */
-#define Faux    false                   /*                              */
-#else
+
 #define Vrai    0x1                     /* bool values  = TRUE          */
 #define Faux    0x0                     /*              = FALSE         */
-#endif
 
 #define Nil     NULL                    /* nil pointer                  */
 
@@ -42,28 +38,7 @@
 #define kBigUInt16      0xffff          /* plus grand 16 bits ~signe    */
 #define kBigUInt32      0xffffffff      /* plus grand 32 bits ~signe    */
 
-#ifdef MAC_OS_C
-/* ==================================================== */
-/*  Types (for Macintosh ThinK C || MWerks)             */
-/* ==================================================== */
 
-                                        /* --- specific sizes --------- */
-typedef long            Int32;          /* Int32  = 32 bits signe       */
-typedef unsigned long   UInt32;         /* UInt32 = 32 bits ~signe      */
-typedef short           Int16;          /* Int16  = 16 bits signe       */
-typedef unsigned short  UInt16;         /* UInt32 = 16 bits ~signe      */
-typedef char            Int8;           /* Int8   = 8 bits signe        */
-typedef unsigned char   UInt8;          /* UInt8  = 8 bits ~signe       */
-
-                                        /* --- default types ---------- */
-
-typedef Boolean         Bool;           /* booleen                      */
-
-typedef long            Int;            /* 'natural' int (>= 32 bits)   */
-
-typedef void            *Ptr;           /* pointeur                     */
-
-#elif ((defined SUN) || (defined SGI) || (defined UNIX))
 /* ==================================================== */
 /*  Types (for Sun & Iris - 32 bits machines)           */
 /* ==================================================== */
@@ -84,14 +59,7 @@ typedef int             Int;            /* 'natural' int (>= 32 bits)   */
 
 typedef void            *Ptr;           /* pointeur                     */
 
-#else 
-/* ==================================================== */
-/*  Types (for undefined machines)                      */
-/* ==================================================== */
 
-#error undefined MACHINE <please edit Gmach.h>
-
-#endif
 
 /* ==================================================== */
 /*  special macro for prototypes                        */

src/libecoPCR/ecorank.c

@@ -34,14 +34,11 @@ ecorankidx_t     *read_rankidx(const char *filename)
 int32_t rank_index(const char* label,ecorankidx_t* ranks)
 {
 	char **rep;
-	
+        fprintf(stderr,"Looking for rank -%s-... ",label);
 	rep = bsearch(label,ranks->label,ranks->count,sizeof(char*),compareRankLabel);
 
 	if (rep)
 		return rep-ranks->label;
-	else
-		ECOERROR(ECO_NOTFOUND_ERROR,"Rank label not found");
-		
 	return -1;
 }
 

src/libecoPCR/ecotax.c

@@ -341,6 +341,9 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 	if (taxonomy && tax!=taxonomy)
 	{
 		rankindex = rank_index("superkingdom",taxonomy->ranks);
+                if (rankindex < 0) {
+		   rankindex = rank_index("domain",taxonomy->ranks);
+                }
 		tax=taxonomy;
 	}
 

tools/ecoPCRFormat.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2.7
 
 import re
 import gzip
@@ -7,12 +7,9 @@ import sys
 import time
 import getopt
 
-try:
-    import psycopg2
-    _dbenable=True
-except ImportError:
 _dbenable=False
 
+
 #####
 #
 #
@@ -221,55 +218,6 @@ def readTaxonomyDump(taxdir):
     
     return taxonomy,ranks,alternativeName,index
 
-def readTaxonomyDB(dbname):
-    connection = psycopg2.connect(database=dbname)
-    
-    cursor = connection.cursor()
-    cursor.execute("select numid,rank,parent from ncbi_taxonomy.taxon")
-    taxonomy=[list(x) for x in cursor]
-
-    cursor.execute("select rank_class from ncbi_taxonomy.taxon_rank_class order by rank_class")
-    ranks=cursor.fetchall()
-    ranks = dict(map(None,(x[0] for x in ranks),xrange(len(ranks))))
-    
-    print >>sys.stderr,"Sorting taxons..."
-    taxonomy.sort(taxonCmp)
-
-    print >>sys.stderr,"Indexing taxonomy..."
-    index = {}
-    for t in taxonomy:
-        index[t[0]]=bsearchTaxon(taxonomy, t[0])
-    
-    print >>sys.stderr,"Indexing parent and rank..."
-    for t in taxonomy:
-        t[1]=ranks[t[1]]
-        try:
-            t[2]=index[t[2]]
-        except KeyError,e:
-            if t[2] is None and t[0]==1:
-                t[2]=index[t[0]]
-            else:
-                raise e
-        
-    cursor.execute("select taxid,name,category from ncbi_taxonomy.name")
-    
-    alternativeName=[]
-    for taxid,name,classname in cursor:
-        alternativeName.append((name,classname,index[taxid]))
-        if classname == 'scientific name':
-            taxonomy[index[taxid]].append(name)
-    
-    cursor.execute("select old_numid,current_numid from ncbi_taxonomy.taxon_id_alias")
- 
-    print >>sys.stderr,"Adding taxid alias..."
-    for taxid,current in cursor:
-        if current is not None:
-            index[taxid]=index[current]
-        else:
-            index[taxid]=None
-            
-       
-    return taxonomy,ranks,alternativeName,index
 
 #####
 #
@@ -585,10 +533,9 @@ def ecoParseOptions(arguments):
            }
     
     o,filenames = getopt.getopt(arguments,
-                                'ht:T:n:gfe',
+                                'ht:n:gfe',
                                 ['help',
                                  'taxonomy=',
-                                 'taxonomy_db=',
                                  'name=',
                                  'genbank',
                                  'fasta',
@@ -601,9 +548,6 @@ def ecoParseOptions(arguments):
         elif name in ('-t','--taxonomy'):
             opt['taxmod']='dump'
             opt['taxdir']=value
-        elif name in ('-T','--taxonomy_db'):
-            opt['taxmod']='db'
-            opt['taxdb']=value
         elif name in ('-n','--name'):
             opt['prefix']=value
         elif name in ('-g','--genbank'):
@@ -622,6 +566,7 @@ def ecoParseOptions(arguments):
 
     return opt,filenames
 
+
 def printHelp():
     print "-----------------------------------"
     print " ecoPCRFormat.py"
@@ -641,11 +586,7 @@ if __name__ == '__main__':
     
     opt,filenames = ecoParseOptions(sys.argv[1:])
     
-    if opt['taxmod']=='dump':
     taxonomy = readTaxonomyDump(opt['taxdir'])
-    elif opt['taxmod']=='db':
-        taxonomy = readTaxonomyDB(opt['taxdb'])
-        
     
     ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])