switch to version 3.0.1b12

unfinished views. Closes #115

python/obitools3/commands/ecopcr.pyx

@@ -175,6 +175,14 @@ def run(config):
     o_dms_name = output[0].name
     o_view_name = output[1]
 
+    # Open the taxonomy DMS
+    taxdms = open_uri(config['obi']['taxoURI'],
+                     dms_only=True)
+    if taxdms is None:
+        raise Exception("Could not open taxonomy DMS")
+    tax_dms = taxdms[0]
+    tax_dms_name = taxdms[0].name
+    
     # Read taxonomy name    
     taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
 
@@ -197,7 +205,8 @@ def run(config):
 
     # TODO: primers in comments?
 
-    if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(taxonomy_name), \
+    if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name), 
+                  tax_dms.name_with_full_path, tobytes(taxonomy_name), \
                   o_dms.name_with_full_path, tobytes(o_view_name), comments, \
                   tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
                   config['ecopcr']['error'], \

python/obitools3/commands/ngsfilter.pyx

@@ -271,7 +271,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
         sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
 
     for seq in sequences:
-        if hasattr(seq, "quality_array"): 
+        if hasattr(seq, "quality_array") and seq.quality_array is not None: 
             q = -reduce(lambda x,y:x+y,(math.log10(z) for z in seq.quality_array),0)/len(seq.quality_array)*10
             seq[b'avg_quality']=q
             q = -reduce(lambda x,y:x+y,(math.log10(z) for z in seq.quality_array[0:10]),0)

python/obitools3/commands/stats.pyx

@@ -119,9 +119,12 @@ def mean(values, options):
 
 def variance(v):
     if len(v)==1: 
-        return 0 
+        return 0
     s = reduce(lambda x,y:(x[0]+y,x[1]+y**2),v,(0.,0.))
-    return s[1]/(len(v)-1) - s[0]**2/len(v)/(len(v)-1)
+    var = round(s[1]/(len(v)-1) - s[0]**2/len(v)/(len(v)-1), 5) # round to go around shady python rounding stuff when var is actually 0
+    if var == -0.0: # then fix -0 to +0 if was rounded to -0
+        var = 0.0
+    return var
 
 
 def varpop(values, options):

python/obitools3/dms/capi/obiecopcr.pxd

@@ -8,6 +8,7 @@ cdef extern from "obi_ecopcr.h" nogil:
 
     int obi_ecopcr(const char* input_dms_name,
                    const char* i_view_name,
+                   const char* tax_dms_name,
                    const char* taxonomy_name,
                    const char* output_dms_name,
                    const char* o_view_name,

python/obitools3/dms/taxo/taxo.pyx

@@ -93,6 +93,8 @@ cdef class Taxonomy(OBIWrapper) :
             raise RuntimeError("Error : Cannot read taxonomy %s" 
                                % tostr(name))
 
+        print("Taxonomy read", file=sys.stderr)
+
         taxo = OBIWrapper.new_wrapper(Taxonomy, pointer)
 
         dms.register(taxo)

python/obitools3/dms/view/view.pyx

@@ -345,7 +345,7 @@ cdef class View(OBIWrapper) :
                                        nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names, 
                                        dict_column=(new_nb_elements_per_line>1), comments=old_column.comments, alias=column_name_b+tobytes('___new___'))
         
-        switch_to_dict = old_column.nb_elements_per_line == 1 and new_nb_elements_per_line > 1
+        switch_to_dict = not old_column.dict_column and new_nb_elements_per_line > 1
         ori_key = old_column._elements_names[0]
         
         for i in range(length) :

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b11'
+serial= '1b12'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/obi_ecopcr.c

@@ -645,7 +645,8 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 
 int obi_ecopcr(const char* i_dms_name,
 		       const char* i_view_name,
-			   const char* taxonomy_name,     // TODO discuss that input dms assumed
+			   const char* tax_dms_name,
+			   const char* taxonomy_name,
 			   const char* o_dms_name,
 			   const char* o_view_name,
 			   const char* o_view_comments,
@@ -678,6 +679,7 @@ int obi_ecopcr(const char* i_dms_name,
 
 	OBIDMS_p          i_dms = NULL;
 	OBIDMS_p          o_dms = NULL;
+	OBIDMS_p          tax_dms = NULL;
 	OBIDMS_taxonomy_p taxonomy = NULL;
 	Obiview_p         i_view = NULL;
 	Obiview_p         o_view = NULL;
@@ -965,8 +967,16 @@ int obi_ecopcr(const char* i_dms_name,
 		return -1;
 	}
 
+	// Open taxonomy DMS
+	tax_dms = obi_open_dms(tax_dms_name, false);
+	if (tax_dms == NULL)
+	{
+		obidebug(1, "\nError opening the taxonomy DMS");
+		return -1;
+	}
+
 	// Open the taxonomy
-	taxonomy = obi_read_taxonomy(i_dms, taxonomy_name, false);
+	taxonomy = obi_read_taxonomy(tax_dms, taxonomy_name, false);
 	if (taxonomy == NULL)
 	{
 		obidebug(1, "\nError opening the taxonomy");

src/obi_ecopcr.h

@@ -77,7 +77,8 @@
  *
  * @param i_dms_name The path to the input DMS.
  * @param i_view_name The name of the input view.
- * @param taxonomy_name The name of the taxonomy in the input DMS.
+ * @param tax_dms_name The path to the DMS containing the taxonomy.
+ * @param taxonomy_name The name of the taxonomy.
  * @param o_dms_name The path to the output DMS.
  * @param o_view_name The name of the output view.
  * @param o_view_comments The comments to associate with the output view.
@@ -106,6 +107,7 @@
  */
 int obi_ecopcr(const char* i_dms_name,
 		       const char* i_view_name,
+			   const char* tax_dms_name,
 			   const char* taxonomy_name,
 			   const char* o_dms_name,
 			   const char* o_view_name,

src/obidms.c

@@ -1417,7 +1417,7 @@ char* obi_dms_formatted_infos(OBIDMS_p dms, bool detailed)
 	char*          view_name = NULL;
 	char*          tax_name = NULL;
 	char*          all_tax_dir_path = NULL;
-	int            i;
+	int            i, last_dot_pos;
 	struct dirent* dp;
 	Obiview_p      view;
 
@@ -1439,17 +1439,21 @@ char* obi_dms_formatted_infos(OBIDMS_p dms, bool detailed)
 		if ((dp->d_name)[0] == '.')
 			continue;
 		i=0;
-		while ((dp->d_name)[i] != '.')
+		while (i < strlen(dp->d_name))
+		{
+			if ((dp->d_name)[i] == '.')
+				last_dot_pos = i;
 			i++;
-		view_name = (char*) malloc((i+1) * sizeof(char));
+		}
+		view_name = (char*) malloc((last_dot_pos+1) * sizeof(char));
 		if (view_name == NULL)
 		{
 			obi_set_errno(OBI_MALLOC_ERROR);
 			obidebug(1, "\nError allocating memory for a view name when getting formatted DMS infos: file %s", dp->d_name);
 			return NULL;
 		}
-		strncpy(view_name, dp->d_name, i);
-		view_name[i] = '\0';
+		strncpy(view_name, dp->d_name, last_dot_pos);
+		view_name[last_dot_pos] = '\0';
 		view = obi_open_view(dms, view_name);
 		if (view == NULL)
 		{

src/obiview.c

@@ -2910,7 +2910,7 @@ int obi_clean_unfinished_views(OBIDMS_p dms)
 		if ((dp->d_name)[0] == '.')
 			continue;
 		i=0;
-		while ((dp->d_name)[i] != '.')
+		while (strncmp((dp->d_name)+i, ".obiview", 8))
 			i++;
 		relative_path = (char*) malloc(strlen(VIEW_DIR_NAME) + strlen(dp->d_name) + 2);
 		strcpy(relative_path, VIEW_DIR_NAME);