Switch to version 3.0.1b9

import of lists, fixed skipping of errors (was not overwriting), and
fixed --no-progress-bar option

python/obitools3/apps/optiongroups/__init__.py

@@ -49,7 +49,13 @@ def __addImportInputOption(optionManager):
                      action="store_const", dest="obi:inputformat",
                      default=None,
                      const=b'silva',
-                     help="Input file is in SILVA fasta format")
+                     help="Input file is in SILVA fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--rdp-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'rdp',
+                     help="Input file is in RDP training set fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
 
     group.add_argument('--embl-input',
                      action="store_const", dest="obi:inputformat",

python/obitools3/commands/addtaxids.pyx

@@ -45,7 +45,7 @@ def addOptions(parser):
                        metavar="<TAXID_TAG>",
                        default=b"TAXID",
                        help="Name of the tag to store the found taxid "
-                            "(default: 'TAXID'.")
+                            "(default: 'TAXID').")
 
     group.add_argument('-n', '--taxon-name-tag', 
                        action="store", 
@@ -53,7 +53,7 @@ def addOptions(parser):
                        metavar="<SCIENTIFIC_NAME_TAG>",
                        default=b"SCIENTIFIC_NAME",
                        help="Name of the tag giving the scientific name of the taxon "
-                            "(default: 'SCIENTIFIC_NAME'.")
+                            "(default: 'SCIENTIFIC_NAME').")
 
     group.add_argument('-g', '--try-genus-match',
                      action="store_true", dest="addtaxids:try_genus_match",
@@ -174,6 +174,7 @@ def run(config):
                 taxid_column[i] = taxon.taxid
                 found_count+=1
             elif try_genus: # try finding genus or other parent taxon from the first word
+                #print(i, o_view[i].id)
                 taxon_name_sp = taxon_name.split(b" ")
                 taxon = taxo.get_taxon_by_name(taxon_name_sp[0], res_anc)
                 if taxon is not None:

python/obitools3/commands/align.pyx

@@ -158,7 +158,7 @@ def run(config):
     i_view_name = i_uri.split(b"/")[0]
     i_column_name = b""
     i_element_name = b""
-    if len(i_uri.split(b"/")) == 2:
+    if len(i_uri.split(b"/")) >= 2:
         i_column_name = i_uri.split(b"/")[1]
     if len(i_uri.split(b"/")) == 3:
         i_element_name = i_uri.split(b"/")[2]
@@ -181,7 +181,7 @@ def run(config):
         i_dms_name_2 = i_dms_2.name
         i_uri_2 = input_2[1]
         original_i_view_name_2 = i_uri_2.split(b"/")[0]
-        if len(i_uri_2.split(b"/")) == 2:
+        if len(i_uri_2.split(b"/")) >= 2:
             i_column_name_2 = i_uri_2.split(b"/")[1]
         if len(i_uri_2.split(b"/")) == 3:
             i_element_name_2 = i_uri_2.split(b"/")[2]

python/obitools3/commands/build_ref_db.pyx

@@ -31,10 +31,9 @@ def addOptions(parser):
     group.add_argument('--threshold','-t',
                       action="store", dest="build_ref_db:threshold",
                       metavar='<THRESHOLD>',
-                      default=0.0,
+                      default=0.99,
                       type=float,
-                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
-                           " (no threshold).")
+                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.99.")
 
 
 def run(config):

python/obitools3/commands/cat.pyx

@@ -97,7 +97,7 @@ def run(config):
             Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
         
     # Initialize multiple elements columns
-    if type(output_0)==BufferedWriter: 
+    if type(output_0)!=BufferedWriter: 
         dict_cols = {}
         for v_uri in config["cat"]["views_to_cat"]:
             v = open_uri(v_uri)[1]

python/obitools3/commands/clean.pyx

@@ -54,11 +54,11 @@ def addOptions(parser):
                        default=False,
                        help="Only sequences labeled as heads are kept in the output. Default: False")
 
-    group.add_argument('--cluster-tags', '-C',
-                       action="store_true", 
-                       dest="clean:cluster-tags",
-                       default=False,
-                       help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
+#    group.add_argument('--cluster-tags', '-C',
+#                       action="store_true", 
+#                       dest="clean:cluster-tags",
+#                       default=False,
+#                       help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
 
     group.add_argument('--thread-count','-p',   # TODO should probably be in a specific option group
                        action="store", dest="clean:thread-count",
@@ -142,4 +142,5 @@ def run(config):
     
     i_dms.close(force=True)
 
-    logger("info", "Done.")
+    logger("info", "Done.")
+    

python/obitools3/commands/count.pyx

@@ -29,6 +29,12 @@ def addOptions(parser):
                         default=False,
                         help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
 
+    group.add_argument('-c','--count-tag',
+                        action="store", dest="count:countcol",
+                        default='COUNT',
+                        type=str,
+                        help="Name of the tag/column associated with the count information (default: COUNT).")
+
     
 def run(config):
     
@@ -41,18 +47,20 @@ def run(config):
     if input is None:
         raise Exception("Could not read input")
     entries = input[1]
-
+    
+    countcol = config['count']['countcol'] 
+    
     count1 = len(entries)
     count2 = 0
     
-    if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
+    if countcol in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
         for e in entries:
             PyErr_CheckSignals()
-            count2+=e[COUNT_COLUMN]
+            count2+=e[countcol]
 
-    if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
+    if countcol in entries and (config['count']['sequence'] == config['count']['all']):
         print(count1,count2)
-    elif COUNT_COLUMN in entries and config['count']['all']:
+    elif countcol in entries and config['count']['all']:
         print(count2)
     else:
         print(count1)

python/obitools3/commands/grep.pyx

@@ -258,6 +258,13 @@ def Filter_generator(options, tax_filter, i_view):
 
 
 def Taxonomy_filter_generator(taxo, options):
+    
+    if (("required_ranks" in options and options["required_ranks"]) or \
+       ("required_taxids" in options and options["required_taxids"]) or \
+       ("ignored_taxids" in options and options["ignored_taxids"])) and \
+       (taxo is None):
+        raise RollbackException("obi grep error: can't use taxonomy options without providing a taxonomy. Rollbacking view")
+    
     if taxo is not None:
         def tax_filter(seq):
             good = True

python/obitools3/commands/import.pyx

@@ -34,14 +34,17 @@ from obitools3.dms.capi.obidms cimport obi_import_view
 from obitools3.dms.capi.obitypes cimport obitype_t, \
                                          OBI_VOID, \
                                          OBI_QUAL, \
-                                         OBI_STR
+                                         OBI_STR, \
+                                         OBI_INT
 
 from obitools3.dms.capi.obierrno cimport obi_errno
 
 from obitools3.apps.optiongroups import addImportInputOption, \
                                         addTabularInputOption, \
                                         addTaxdumpInputOption, \
-                                        addMinimalOutputOption
+                                        addMinimalOutputOption, \
+                                        addNoProgressBarOption, \
+                                        addTaxonomyOption
 
 from obitools3.uri.decode import open_uri
 
@@ -50,6 +53,7 @@ from obitools3.apps.config import logger
 from cpython.exc cimport PyErr_CheckSignals
 
 from io import BufferedWriter
+import ast
 
 
 __title__="Import sequences from different formats into a DMS"
@@ -69,7 +73,9 @@ def addOptions(parser):
     addImportInputOption(parser)
     addTabularInputOption(parser)
     addTaxdumpInputOption(parser)
+    addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group = parser.add_argument_group('obi import specific options')
 
@@ -85,6 +91,10 @@ def addOptions(parser):
                      help="If importing a view into another DMS, do it by importing each line, saving disk space if the original view "
                           "has a line selection associated.")
 
+#    group.add_argument('--only-id',
+#                     action="store", dest="import:onlyid",
+#                     help="only id")
+
 def run(config):
     
     cdef   tuple       input
@@ -97,6 +107,7 @@ def run(config):
     cdef   bint        get_quality
     cdef   bint        NUC_SEQS_view
     cdef   bint        silva
+    cdef   bint        rdp
     cdef   int         nb_elts
     cdef   object      d
     cdef   View        view
@@ -180,6 +191,16 @@ def run(config):
         logger("info", "Done.")
         return
 
+    # Open taxonomy if there is one
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        taxo_uri = open_uri(config['obi']['taxoURI'])
+        if taxo_uri is None or taxo_uri[2] == bytes:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+
+    else :
+        taxo = None
+
     # If importing a view between two DMS and not wanting to save space if line selection in original view, use C API
     if isinstance(input[1], View) and not config['import']['space_priority']:
         if obi_import_view(input[0].name_with_full_path, o_dms.name_with_full_path, input[1].name, tobytes((config['obi']['outputURI'].split('/'))[-1])) < 0 :
@@ -192,8 +213,11 @@ def run(config):
         logger("info", "Done.")
         return
 
-    if entry_count >= 0:
+    # Reinitialize the progress bar
+    if entry_count >= 0 and config['obi']['noprogressbar'] == False:
         pb = ProgressBar(entry_count, config)
+    else:
+        pb = None
         
     NUC_SEQS_view = False
     if isinstance(output[1], View) :
@@ -202,20 +226,25 @@ def run(config):
             NUC_SEQS_view = True
     else: 
         raise NotImplementedError()
-        
+
     # Save basic columns in variables for optimization
     if NUC_SEQS_view :
         id_col = view[ID_COLUMN]
         def_col = view[DEFINITION_COLUMN]
         seq_col = view[NUC_SEQUENCE_COLUMN]
 
-    # Prepare taxon scientific name if SILVA file
-    if 'inputformat' in config['obi'] and config['obi']['inputformat'] == b"silva":
+    # Prepare taxon scientific name and taxid refs if RDP or SILVA file
+    silva = False
+    rdp = False
+    if 'inputformat' in config['obi'] and (config['obi']['inputformat'] == b"silva" or config['obi']['inputformat'] == b"rdp"):
+        #if taxo is None:
+        #    raise Exception("A taxonomy (as built by 'obi import --taxdump') must be provided for SILVA and RDP files")
         silva = True
-        sci_name_col = Column.new_column(view, SCIENTIFIC_NAME_COLUMN, OBI_STR)
-    else:
-        silva = False
-    
+        rdp = True
+        if taxo is not None:
+            sci_name_col = Column.new_column(view, SCIENTIFIC_NAME_COLUMN, OBI_STR)
+            taxid_col = Column.new_column(view, TAXID_COLUMN, OBI_INT)
+
     dcols = {}
 
     # First read through the entries to prepare columns with dictionaries as they are very time-expensive to rewrite
@@ -265,8 +294,13 @@ def run(config):
         # Reinitialize the input
         if isinstance(input[0], CompressedFile):
             input_is_file = True
-        if entry_count >= 0:
+        
+        # Reinitialize the progress bar
+        if entry_count >= 0 and config['obi']['noprogressbar'] == False:
             pb = ProgressBar(entry_count, config)
+        else:
+            pb = None
+
         try:
             input[0].close()
         except AttributeError:
@@ -275,6 +309,11 @@ def run(config):
         if input is None:
             raise Exception("Could not open input URI")
     
+#    if 'onlyid' in config['import']:
+#        onlyid = tobytes(config['import']['onlyid'])
+#    else:
+#        onlyid = None
+    
     entries = input[1]
     i = 0
     for entry in entries :
@@ -292,6 +331,9 @@ def run(config):
         elif not i%50000:
             logger("info", "Imported %d entries", i)
         
+#        if onlyid is not None and entry.id != onlyid:
+#            continue
+        
         try:
              
             if NUC_SEQS_view: 
@@ -307,11 +349,18 @@ def run(config):
                 if get_quality:
                     qual_col[i] = entry.quality
                     
-                # Parse taxon scientific name if SILVA file
-                if silva:
-                    sci_name = entry.definition.split(b";")[-1]
-                    sci_name_col[i] = sci_name
-             
+                # Parse taxon scientific name if RDP file
+                if (rdp or silva) and taxo is not None:
+                    sci_names = entry.definition.split(b";")
+                    for sci_name in reversed(sci_names):
+                        if sci_name.split()[0] != b'unidentified' and sci_name.split()[0] != b'uncultured' and sci_name.split()[0] != b'metagenome' :
+                            taxon = taxo.get_taxon_by_name(sci_name)
+                            if taxon is not None:
+                                sci_name_col[i] = taxon.name
+                                taxid_col[i] = taxon.taxid
+                                #print(taxid_col[i], sci_name_col[i])
+                                break
+
             for tag in entry :
                 
                 if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
@@ -323,27 +372,39 @@ def run(config):
                         tag = COUNT_COLUMN
                     if tag[:7] == b"merged_":
                         tag = MERGED_PREFIX+tag[7:]
-                        
+
+                    if type(value) == bytes and value[:1]==b"[" :
+                        try:
+                            if type(eval(value)) == list:
+                                value = eval(value)
+                                #print(value)
+                        except:
+                            pass
+                    
                     if tag not in dcols :
-                         
+                                                
                         value_type = type(value)
                         nb_elts = 1
                         value_obitype = OBI_VOID
                         dict_col = False
-                         
-                        if value_type == dict or value_type == list :
+                        
+                        if value_type == dict :
                             nb_elts = len(value)
                             elt_names = list(value)
-                            if value_type == dict :
-                                dict_col = True
+                            dict_col = True
                         else :
                             nb_elts = 1
                             elt_names = None
-                         
+                        
+                        if value_type == list :
+                            tuples = True
+                        else:
+                            tuples = False
+                        
                         value_obitype = get_obitype(value)
-                         
+                                                
                         if value_obitype != OBI_VOID :
-                            dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col), value_obitype)
+                            dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col, tuples=tuples), value_obitype)
                                                      
                             # Fill value
                             dcols[tag][0][i] = value
@@ -419,11 +480,12 @@ def run(config):
                                 dcols[tag][0][i] = value
         
         except Exception as e:
-            print("\nCould not import sequence:", entry, "(error raised:", e, ")")
+            print("\nCould not import sequence:", repr(entry), "(error raised:", e, ")")
             if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
                 raise e
             else:
                 pass
+                i-=1  # overwrite problematic entry
         
         i+=1
  

python/obitools3/commands/stats.pyx

@@ -154,7 +154,7 @@ def run(config):
     else :
         taxo = None
 
-    statistics = set(config['stats']['minimum']) | set(config['stats']['maximum']) | set(config['stats']['mean'])
+    statistics = set(config['stats']['minimum']) | set(config['stats']['maximum']) | set(config['stats']['mean']) | set(config['stats']['var']) | set(config['stats']['sd'])
     total = 0
     catcount={}
     totcount={}
@@ -195,7 +195,7 @@ def run(config):
         except KeyError:
             totcount[category]=totcount.get(category,0)+1
         for var in statistics:
-            if var in line:
+            if var in line and line[var] is not None:
                 v = line[var]
                 if var not in values:
                     values[var]={}
@@ -238,14 +238,34 @@ def run(config):
     else:
         sdvar= "%s"
         
-    hcat = "\t".join([pcat % x for x in config['stats']['categories']]) + \
-           "\t".join([minvar % x for x in config['stats']['minimum']])  + \
-           "\t".join([maxvar % x for x in config['stats']['maximum']])  + \
-           "\t".join([meanvar % x for x in config['stats']['mean']])  + \
-           "\t".join([varvar % x for x in config['stats']['var']])  + \
-           "\t".join([sdvar % x for x in config['stats']['sd']]) + \
-           "count\t" + \
-           "total" 
+    hcat = ""
+    
+    for x in config['stats']['categories']:
+        hcat += pcat % x
+        hcat += "\t"
+    
+    for x in config['stats']['minimum']:
+        hcat += minvar % x
+        hcat += "\t"
+
+    for x in config['stats']['maximum']:
+        hcat += maxvar % x
+        hcat += "\t"
+
+    for x in config['stats']['mean']:
+        hcat += meanvar % x
+        hcat += "\t"
+    
+    for x in config['stats']['var']:
+        hcat += varvar % x
+        hcat += "\t"
+
+    for x in config['stats']['sd']:
+        hcat += sdvar % x
+        hcat += "\t"
+
+    hcat += "count\ttotal" 
+    
     print(hcat)
     sorted_stats = sorted(catcount.items(), key = lambda kv:(totcount[kv[0]]), reverse=True)
     for i in range(len(sorted_stats)):

python/obitools3/dms/view/view.pyx

@@ -77,7 +77,7 @@ cdef class View(OBIWrapper) :
  
  
     @staticmethod
-    def import_view(object dms_1, object dms_2, object view_name_1, object view_name_2):
+    def import_view(object dms_1, object dms_2, object view_name_1, object view_name_2): # TODO argument to import line by line to avoid huge AVL copy
         if obi_import_view(tobytes(dms_1), tobytes(dms_2), tobytes(view_name_1), tobytes(view_name_2)) < 0 :
             raise Exception("Error importing a view")
 

python/obitools3/uri/decode.pyx

@@ -192,7 +192,7 @@ def open_uri(uri,
     
     config = getConfiguration()
     urip = urlparse(urib)
-            
+        
     if 'obi' not in config:
         config['obi']={}
     
@@ -209,13 +209,14 @@ def open_uri(uri,
     scheme = urip.scheme
     
     error = None
-    
-    if urib != b"-" and \
+        
+    if b'/taxonomy/' in urib or \
+        (urib != b"-" and \
         (scheme==b"dms" or \
          (scheme==b"" and \
           (((not input) and "outputformat" not in config["obi"]) or \
-          (input and "inputformat" not in config["obi"])))):   # TODO maybe not best way
-        
+          (input and "inputformat" not in config["obi"]))))):   # TODO maybe not best way
+                
         if default_dms is not None and b"/" not in urip.path:   # assuming view to open in default DMS (TODO discuss)
             dms=(default_dms, urip.path)
         else:
@@ -223,7 +224,7 @@ def open_uri(uri,
         
         if dms is None and default_dms is not None:
             dms=(default_dms, urip.path)
-
+                
         if dms is not None:
             if dms_only:
                 return (dms[0],
@@ -248,7 +249,7 @@ def open_uri(uri,
                 
                 if default_dms is None:
                     config["obi"]["defaultdms"]=resource[0]
-                                
+                
                 return (resource[0],
                         resource[1],
                         type(resource[1]),
@@ -464,7 +465,7 @@ def open_uri(uri,
         if format is not None:
             if seqtype==b"nuc":
                 objclass = Nuc_Seq    # Nuc_Seq_Stored? TODO
-                if format==b"fasta" or format==b"silva":
+                if format==b"fasta" or format==b"silva" or format==b"rdp":
                     if input:
                         iseq = fastaNucIterator(file, 
                                                 skip=skip, 

python/obitools3/utils.pxd

@@ -18,7 +18,7 @@ cdef object clean_empty_values_from_object(object value, exclude=*)
 
 cdef obitype_t get_obitype_single_value(object value)
 cdef obitype_t update_obitype(obitype_t obitype, object new_value)
-cdef obitype_t get_obitype_iterable_value(object value)
+cdef obitype_t get_obitype_iterable_value(object value, type t)
 cdef obitype_t get_obitype(object value)
 
 cdef object __etag__(bytes x, bytes nastring=*)

python/obitools3/utils.pyx

@@ -260,38 +260,51 @@ cdef obitype_t update_obitype(obitype_t obitype, object new_value) :
     
     new_type = type(new_value)
     
-    if obitype == OBI_INT :
-        if new_type == float or new_value > OBI_INT_MAX :
-            return OBI_FLOAT
+    #if new_type == NoneType:  # doesn't work because Cython sucks
+    if new_value == None or new_type==list or new_type==dict or new_type==tuple:
+        return obitype
+    
     # TODO BOOL vers INT/FLOAT
-    elif new_type == str or new_type == bytes :
+    if new_type == str or new_type == bytes :
         if obitype == OBI_SEQ and is_a_DNA_seq(tobytes(new_value)) :
             pass
         else :
             return OBI_STR
-    
+    elif obitype == OBI_INT :
+        if new_type == float or new_value > OBI_INT_MAX :
+            return OBI_FLOAT
+        
     return obitype
 
 
-cdef obitype_t get_obitype_iterable_value(object value) :
+cdef obitype_t get_obitype_iterable_value(object value, type t) :
     
     cdef obitype_t value_obitype
     
     value_obitype = OBI_VOID
     
-    for k in value :
-        if value_obitype == OBI_VOID :
-            value_obitype = get_obitype_single_value(value[k])
-        else :
-            value_obitype = update_obitype(value_obitype, value[k])
+    if t == dict:
+        for k in value :
+            if value_obitype == OBI_VOID :
+                value_obitype = get_obitype_single_value(value[k])
+            else :
+                value_obitype = update_obitype(value_obitype, value[k])
+    
+    elif t == list or t == tuple:
+        for v in value :
+            if value_obitype == OBI_VOID :
+                value_obitype = get_obitype_single_value(v)
+            else :
+                value_obitype = update_obitype(value_obitype, v)
     
     return value_obitype
 
 
 cdef obitype_t get_obitype(object value) :
     
-    if type(value) == dict or type(value) == list or type(value) == tuple :
-        return get_obitype_iterable_value(value)
+    t = type(value)
+    if t == dict or t == list or t == tuple :
+        return get_obitype_iterable_value(value, t)
     
     else :
         return get_obitype_single_value(value)

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b7'
+serial= '1b9'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/build_reference_db.c

@@ -863,7 +863,8 @@ int build_reference_db(const char* dms_name,
 	fprintf(stderr,"\rDone : 100 %%           \n");
 
 	// Add information about the threshold used to build the DB
-	snprintf(threshold_str, 5, "%f", threshold);
+#define snprintf_nowarn(...) (snprintf(__VA_ARGS__) < 0 ? abort() : (void)0)
+	snprintf_nowarn(threshold_str, 5, "%f", threshold);
 
 	new_comments = obi_add_comment((o_view->infos)->comments, DB_THRESHOLD_KEY_IN_COMMENTS, threshold_str);
 	if (new_comments == NULL)

src/obi_ecotag.c

@@ -233,7 +233,7 @@ int obi_ecotag(const char* dms_name,
 		// Write result (max score, threshold, LCA assigned, list of the ids of the best matches)
 
 
-	index_t         i, j, k;
+	index_t         i, j, k, t;
 	ecotx_t*        lca;
 	ecotx_t*        lca_in_array;
 	ecotx_t*        best_match;
@@ -259,16 +259,20 @@ int obi_ecotag(const char* dms_name,
 	int32_t*   		best_match_taxids;
 	int32_t*		best_match_taxids_to_store;
 	int				best_match_count;
+	int				best_match_taxid_count;
 	int             buffer_size;
 	int 			best_match_ids_buffer_size;
 	index_t         best_match_idx;
 	int32_t         lca_array_length;
 	int32_t         lca_taxid;
 	int32_t         taxid_best_match;
+	int32_t         taxid;
+	int32_t         taxid_to_store;
 	bool   			assigned;
 	const char*		lca_name;
 	const char*		id;
 	int				id_len;
+	bool			already_in;
 
 	OBIDMS_p          dms = NULL;
 	OBIDMS_p		  ref_dms = NULL;
@@ -488,10 +492,11 @@ int obi_ecotag(const char* dms_name,
 
 	for (i=0; i < query_count; i++)
 	{
-		if (i%1000 == 0)
+		if (i%10 == 0)
 			fprintf(stderr,"\rDone : %f %%       ", (i / (float) query_count)*100);
 
 		best_match_count = 0;
+		best_match_taxid_count = 0;
 		best_match_ids_length = 0;
 		threshold = ecotag_threshold;
 		best_score = 0.0;
@@ -543,6 +548,7 @@ int obi_ecotag(const char* dms_name,
 					// Reset the array with that match
 					best_match_ids_length = 0;
 					best_match_count = 0;
+					best_match_taxid_count = 0;
 				}
 
 				// Store in best match array
@@ -585,8 +591,27 @@ int obi_ecotag(const char* dms_name,
 
 				// Save match
 				best_match_array[best_match_count] = j;
-				best_match_taxids[best_match_count] = obi_get_int_with_elt_idx_and_col_p_in_view(ref_view, ref_taxid_column, j, 0);
 				best_match_count++;
+
+				// Save best match taxid only if not already in array
+				taxid_to_store = obi_get_int_with_elt_idx_and_col_p_in_view(ref_view, ref_taxid_column, j, 0);
+				already_in = false;
+				for (t=0; t<best_match_taxid_count; t++)
+				{
+					taxid = best_match_taxids[t];
+					//fprintf(stderr, "\ntaxid %d, taxid_to_store %d\n", taxid, taxid_to_store);
+					if (taxid == taxid_to_store)
+					{
+						already_in = true;
+						break;
+					}
+				}
+				if (! already_in)
+				{
+					best_match_taxids[best_match_taxid_count] = taxid_to_store;
+					best_match_taxid_count++;
+				}
+
 				strcpy(best_match_ids+best_match_ids_length, id);
 				best_match_ids_length = best_match_ids_length + id_len + 1;
 			}
@@ -693,7 +718,7 @@ int obi_ecotag(const char* dms_name,
 									assigned_name_column, lca_name,
 									assigned_status_column, assigned,
 									best_match_ids_column, best_match_ids_to_store, best_match_ids_length,
-									best_match_taxids_column, best_match_taxids_to_store, best_match_count,
+									best_match_taxids_column, best_match_taxids_to_store, best_match_taxid_count,
 									score_column, best_score
 									) < 0)
 							return -1;

src/obidmscolumn.h

@@ -36,7 +36,7 @@
 										   	   	 */
 #define COLUMN_GROWTH_FACTOR (2)	 	  		/**< The growth factor when a column is enlarged.
                                 	   	   	   	 */
-#define MAXIMUM_LINE_COUNT (1000000000)   		/**< The maximum line count for the data of a column (1E9). //TODO
+#define MAXIMUM_LINE_COUNT (1000000000000)      /**< The maximum line count for the data of a column (1E12). //TODO
                                 	       	   	 */
 #define COMMENTS_MAX_LENGTH (4096)        		/**< The maximum length for comments.
  	 	 	 	 	 	 	 	 	       	   	 */