switch to version 3.0.0b25

displaying an error

MANIFEST.in

@@ -6,7 +6,7 @@ recursive-include doc/sphinx/source *.txt *.rst *.py
 recursive-include doc/sphinx/sphinxext *.py
 include doc/sphinx/Makefile
 include doc/sphinx/Doxyfile
-include README.txt
+include README.md
 include requirements.txt
 include scripts/obi
 

python/obitools3/commands/ecopcr.pyx

@@ -35,12 +35,14 @@ def addOptions(parser):
                        action="store", dest="ecopcr:primer1",
                        metavar='<PRIMER>',
                        type=str,
+                       required=True,
                        help="Forward primer, length must be less than or equal to 32")
 
     group.add_argument('--primer2', '-R',
                        action="store", dest="ecopcr:primer2",
                        metavar='<PRIMER>',
                        type=str,
+                       required=True,
                        help="Reverse primer, length must be less than or equal to 32")
 
     group.add_argument('--error', '-e',

python/obitools3/commands/grep.pyx

@@ -161,8 +161,7 @@ def obi_eval(compiled_expr, loc_env, line):
     return obi_eval_result
     
 
-def Filter_generator(options, tax_filter):
-    #taxfilter = taxonomyFilterGenerator(options)
+def Filter_generator(options, tax_filter, i_view):
 
     # Initialize conditions
     predicates = None
@@ -171,6 +170,9 @@ def Filter_generator(options, tax_filter):
     attributes = None
     if "attributes" in options and len(options["attributes"]) > 0:
         attributes = options["attributes"]
+        for attribute in attributes:
+            if attribute not in i_view:
+                return None
     lmax = None
     if "lmax" in options:
         lmax = options["lmax"]
@@ -196,6 +198,8 @@ def Filter_generator(options, tax_filter):
     if "attribute_patterns" in options and len(options["attribute_patterns"]) > 0:
         for p in options["attribute_patterns"]:
             attribute, pattern = p.split(":", 1)
+            if attribute not in i_view:
+                return None
             attribute_patterns[tobytes(attribute)] = re.compile(tobytes(pattern))
     
     def filter(line, loc_env):
@@ -324,21 +328,29 @@ def run(config):
  
     # Apply filter
     tax_filter = Taxonomy_filter_generator(taxo, config["grep"])
-    filter = Filter_generator(config["grep"], tax_filter)
+    filter = Filter_generator(config["grep"], tax_filter, i_view)        
     selection = Line_selection(i_view)
-    for i in range(len(i_view)):
-        PyErr_CheckSignals()
-        pb(i)
-        line = i_view[i]
-                 
-        loc_env = {"sequence": line, "line": line, "taxonomy": taxo, "obi_eval_result": False}
-        
-        good = filter(line, loc_env)
- 
-        if good :
-            selection.append(i)
-
-    pb(i, force=True)
+    
+    if filter is None and config["grep"]["invert_selection"]: # all sequences are selected: filter is None if no line will be selected because some columns don't exist
+        for i in range(len(i_view)):
+            PyErr_CheckSignals()
+            pb(i)
+            selection.append(i)        
+    
+    elif filter is not None :   # filter is None if no line will be selected because some columns don't exist
+        for i in range(len(i_view)):
+            PyErr_CheckSignals()
+            pb(i)
+            line = i_view[i]
+                     
+            loc_env = {"sequence": line, "line": line, "taxonomy": taxo, "obi_eval_result": False}
+            
+            good = filter(line, loc_env)
+     
+            if good :
+                selection.append(i)
+    
+    pb(len(i_view), force=True)
     print("", file=sys.stderr)
 
     # Create output view with the line selection

python/obitools3/commands/import.pyx

@@ -73,7 +73,7 @@ def addOptions(parser):
                      action="store_true", dest="import:preread",
                      default=False,
                      help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for "
-                          "a much faster import.")
+                          "a much faster import. This option is not recommended and will slow down the import in any other case.")
 
 
 def run(config):
@@ -236,7 +236,7 @@ def run(config):
             dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \
                               nb_elements_per_line=len(dict_dict[tag][0]), \
                               elements_names=list(dict_dict[tag][0])), \
-                          value_obitype)
+                          dict_dict[tag][1])
     
         
         # Reinitialize the input
@@ -260,7 +260,6 @@ def run(config):
 
         if entry is None:  # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
             if config['obi']['skiperror']:
-                i-=1
                 continue
             else:
                 raise RollbackException("obi import error, rollbacking view", view)
@@ -269,125 +268,134 @@ def run(config):
             pb(i)
         elif not i%50000:
             logger("info", "Imported %d entries", i)
-              
-        if NUC_SEQS_view: 
-            id_col[i] = entry.id
-            def_col[i] = entry.definition
-            seq_col[i] = entry.seq
-            # Check if there is a sequencing quality associated by checking the first entry    # TODO haven't found a more robust solution yet
-            if i == 0:
-                get_quality = QUALITY_COLUMN in entry
+        
+        try:
+             
+            if NUC_SEQS_view: 
+                id_col[i] = entry.id
+                def_col[i] = entry.definition
+                seq_col[i] = entry.seq
+                # Check if there is a sequencing quality associated by checking the first entry    # TODO haven't found a more robust solution yet
+                if i == 0:
+                    get_quality = QUALITY_COLUMN in entry
+                    if get_quality:
+                        Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
+                        qual_col = view[QUALITY_COLUMN]
                 if get_quality:
-                    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
-                    qual_col = view[QUALITY_COLUMN]
-            if get_quality:
-                qual_col[i] = entry.quality
-         
-        for tag in entry :
-            
-            if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
-                                
-                value = entry[tag]
-                if tag == b"taxid":
-                    tag = TAXID_COLUMN
-                if tag == b"count":
-                    tag = COUNT_COLUMN
-                if tag[:7] == b"merged_":
-                    tag = MERGED_PREFIX+tag[7:]
-                    
-                if tag not in dcols :
-                     
-                    value_type = type(value)
-                    nb_elts = 1
-                    value_obitype = OBI_VOID
-                     
-                    if value_type == dict or value_type == list :
-                        nb_elts = len(value)
-                        elt_names = list(value)
-                    else :
-                        nb_elts = 1
-                        elt_names = None
-                     
-                    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), value_obitype)
-                                                 
-                        # Fill value
-                        if value_type == dict and nb_elts == 1:  # special case that makes the OBI3 create a 1 elt/line column which won't read a dict value
-                            value = value[list(value.keys())[0]]       # The solution is to transform the value in a simple atomic one acceptable by the column
-                        dcols[tag][0][i] = value
-                     
-                    # TODO else log error?
- 
-                else :
-         
-                    rewrite = False
- 
-                    # Check type adequation
-                    old_type = dcols[tag][1]
-                    new_type = OBI_VOID
-                    new_type = update_obitype(old_type, value)
-                    if old_type != new_type :
-                        rewrite = True
- 
-                    try:
-                        # Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key                        
-                        if type(value) == dict and \
-                            dcols[tag][0].nb_elements_per_line == 1 \
-                            and set(dcols[tag][0].elements_names) != set(value.keys()) :
-                            raise IndexError  # trigger column rewrite
+                    qual_col[i] = entry.quality
+             
+            for tag in entry :
+                
+                if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
+                                    
+                    value = entry[tag]
+                    if tag == b"taxid":
+                        tag = TAXID_COLUMN
+                    if tag == b"count":
+                        tag = COUNT_COLUMN
+                    if tag[:7] == b"merged_":
+                        tag = MERGED_PREFIX+tag[7:]
                         
-                        # Fill value
-                        dcols[tag][0][i] = value
-                     
-                    except IndexError :
-                                                 
+                    if tag not in dcols :
+                         
                         value_type = type(value)
-                        old_column = dcols[tag][0]
-                        old_nb_elements_per_line = old_column.nb_elements_per_line
-                        new_nb_elements_per_line = 0
-                        old_elements_names = old_column.elements_names
-                        new_elements_names = None
+                        nb_elts = 1
+                        value_obitype = OBI_VOID
+                         
+                        if value_type == dict or value_type == list :
+                            nb_elts = len(value)
+                            elt_names = list(value)
+                        else :
+                            nb_elts = 1
+                            elt_names = None
+                         
+                        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), value_obitype)
+                                                     
+                            # Fill value
+                            if value_type == dict and nb_elts == 1:  # special case that makes the OBI3 create a 1 elt/line column which won't read a dict value
+                                value = value[list(value.keys())[0]]       # The solution is to transform the value in a simple atomic one acceptable by the column
+                            dcols[tag][0][i] = value
+                         
+                        # TODO else log error?
      
-                        #####################################################################
-                         
-                        # Check the length and keys of column lines if needed
-                        if value_type == dict :    # Check dictionary keys
-                            for k in value :
-                                if k not in old_elements_names :
-                                    new_elements_names = list(set(old_elements_names+[tobytes(k) for k in value]))
-                                    rewrite = True
-                                    break
-                         
-                        elif value_type == list or value_type == tuple :  # Check vector length
-                            if old_nb_elements_per_line < len(value) :
-                                new_nb_elements_per_line = len(value)
-                                rewrite = True
-                         
-                        #####################################################################
-                         
-                        if rewrite :
-                            if new_nb_elements_per_line == 0 and new_elements_names is not None :
-                                new_nb_elements_per_line = len(new_elements_names)
-                             
-                            # Reset obierrno 
-                            obi_errno = 0
- 
-                            dcols[tag] = (view.rewrite_column_with_diff_attributes(old_column.name, 
-                                                                                   new_data_type=new_type, 
-                                                                                   new_nb_elements_per_line=new_nb_elements_per_line,
-                                                                                   new_elements_names=new_elements_names,
-                                                                                   rewrite_last_line=False), 
-                                          new_type)
-                             
-                            # Update the dictionary:
-                            for t in dcols :
-                                dcols[t] = (view[t], dcols[t][1])
-                             
+                    else :
+             
+                        rewrite = False
+     
+                        # Check type adequation
+                        old_type = dcols[tag][1]
+                        new_type = OBI_VOID
+                        new_type = update_obitype(old_type, value)
+                        if old_type != new_type :
+                            rewrite = True
+     
+                        try:
+                            # Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key                        
+                            if type(value) == dict and \
+                                dcols[tag][0].nb_elements_per_line == 1 \
+                                and set(dcols[tag][0].elements_names) != set(value.keys()) :
+                                raise IndexError  # trigger column rewrite
+                            
                             # Fill value
                             dcols[tag][0][i] = value
-                                    
+                         
+                        except IndexError :
+                                                     
+                            value_type = type(value)
+                            old_column = dcols[tag][0]
+                            old_nb_elements_per_line = old_column.nb_elements_per_line
+                            new_nb_elements_per_line = 0
+                            old_elements_names = old_column.elements_names
+                            new_elements_names = None
+         
+                            #####################################################################
+                             
+                            # Check the length and keys of column lines if needed
+                            if value_type == dict :    # Check dictionary keys
+                                for k in value :
+                                    if k not in old_elements_names :
+                                        new_elements_names = list(set(old_elements_names+[tobytes(k) for k in value]))
+                                        rewrite = True
+                                        break
+                             
+                            elif value_type == list or value_type == tuple :  # Check vector length
+                                if old_nb_elements_per_line < len(value) :
+                                    new_nb_elements_per_line = len(value)
+                                    rewrite = True
+                             
+                            #####################################################################
+                             
+                            if rewrite :
+                                if new_nb_elements_per_line == 0 and new_elements_names is not None :
+                                    new_nb_elements_per_line = len(new_elements_names)
+                                 
+                                # Reset obierrno 
+                                obi_errno = 0
+     
+                                dcols[tag] = (view.rewrite_column_with_diff_attributes(old_column.name, 
+                                                                                       new_data_type=new_type, 
+                                                                                       new_nb_elements_per_line=new_nb_elements_per_line,
+                                                                                       new_elements_names=new_elements_names,
+                                                                                       rewrite_last_line=False), 
+                                              new_type)
+                                 
+                                # Update the dictionary:
+                                for t in dcols :
+                                    dcols[t] = (view[t], dcols[t][1])
+                                 
+                                # Fill value
+                                dcols[tag][0][i] = value
+        
+        except Exception as e:
+            print("\nCould not import sequence id:", entry.id, "(error raised:", e, ")")
+            if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
+                raise e
+            else:
+                pass
+        
         i+=1
  
     if pb is not None:

python/obitools3/commands/ls.pyx

@@ -34,9 +34,10 @@ def run(config):
     if input[2] == DMS and not config['ls']['longformat']:
         dms = input[0]
         l = []
-        for view in input[0]:
-            l.append(tostr(view) + "\t(Date created: " + str(bytes2str_object(dms[view].comments["Date created"]))+")")
-            dms[view].close()
+        for viewname in input[0]:
+            view = dms[viewname]
+            l.append(tostr(viewname) + "\t(Date created: " + str(bytes2str_object(view.comments["Date created"]))+")")
+            view.close()
         l.sort()
         for v in l:
             print(v)

python/obitools3/commands/ngsfilter.pyx

@@ -42,6 +42,7 @@ def addOptions(parser):
                      metavar="<URI>",
                      type=str,
                      default=None,
+                     required=True,
                      help="URI to the view containing the samples definition (with tags, primers, sample names,...).\n"
                           "\nWarning: primer lengths must be less than or equal to 32")
 
@@ -505,7 +506,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
                     sample=None
         
         if sample is None:
-            sequences[0][b'error']=b"No tags found"
+            sequences[0][b'error']=b"No sample with that tag combination"
             return False, sequences[0]
     
         sequences[0].update(sample)

python/obitools3/commands/uniq.pyx

@@ -419,12 +419,12 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
     print("")
     logger("info", "Second browsing through the input")
     # Initialize the progress bar
-    pb = ProgressBar(len(uniques), seconde=5)
+    pb = ProgressBar(len(view), seconde=5)
     o_idx = 0
+    total_treated = 0
     
     for unique_id in uniques :
         PyErr_CheckSignals()
-        pb(o_idx)
         
         merged_sequences = uniques[unique_id]
         
@@ -453,7 +453,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
             merged_dict[mkey] = {}
 
         for i_idx in merged_sequences:
-                        
+            pb(total_treated)
+ 
             i_id = i_id_col[i_idx]
             i_seq = view[i_idx]
 
@@ -504,7 +505,9 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
                 if key != COUNT_COLUMN and key != ID_COLUMN and key != NUC_SEQUENCE_COLUMN and key in o_seq and o_seq[key] != i_seq[key] \
                     and key not in merged_dict :
                     o_seq[key] = None
-
+            
+            total_treated += 1
+            
         # Write merged dicts
         for mkey in merged_dict: 
             if mkey in str_merged_cols:
@@ -526,7 +529,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
         o_count_col[o_idx] = o_count
         o_idx += 1
     
-    pb(len(uniques), force=True)
+    pb(len(view), force=True)
     
     # Deletes quality columns if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
     if QUALITY_COLUMN in view:
@@ -588,10 +591,11 @@ def run(config):
     # Initialize the progress bar
     pb = ProgressBar(len(entries), config, seconde=5)
     
-    try:
-        uniq_sequences(entries, o_view, pb, config, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])       
-    except Exception, e:
-        raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
+    if len(entries) > 0:
+        try:
+            uniq_sequences(entries, o_view, pb, config, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])       
+        except Exception, e:
+            raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
     
     print("", file=sys.stderr)
 

python/obitools3/dms/capi/obidmscolumn.pxd

@@ -63,6 +63,8 @@ cdef extern from "obidmscolumn.h" nogil:
     
     char* obi_get_elements_names(OBIDMS_column_p column)
     
+    char* obi_column_formatted_infos(OBIDMS_column_p column)
+
     index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
     
     int obi_column_write_comments(OBIDMS_column_p column, const char* comments)

python/obitools3/dms/column/column.pyx

@@ -14,6 +14,7 @@ from ..capi.obidms cimport obi_import_column
 from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
                                  obi_close_column, \
                                  obi_get_elements_names, \
+                                 obi_column_formatted_infos, \
                                  obi_column_write_comments
                                      
 from ..capi.obiutils cimport obi_format_date
@@ -38,7 +39,7 @@ from obitools3.utils cimport tobytes, \
  
 from obitools3.dms.column import typed_column
  
-from libc.stdlib  cimport free
+from libc.stdlib cimport free
  
 import importlib
 import inspect
@@ -288,9 +289,15 @@ cdef class Column(OBIWrapper) :
     @OBIWrapper.checkIsActive
     def __repr__(self) :
         cdef bytes s
+        #cdef char* s_b
+        #cdef str s_str
+        #s_b = obi_column_formatted_infos(self.pointer())
+        #s_str = bytes2str(s_b)
+        #free(s_b)
         s = self._alias + b", data type: " + self.data_type
+        #return s_str
         return bytes2str(s)
-
+    
          
     def close(self):  # TODO discuss, can't be called bc then bug when closing view that tries to close it in C
     

python/obitools3/dms/dms.pyx

@@ -227,7 +227,9 @@ cdef class DMS(OBIWrapper):
         cdef str s 
         s=""
         for view_name in self.keys():
-            s = s + repr(self.get_view(view_name)) + "\n"
+            view = self.get_view(view_name)
+            s = s + repr(view) + "\n"
+            view.close()
         return s
     
 

python/obitools3/dms/view/view.pyx

@@ -533,6 +533,7 @@ cdef class View(OBIWrapper) :
             for command in command_list:
                 s+=b"obi "
                 s+=command
+                s+=b"\n"
         return s
 
 

python/obitools3/libalign/_solexapairend.pyx

@@ -188,7 +188,7 @@ def buildConsensus(ali, seq, ref_tags=None):
         seq[b'shift']=ali.shift
     else:
         if len(ali[0])>999:   # TODO why?
-            raise AssertionError,"Too long alignemnt"
+            raise AssertionError,"Too long alignment"
     
         ic=IterOnConsensus(ali)
     
@@ -250,11 +250,21 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
     quality.extend(reverse.quality)
     seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality)
     seq[b"score"]=ali.score
-    seq[b"ali_direction"]=ali.direction
+    if len(ali.direction) > 0:
+        seq[b"ali_direction"]=ali.direction
+    else:
+        seq[b"ali_direction"]=None
     seq[b"mode"]=b"joined"
-    seq[b"pairedend_limit"]=len(forward)    
+    seq[b"pairedend_limit"]=len(forward)
+    seq[b"ali_length"] = ali.consensus_len
+    if ali.consensus_len > 0:
+        seq[b"score_norm"]=float(ali.score)/ali.consensus_len
+    else:
+        seq[b"score_norm"]=0.0
+  
     for tag in forward:
-        if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN:
+        if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
+            tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
             seq[tag] = forward[tag]
     return seq
 

python/obitools3/parsers/embl.pyx

@@ -177,7 +177,7 @@ def emblIterator_dir(dir_path,
     for filename in files:
         if read==only:
             return
-        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files, len(files)))
+        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files+1, len(files)))
         f = uopen(filename)
         if only is not None:
             only_f = only-read

python/obitools3/parsers/genbank.pyx

@@ -25,8 +25,9 @@ from libc.string cimport strcpy, strlen
 _featureMatcher = re.compile(b'^FEATURES.+\n(?=ORIGIN)',re.DOTALL + re.M)
 
 _headerMatcher = re.compile(b'^LOCUS.+(?=\nFEATURES)', re.DOTALL + re.M)
-_seqMatcher    = re.compile(b'(?<=ORIGIN).+(?=//\n)', re.DOTALL + re.M)
-_cleanSeq      = re.compile(b'[ \n0-9]+')
+_seqMatcher    = re.compile(b'ORIGIN.+(?=//\n)', re.DOTALL + re.M)
+_cleanSeq1     = re.compile(b'ORIGIN.+\n')
+_cleanSeq2     = re.compile(b'[ \n0-9]+')
 _acMatcher     = re.compile(b'(?<=^ACCESSION   ).+',re.M)
 _deMatcher     = re.compile(b'(?<=^DEFINITION  ).+\n( .+\n)*',re.M)
 _cleanDe       = re.compile(b'\n *')
@@ -42,7 +43,8 @@ def genbankParser(bytes text):
         ft     = _featureMatcher.search(text).group()
         
         s      = _seqMatcher.search(text).group()
-        s      = _cleanSeq.sub(b'', s).upper()
+        s      = _cleanSeq1.sub(b'', s)
+        s      = _cleanSeq2.sub(b'', s)
         
         acs    = _acMatcher.search(text).group()
         acs    = acs.split()
@@ -51,23 +53,23 @@ def genbankParser(bytes text):
         
         de     = _deMatcher.search(header).group()
         de     = _cleanDe.sub(b' ',de).strip().strip(b'.')
-
+    
+        tags = {}
+        extractTaxon(ft, tags)
+            
+        seq = Nuc_Seq(ac,
+                      s,
+                      definition=de,
+                      quality=None,
+                      offset=-1,
+                      tags=tags)
+    
     except Exception as e:
         print("\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")")
         # Do not raise any Exception if you need the possibility to resume the generator
         # (Python generators can't resume after any exception is raised)
         return None
-    
-    tags = {}
-    extractTaxon(ft, tags)
-        
-    seq = Nuc_Seq(ac,
-                  s,
-                  definition=de,
-                  quality=None,
-                  offset=-1,
-                  tags=tags)
-    
+
     return seq
 
 
@@ -171,10 +173,12 @@ def genbankIterator_dir(dir_path,
     read = 0
     read_files = 0
     files = [filename for filename in glob.glob(os.path.join(path, b'*.gbff*'))]
+    files.extend([filename for filename in glob.glob(os.path.join(path, b'*.seq*'))])  # new genbank extension
+    files = list(set(files))
     for filename in files:
         if read==only:
             return
-        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files, len(files)))
+        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files+1, len(files)))
         f = uopen(filename)
         if only is not None:
             only_f = only-read

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0-beta17'
+serial= '0b25'
 
-version ="%d.%02d.%s" % (major,minor,serial)
+version ="%d.%d.%s" % (major,minor,serial)

requirements.txt

@@ -0,0 +1,5 @@
+--extra-index-url https://pypi.python.org/simple/
+Cython>=0.24
+Sphinx>=1.2.0
+ipython>=3.0.0
+breathe>=4.0.0

setup.py

@@ -5,8 +5,9 @@ import re
 import subprocess
 
 from distutils import log
-from distutils.core import setup
-    
+#from distutils.core import setup
+from setuptools import setup    # to work with pip
+
 from distutils.core import Extension
 from distutils.sysconfig import get_python_lib
 
@@ -26,10 +27,11 @@ class Distribution(ori_Distribution):
         
         ori_Distribution.__init__(self, attrs)
         
-        self.global_options.insert(0,('cobitools3', None, "intall location of the C library"
+        self.global_options.insert(0,('cobitools3', None, "install location of the C library"
                                      ))
 
 from distutils.command.build import build as build_ori
+from setuptools.command.bdist_egg import bdist_egg as bdist_egg_ori
 from distutils.core import Command
 
 
@@ -70,6 +72,12 @@ class build(build_ori):
         build_ori.run(self)
 
 
+class bdist_egg(bdist_egg_ori):
+    def run(self):
+        self.run_command('build_clib')
+        bdist_egg_ori.run(self)
+
+
 sys.path.append(os.path.abspath("python"))
 
 
@@ -88,9 +96,10 @@ PACKAGE     = "OBITools3"
 VERSION     = version
 AUTHOR      = 'Celine Mercier'
 EMAIL       = 'celine.mercier@metabarcoding.org'
-URL         = "http://metabarcoding.org/obitools3"
+URL         = "https://metabarcoding.org/obitools3"
+PLATFORMS   = "posix"
 LICENSE     = "CeCILL-V2"
-DESCRIPTION = "Tools and library for DNA metabarcoding",
+DESCRIPTION = "A package for the management of analyses and data in DNA metabarcoding."
 PYTHONMIN   = '3.5'
 
 SRC       = 'python'
@@ -147,17 +156,24 @@ classifiers=['Development Status :: 4 - Beta',
              'Topic :: Utilities',
              ]
 
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
 setup(name=PACKAGE,
       description=DESCRIPTION,
+      long_description=long_description,
+      long_description_content_type="text/markdown",
       classifiers=classifiers,
       version=VERSION,
       author=AUTHOR,
       author_email=EMAIL,
+      platforms=PLATFORMS,
       license=LICENSE,
       url=URL,
       ext_modules=xx,
       distclass=Distribution,
       cmdclass={'build': build,
+                'bdist_egg': bdist_egg,
                 'build_clib': build_clib},
       cobitools3=get_python_lib(),
       packages = findPackage('python'),

src/kmer_similarity.c

@@ -413,7 +413,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	 	return NULL;
 	}
 
-	score = max_common_kmers + kmer_size - 1;  // aka the number of nucleotides in the longest stretch of kmers perfectly matching
+	if (max_common_kmers > 0)
+		score = max_common_kmers + kmer_size - 1;  // aka the number of nucleotides in the longest stretch of kmers perfectly matching
+	else
+		score = 0;
 	abs_shift = abs(best_shift);
 
 	// Save result in Obi_ali structure
@@ -423,10 +426,15 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	ali->shift = abs_shift;
 	ali->consensus_seq = NULL;
 	ali->consensus_qual = NULL;
-	if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
-		strcpy(ali->direction, "left");
+	if (score == 0)
+		ali->direction[0] = '\0';
 	else
-		strcpy(ali->direction, "right");
+	{
+		if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
+			strcpy(ali->direction, "left");
+		else
+			strcpy(ali->direction, "right");
+	}
 
 	// Build the consensus sequence if asked
 	if (build_consensus)

src/obi_ecotag.c

@@ -71,9 +71,12 @@ static int create_output_columns(Obiview_p o_view);
  * @param name The assigned scientific name.
  * @param assigned_status_column A pointer on the column where the assigned status should be written.
  * @param assigned The assigned status (whether the sequence was assigned to a taxon or not).
- * @param best_match_column A pointer on the column where the list of ids of the best matches should be written.
+ * @param best_match_ids_column A pointer on the column where the list of ids of the best matches should be written.
  * @param best_match_ids The list of ids of the best matches as an array of the concatenated ids separated by '\0'.
  * @param best_match_ids_length The total length of the array of ids of best matches.
+ * @param best_match_taxids_column A pointer on the column where the list of taxids of the best matches should be written.
+ * @param best_match_taxids The list of taxids of the best matches as an array of the taxids.
+ * @param best_match_taxids_length The length of the array of taxids of best matches.
  * @param score_column A pointer on the column where the score should be written.
  * @param score The similarity score of the sequence with its best match(es).
  *
@@ -87,7 +90,8 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 							OBIDMS_column_p assigned_taxid_column, int32_t taxid,
 							OBIDMS_column_p assigned_name_column, const char* name,
 							OBIDMS_column_p assigned_status_column, bool assigned,
-							OBIDMS_column_p best_match_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_ids_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_taxids_column, const int32_t* best_match_taxids, int best_match_taxids_length,
 							OBIDMS_column_p score_column, double score);
 
 
@@ -130,7 +134,14 @@ static int create_output_columns(Obiview_p o_view)
 	// Column for array of best match ids
 	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, true, false, NULL, NULL, -1, "{}", true) < 0)
 	{
-		obidebug(1, "\nError creating the column for the array of ids of the best match in ecotag");
+		obidebug(1, "\nError creating the column for the array of ids of best matches in ecotag");
+		return -1;
+	}
+
+	// Column for array of best match taxids
+	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, true, false, NULL, NULL, -1, "{}", true) < 0)
+	{
+		obidebug(1, "\nError creating the column for the array of taxids of best matches in ecotag");
 		return -1;
 	}
 
@@ -142,7 +153,8 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 							OBIDMS_column_p assigned_taxid_column, int32_t taxid,
 							OBIDMS_column_p assigned_name_column, const char* name,
 							OBIDMS_column_p assigned_status_column, bool assigned,
-							OBIDMS_column_p best_match_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_ids_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_taxids_column, const int32_t* best_match_taxids, int best_match_taxids_length,
 							OBIDMS_column_p score_column, double score)
 {
 	// Write the assigned taxid
@@ -167,9 +179,16 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 	}
 
 	// Write the best match ids
-	if (obi_set_array_with_col_p_in_view(output_view, best_match_column, line, best_match_ids, (uint8_t)(sizeof(char)*8), best_match_ids_length) < 0)
+	if (obi_set_array_with_col_p_in_view(output_view, best_match_ids_column, line, best_match_ids, (uint8_t)(sizeof(char)*8), best_match_ids_length) < 0)
 	{
-		obidebug(1, "\nError writing a assignment status in a column when writing ecotag results");
+		obidebug(1, "\nError writing the array of best match ids in a column when writing ecotag results");
+		return -1;
+	}
+
+	// Write the best match taxids
+	if (obi_set_array_with_col_p_in_view(output_view, best_match_taxids_column, line, best_match_taxids, (uint8_t)(sizeof(OBI_INT)*8), best_match_taxids_length) < 0)
+	{
+		obidebug(1, "\nError writing the array of best match taxids in a column when writing ecotag results");
 		return -1;
 	}
 
@@ -235,6 +254,8 @@ int obi_ecotag(const char* dms_name,
 	char*     		best_match_ids;
 	char*			best_match_ids_to_store;
 	int32_t         best_match_ids_length;
+	int32_t*   		best_match_taxids;
+	int32_t*		best_match_taxids_to_store;
 	int				best_match_count;
 	int             buffer_size;
 	int 			best_match_ids_buffer_size;
@@ -263,7 +284,8 @@ int obi_ecotag(const char* dms_name,
 	OBIDMS_column_p assigned_taxid_column = NULL;
 	OBIDMS_column_p assigned_name_column = NULL;
 	OBIDMS_column_p assigned_status_column = NULL;
-	OBIDMS_column_p best_match_column = NULL;
+	OBIDMS_column_p best_match_ids_column = NULL;
+	OBIDMS_column_p best_match_taxids_column = NULL;
 	OBIDMS_column_p lca_taxid_a_column = NULL;
 	OBIDMS_column_p score_a_column = NULL;
 	OBIDMS_column_p ref_taxid_column = NULL;
@@ -396,7 +418,8 @@ int obi_ecotag(const char* dms_name,
 	assigned_taxid_column = obi_view_get_column(output_view, ECOTAG_TAXID_COLUMN_NAME);
 	assigned_name_column = obi_view_get_column(output_view, ECOTAG_NAME_COLUMN_NAME);
 	assigned_status_column = obi_view_get_column(output_view, ECOTAG_STATUS_COLUMN_NAME);
-	best_match_column = obi_view_get_column(output_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME);
+	best_match_ids_column = obi_view_get_column(output_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME);
+	best_match_taxids_column = obi_view_get_column(output_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME);
 	score_column = obi_view_get_column(output_view, ECOTAG_SCORE_COLUMN_NAME);
 
 	// Open the used reference columns
@@ -453,6 +476,14 @@ int obi_ecotag(const char* dms_name,
 		return -1;
 	}
 
+	best_match_taxids = (int32_t*) malloc(buffer_size* sizeof(int32_t));
+	if (best_match_taxids == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for the best match taxid array in ecotag");
+		return -1;
+	}
+
 	for (i=0; i < query_count; i++)
 	{
 		if (i%1000 == 0)
@@ -514,7 +545,7 @@ int obi_ecotag(const char* dms_name,
 
 				// Store in best match array
 
-				// Grow match array if needed
+				// Grow match and taxid array if needed
 				if (best_match_count == buffer_size)
 				{
 					buffer_size = buffer_size*2;
@@ -525,6 +556,13 @@ int obi_ecotag(const char* dms_name,
 						obidebug(1, "\nError reallocating match array when assigning");
 						return -1;
 					}
+					best_match_taxids = (int32_t*) realloc(best_match_taxids, buffer_size*sizeof(int32_t));
+					if (best_match_taxids == NULL)
+					{
+						obi_set_errno(OBI_MALLOC_ERROR);
+						obidebug(1, "\nError reallocating match taxids array when assigning");
+						return -1;
+					}
 				}
 
 				id = obi_get_str_with_elt_idx_and_col_p_in_view(ref_view, ref_id_column, j, 0);
@@ -545,6 +583,7 @@ 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++;
 				strcpy(best_match_ids+best_match_ids_length, id);
 				best_match_ids_length = best_match_ids_length + id_len + 1;
@@ -629,6 +668,7 @@ int obi_ecotag(const char* dms_name,
 			else
 				lca_name = lca->name;
 			best_match_ids_to_store = best_match_ids;
+			best_match_taxids_to_store = best_match_taxids;
 		}
 		else
 		{
@@ -636,6 +676,7 @@ int obi_ecotag(const char* dms_name,
 			lca_name = OBIStr_NA;
 			lca_taxid = OBIInt_NA;
 			best_match_ids_to_store = OBITuple_NA;
+			best_match_taxids_to_store = OBITuple_NA;
 			score = OBIFloat_NA;
 		}
 
@@ -644,7 +685,8 @@ int obi_ecotag(const char* dms_name,
 								    assigned_taxid_column, lca_taxid,
 									assigned_name_column, lca_name,
 									assigned_status_column, assigned,
-									best_match_column, best_match_ids_to_store, best_match_ids_length,
+									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,
 									score_column, best_score
 									) < 0)
 							return -1;
@@ -652,6 +694,7 @@ int obi_ecotag(const char* dms_name,
 
 	free(best_match_array);
 	free(best_match_ids);
+	free(best_match_taxids);
 
 	obi_close_taxonomy(taxonomy);
 	obi_save_and_close_view(query_view);

src/obi_ecotag.h

@@ -23,7 +23,8 @@
 #define ECOTAG_TAXID_COLUMN_NAME "TAXID"
 #define ECOTAG_NAME_COLUMN_NAME "SCIENTIFIC_NAME"
 #define ECOTAG_STATUS_COLUMN_NAME "ID_STATUS"
-#define ECOTAG_BEST_MATCH_IDS_COLUMN_NAME "BEST_MATCH"
+#define ECOTAG_BEST_MATCH_IDS_COLUMN_NAME "BEST_MATCH_IDS"
+#define ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME "BEST_MATCH_TAXIDS"
 #define ECOTAG_SCORE_COLUMN_NAME "BEST_IDENTITY"
 
 

src/obidms.c

@@ -1496,7 +1496,7 @@ obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, c
 	memcpy(column_2->data, column_1->data, header_1->data_size);
 
 	// Copy the AVL files if there are some (overwriting the automatically created files)
-	if ((header_1->returned_data_type == OBI_STR) || (header_1->returned_data_type == OBI_SEQ) || (header_1->returned_data_type == OBI_QUAL))
+	if ((header_1->tuples) || ((header_1->returned_data_type == OBI_STR) || (header_1->returned_data_type == OBI_SEQ) || (header_1->returned_data_type == OBI_QUAL)))
 	{
 		avl_name_1 = (char*) malloc((strlen(header_1->indexer_name) + 1)  * sizeof(char));
 		if (avl_name_1 == NULL)

src/obidmscolumn.c

@@ -1350,6 +1350,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 		}
 		strncpy(header->indexer_name, final_indexer_name, INDEXER_MAX_NAME);
 	}
+	else
+		new_column->indexer = NULL;
 
 	// Fill the data with NA values
 	obi_ini_to_NA_values(new_column, 0, nb_lines);
@@ -1558,6 +1560,8 @@ OBIDMS_column_p obi_open_column(OBIDMS_p     dms,
 			return NULL;
 		}
 	}
+	else
+		column->indexer = NULL;
 
 	if (close(column_file_descriptor) < 0)
 	{
@@ -1693,8 +1697,8 @@ int obi_close_column(OBIDMS_column_p column)
 		if (obi_dms_unlist_column(column->dms, column) < 0)
 			ret_val = -1;
 
-		// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
-		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
+		// If it's a tuple column or the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
+		if ((column->indexer) != NULL)
 			if (obi_close_indexer(column->indexer) < 0)
 				ret_val = -1;