add --locus_numbering_start to be able to continue numbering (like to…

… add mitochondrial part into the same flat file later) + modification of combine method + Fix bug setting start_codon into the CDS feature (bug difficult to see because detected only by the validator own by ENA and not the public one available in their repository)

EMBLmyGFF3/EMBLmyGFF3.py

@@ -40,7 +40,6 @@
 SCRIPT_DIR=os.path.dirname(__file__)
 FEATURE_DIR=SCRIPT_DIR + "/modules/features"
 QUALIFIER_DIR=SCRIPT_DIR + "/modules/qualifiers"
-CPT_LOCUS_GLB=0
 
 class EMBL( object ):
     """
@@ -756,9 +755,10 @@ def FT(self):
             #manage locus_tag
             locus_tag=None
             if feature.type.lower() != "source" and feature.type.lower() != "gap":
-                global CPT_LOCUS_GLB
-                CPT_LOCUS_GLB+=1
-                locus_tag_suffix="locus"+str(CPT_LOCUS_GLB)
+                cpt_locus = self.PREVIOUS_VALUES['locus_numbering_start']
+                locus_tag_suffix="LOCUS"+str(cpt_locus)
+                # now the locus has been used we can increment the locus value
+                self.PREVIOUS_VALUES['locus_numbering_start'] += 1
 
                 # replace locus_tag_suffix by the value of the locus_tag qualifier if this one exists
                 for qualifier in feature.qualifiers:
@@ -999,7 +999,7 @@ def set_keywords(self, keywords = []):
 
     def set_locus_tag(self, locus_tag = ""):
         """
-        Sets the entry locus_tag numbers, or parses it from the current record
+        Sets the entry locus_tag value, or parses it from the current record
         """
         if "locus_tag" in EMBL.PREVIOUS_VALUES:
             self.locus_tag = EMBL.PREVIOUS_VALUES["locus_tag"]
@@ -1017,6 +1017,15 @@ def set_locus_tag(self, locus_tag = ""):
                 self.locus_tag = locus_tag
                 EMBL.PREVIOUS_VALUES["locus_tag"] = locus_tag
 
+    def set_locus_numbering_start (self, locus_numbering_start = 1):
+        """
+        Sets the entry locus_numbering_start numbers
+        """
+        if "locus_numbering_start" in EMBL.PREVIOUS_VALUES:
+            self.set_locus_numbering_start = EMBL.PREVIOUS_VALUES["locus_numbering_start"]
+        else:
+            EMBL.PREVIOUS_VALUES["locus_numbering_start"] = locus_numbering_start
+
     def set_molecule_type(self, molecule_type = None):
         """
         Sets the sample molecule type, or parses it from the current record.
@@ -1259,6 +1268,7 @@ def main():
     parser.add_argument("--interleave_genes", action="store_false", help="Print gene features with interleaved mRNA and CDS features.")
     parser.add_argument("--force_unknown_features", action="store_true", help="Force to keep feature types not accepted by EMBL. /!\ Option not suitable for submission purpose.")
     parser.add_argument("--force_uncomplete_features", action="store_true", help="Force to keep features whithout all the mandatory qualifiers. /!\ Option not suitable for submission purpose.")
+    parser.add_argument("--locus_numbering_start", default=1, type=int, help="Start locus numbering with the provided value.")
 
     parser.add_argument("--email", default=None, help="Email used to fetch information from NCBI taxonomy database.")
     parser.add_argument("--shame", action="store_true", help="Suppress the shameless plug.")
@@ -1319,6 +1329,7 @@ def main():
         writer.set_keep_duplicates( args.keep_duplicates )
         writer.set_keywords( args.keyword )
         writer.set_locus_tag( args.locus_tag )
+        writer.set_locus_numbering_start(args.locus_numbering_start)
         writer.set_molecule_type( args.molecule_type )
         writer.set_organelle( args.organelle )
         writer.set_project_id( args.project_id )

EMBLmyGFF3/modules/feature.py

@@ -297,7 +297,7 @@ def _load_definition(self, filename):
                     if "qualifier" in key:
                         for item, definition in value.iteritems():
                             #logging.error("item:%s definition:%s",item,definition)
-                            self.legal_qualifiers += [key]
+                            self.legal_qualifiers += [item]
                             mandatory = "mandatory" in key
                             self.qualifiers[item] = Qualifier(item, mandatory = mandatory, qualifier_definition_dir=self.qualifier_definition_dir)
                     else:
@@ -462,7 +462,17 @@ def add_qualifier(self, gff_qualifier, value):
         if self.qualifier_suffix.get(gff_qualifier, None):
             value = ["%s%s" % (v, self.qualifier_suffix[gff_qualifier]) for v in value]
 
-        self.qualifiers[qualifier].add_value(value)
+        ###########################################
+        # add the value only if not already present         
+        # List case
+        if isinstance(value, list):
+            for val in value:
+                if val not in self.qualifiers[qualifier].value:
+                    self.qualifiers[qualifier].add_value(val)
+        # Scalar case
+        else:
+            if value not in self.qualifiers[qualifier].value:
+                self.qualifiers[qualifier].add_value(value)
 
     def combine(self, other):
         """
@@ -472,23 +482,24 @@ def combine(self, other):
         # add new location
         self.location += other.location
 
-        # combine qualifiers
-        for name, qualifier in self.qualifiers.iteritems():
-            other_qualifier = other.qualifiers.get(name, None)
-            for val in getattr(other_qualifier, "value", []):
-                if val not in qualifier.value:
-                    self.qualifiers[name].add_value(other_value)
-
-        # Sort out phase
-        current_phase = int(self.qualifiers.get("phase", [0])[0])
-        other_phase = int(other.qualifiers.get("phase", [0])[0])
-
-        phase = current_phase if self.location.start < other.location.start else other_phase
-        if "codon_start" in self.legal_qualifiers:
-            if not "codon_start" in self.qualifiers:
-                self.qualifiers["codon_start"] = Qualifier("codon_start", phase, qualifier_definition_dir = self.qualifier_definition_dir)
+        # combine qualifier except codon start
+        for gff_qualifier, list_val_other in other.qualifiers.iteritems():
+            other_qualifier = self._from_gff_qualifier(gff_qualifier) # get the real qualifier name in EMBL format to be able to compare with the one alredy saved
+            if other_qualifier != "codon_start":
+                self.add_qualifier(gff_qualifier, list_val_other)
             else:
-                self.qualifiers["codon_start"].set_value(phase)
+                # as the feature are sorted by increasing order location if + strand the first CDS codon_start qualifier was the good one
+                # Of we are in a minus strand case we have to replace the start_codon, only hte last one will left
+                if self.location.strand < 0:
+                    # get phase of the last CDS
+                    phase = int(other.qualifiers.get("phase", [0])[0])
+
+                    if "codon_start" in self.legal_qualifiers:
+
+                        if not "codon_start" in self.qualifiers:
+                            self.qualifiers["codon_start"] = Qualifier("codon_start", phase, qualifier_definition_dir = self.qualifier_definition_dir)
+                        else:
+                            self.qualifiers["codon_start"].set_value(phase)
 
     def CDS_report(self, out = sys.stdout, parts = False, codon_info = True):
         """