3-terms-species fix

Author: Francesca

thoraxe/transcript_query/transcript_query.py

@@ -230,10 +230,20 @@ def _species2ensembldataset(species_name):
 
     >>> _species2ensembldataset('homo_sapiens')
     ['hsapiens_gene_ensembl', 'hsapiens_eg_gene']
+    >>> _species2ensembldataset('anas_platyrhynchos_platyrhynchos')
+    ['applatyrhynchos_gene_ensembl', 'applatyrhynchos_eg_gene']
     """
     utils.species.check_species_name(species_name)
     names = species_name.split("_")
-    species = names[0][0] + names[1]
+    # DEPRECATED: only handled binomial names
+    # species = names[0][0] + names[1]
+    # 3-TERM-SPECIES FIX: handle both binomial and trinomial names
+    # Binomial:  homo_sapiens           -> hsapiens
+    # Trinomial: canis_lupus_familiaris -> clfamiliaris
+    if len(names) == 2:
+        species = names[0][0] + names[1]
+    else:
+        species = names[0][0] + names[1][0] + "".join(names[2:])
     return [species + "_gene_ensembl", species + "_eg_gene"]
 
 
@@ -450,8 +460,10 @@ def get_orthologs(species, ensgeneid, **params):
     if not dortho:
         raise Exception(
             f"Ensembl does not have annotated orthologs for {ensgeneid}")
-    # keep only binomial species names:
-    dortho = [d for d in dortho if len(d['target']['species'].split('_')) == 2]
+    # DEPRECATED: used to keep only binomial species names
+    # dortho = [d for d in dortho if len(d['target']['species'].split('_')) == 2]
+    # 3-TERM-SPECIES FIX: keep binomial and trinomial species names (>= 2 parts)
+    dortho = [d for d in dortho if len(d['target']['species'].split('_')) >= 2]
     return dortho
 
 

thoraxe/utils/species.py

@@ -18,9 +18,9 @@ def check_species_name(species_name):
     >>> check_species_name('homo_sapiens')
     True
     >>> check_species_name('colobus_angolensis_palliatus')
-    False
+    True
     >>> check_species_name('cricetulus_griseus_chok1gshd')
-    False
+    True
     """
     result = re.match('^[a-z]+_[a-z]+(_[0-9a-z]+)?$', species_name)
 
@@ -30,10 +30,22 @@ def check_species_name(species_name):
             ' with spaces replaced by underscores e.g. Homo sapiens should be '
             f'homo_sapiens. {species_name} do not conform the format.')
 
-    if len(species_name.split('_')) != 2:
-        warnings.warn(
-            f'Only binomial names are used. Skipping {species_name}.')
-        return False
+    # DEPRECATED: trinomial names were previously skipped
+    # if len(species_name.split('_')) != 2:
+    #     warnings.warn(
+    #         f'Only binomial names are used. Skipping {species_name}.')
+    #     return False
+
+    # 3-TERM-SPECIES FIX: accept trinomial names (e.g. anas_platyrhynchos_platyrhynchos)
+    n_parts = len(species_name.split('_'))
+    if n_parts < 2:
+        raise ValueError(
+            f'Species name must have at least 2 parts (genus_species). '
+            f'Got: {species_name}')
+    # if n_parts > 2:
+    #     warnings.warn(
+    #         f'Trinomial species name detected: {species_name}. '
+    #         f'Attempting to use it.')
 
     return True