Merge branch 'master' into dev

PanACoTA/align_module/post_align.py

@@ -320,10 +320,21 @@ def get_genome(header, all_genomes):
         name of genome from which the header is
         None if no genome found
     """
+    # Name of protein is not always genome-name_num
+    # Ex: in gembase complete DB: >TOTO.0215.00002.i006_00065 is from genome TOTO.0215.00002
+    # So, genome name cannot be deduced directly from header. But it is always included in header
     header = header.split(">")[1].split()[0]
+
     for genome in all_genomes:
         if genome in header:
-            return genome
+            # header should be genome<something>_num
+            # -> header.split(genome) should be empty for the first field
+            # If not empty, means that genome name is included into another genome name, so
+            # we must not return this genome.
+            # For example, genome "8-KG" is in header "98-KG_xxx", but the correct genome for this
+            # header is "98-KG"
+            if not header.split(genome)[0]:
+                return genome
     logger.error((f"Protein {header} does not correspond to any genome name "
                   f"given... {all_genomes}"))
     return None

test/test_unit/test_align/test_postalign.py

@@ -55,14 +55,22 @@ def test_get_genome():
     assert pal.get_genome(header, genomes) == "TOTO.0215.00002"
 
 
-def test_get_genome_not_start():
+def test_get_genome_included():
     """
-    Given a header and a list of genomes, check that it returns the expected genome. The genome
-    name is not at the beginning of the protein name
+    Given a header and a list of genomes, check that it returns the expected genome
     """
-    header = ">mongenome,TOTO.0215.00002.i006_00065"
-    genomes = ["TOTO.0315.00001", "ESCO.0215.00002", "ESCO.0215.00001", "TOTO.0215.00002"]
-    assert pal.get_genome(header, genomes) == "TOTO.0215.00002"
+    header = ">aTOTO.0215.00002.i006_00065"
+    genomes = [ "TOTO.0215.00002", "TOTO.0315.00001", "ESCO.0215.00002", "aTOTO.0215.00002"]
+    assert pal.get_genome(header, genomes) == "aTOTO.0215.00002"
+
+# def test_get_genome_not_start():
+#     """
+#     Given a header and a list of genomes, check that it returns the expected genome. The genome
+#     name is not at the beginning of the protein name
+#     """
+#     header = ">mongenome,TOTO.0215.00002.i006_00065"
+#     genomes = ["TOTO.0315.00001", "ESCO.0215.00002", "ESCO.0215.00001", "TOTO.0215.00002"]
+#     assert pal.get_genome(header, genomes) == "TOTO.0215.00002"
 
 
 def test_get_genome_notfound(caplog):