Merge branch 'dev' of gitlab.pasteur.fr:aperrin/pipeline_annotation into dev

PanACoTA/align_module/pan_to_pergenome.py

@@ -226,8 +226,7 @@ def write_genome_file(listdir, aldir, dname, strain, member, several):
                        "option -F (or --force).".format(strain, geprtfile, gegenfile))
         return
 
-    # If one of the 2 files already exists, overwrite both files (same behaviour
-    # as if no file exists)
+    # If at least one of the 2 files already exists, overwrite both files
     with open(gegenfile, "w") as gegf, open(geprtfile, "w") as gepf:
         for mem, fam in member.items():
             if strain not in several[fam]:
@@ -256,8 +255,12 @@ def write_missing_genomes(fam_genomes, several, all_genomes, aldir, dname):
         name of dataset
     """
     for fam, genomes in fam_genomes.items():
-        missfile = os.path.join(aldir, dname + "-current." + fam + ".miss.lst")
+        # File where missing genomes will be written
+        missfile = os.path.join(aldir, f"{dname}-current.{fam}.miss.lst")
         with open(missfile, "w") as mff:
+            # missing = missing or several members:
+            # miss: all genomes - genomes in the family
+            # several: add to 'miss' genomes with several members in the family
             missing = (set(all_genomes) - set(genomes)).union(set(several[fam]))
             if missing:
                 mff.write("\n".join(missing) + "\n")

test/data/align/exp_files/exp_getentry-gen-ESCO4.txt

-ESCO4_00001 Aldir/TEST6-current.1.gen
-ESCO4_00003 Aldir/TEST6-current.3.gen
-ESCO4_00004 Aldir/TEST6-current.2.gen
+ESCO4_00001 test/data/align/generated_by_unit-tests/Aldir/test_write_genome-current.1.gen
+ESCO4_00003 test/data/align/generated_by_unit-tests/Aldir/test_write_genome-current.3.gen
+ESCO4_00004 test/data/align/generated_by_unit-tests/Aldir/test_write_genome-current.2.gen

test/data/align/exp_files/exp_getentry-prt-ESCO4.txt

-ESCO4_00001 Aldir/TEST6-current.1.prt
-ESCO4_00003 Aldir/TEST6-current.3.prt
-ESCO4_00004 Aldir/TEST6-current.2.prt
+ESCO4_00001 test/data/align/generated_by_unit-tests/Aldir/test_write_genome-current.1.prt
+ESCO4_00003 test/data/align/generated_by_unit-tests/Aldir/test_write_genome-current.3.prt
+ESCO4_00004 test/data/align/generated_by_unit-tests/Aldir/test_write_genome-current.2.prt

test/test_unit/utilities_for_tests.py

@@ -71,3 +71,20 @@ def compare_order_content(file1, file2):
                 print(f"'{line1}' vs {line2} do not correspond.")
                 return False
     return True
+
+
+def compare_file_to_list(file1, exp):
+    """
+    Check that the file contains the same lines as the list 'exp', in any order
+    """
+    missing = []
+    with open(file1, "r") as outf:
+        for line in outf:
+            missing.append(line.strip())
+    if len(missing) != len(exp):
+        print(f"{len(missing)} lines in {file1}, {len(exp)} lines expected")
+        return False
+    if set(missing) != set(exp):
+        print("Not same lines")
+        return False
+    return True