Always get uniq contig IDs with prokka

use --centre prokka option

PanACoTA/annotate_module/annotation_functions.py

@@ -258,7 +258,7 @@ def run_prokka(arguments):
     #     - if outdir exists exists but force, remove this outdir.
     # So, outdir does not exist -> run prokka
     cmd = (f"prokka --outdir {prok_dir} --cpus {threads} "
-           f"--prefix {name} {gpath}")
+           f"--prefix {name} --centre prokka {gpath}")
     error = (f"Error while trying to run prokka on {name} from {gpath}")
     logger.details("Prokka command: " + cmd)
     prokf = open(prok_logfile, "w")

test/test_unit/test_annotate/test_annotation_functions-prokka.py

@@ -490,9 +490,13 @@ def test_run_prokka_out_exists_force():
     # we cannot compare the whole file.
     with open(out_tbl, "r") as outt:
         lines = [line.strip() for line in outt.readlines()]
-        assert ">Feature H561_S27" in lines
-        assert ">Feature H561_S28" in lines
-        assert ">Feature H561_S29" in lines
+        # Check that there are 3 contigs
+        feature = 0
+        for line in lines:
+            if 'Feature' in line:
+                feature += 1
+        assert feature == 3
+        # Check that there are 16 CDS
         CDS = 0
         for line in lines:
             if "CDS" in line:
@@ -512,7 +516,7 @@ def test_run_prokka_out_exists_force():
     assert q.get().message == ("Prokka command: prokka "
                                "--outdir test/data/annotate/generated_by_unit-tests/"
                                "H299_H561.fasta-prokkaRes --cpus 2 --prefix test_runprokka_H299 "
-                               "test/data/annotate/genomes/H299_H561.fasta")
+                               "--centre prokka test/data/annotate/genomes/H299_H561.fasta")
     assert q.get() .message.startswith("End annotating test_runprokka_H299 "
                                        "from test/data/annotate/genomes/H299_H561.fasta")
 
@@ -547,9 +551,13 @@ def test_run_prokka_out_doesnt_exist_ok():
     # we cannot compare the whole file.
     with open(out_tbl, "r") as outt:
         lines = [line.strip() for line in outt.readlines()]
-        assert ">Feature H561_S27" in lines
-        assert ">Feature H561_S28" in lines
-        assert ">Feature H561_S29" in lines
+        # Check that there are 3 contigs
+        feature = 0
+        for line in lines:
+            if 'Feature' in line:
+                feature += 1
+        assert feature == 3
+        # Check that there are 16 CDS
         CDS = 0
         for line in lines:
             if "CDS" in line:
@@ -566,7 +574,7 @@ def test_run_prokka_out_doesnt_exist_ok():
     assert q.get().message == ("Prokka command: prokka "
                                "--outdir test/data/annotate/generated_by_unit-tests/"
                                "H299_H561.fasta-prokkaRes --cpus 2 --prefix test_runprokka_H299 "
-                               "test/data/annotate/genomes/H299_H561.fasta")
+                               "--centre prokka test/data/annotate/genomes/H299_H561.fasta")
     assert q.get().message.startswith("End annotating")
 
 
@@ -592,6 +600,6 @@ def test_run_prokka_out_problem_running():
                                "--outdir test/data/annotate/generated_by_unit-tests/"
                                "H299_H561bis.fasta-prokkaRes --cpus 2 "
                                "--prefix test_runprokka_H299-error "
-                               "test/data/annotate/genomes/H299_H561bis.fasta")
+                               "--centre prokka test/data/annotate/genomes/H299_H561bis.fasta")
     assert q.get().message == ("Error while trying to run prokka on test_runprokka_H299-error "
                                "from test/data/annotate/genomes/H299_H561bis.fasta")

test/test_unit/test_annotate/test_format_func.py

@@ -35,7 +35,12 @@ def setup_teardown_module():
     - remove directory with generated results
     """
     # utils.init_logger(LOGFILE_BASE, 0, 'test_fastme', verbose=1)
-    os.mkdir(GENEPATH)
+    if os.path.isdir(GENEPATH):
+        content = os.listdir(GENEPATH)
+        for f in content:
+            assert f.startswith(".fuse")
+    else:
+        os.mkdir(GENEPATH)
     print("setup")
 
     yield