fixed neiserria point mutations, version bump and tested

abritamr/AmrSetup.py

@@ -46,7 +46,7 @@ def __init__(self, args):
 
 
         # for amr
-        self.species_list = ['Acinetobacter_baumannii','Clostridioides_difficile', "Campylobacter", "Enterococcus_faecalis", "Enterococcus_faecium", "Escherichia", "Klebsiella", "Salmonella", "Staphylococcus_aureus", "Staphylococcus_pseudintermedius", "Streptococcus_agalactiae", "Streptococcus_pneumoniae", "Streptococcus_pyogenes", "Vibrio_cholerae"]
+        self.species_list = ["Burkholderia_cepacia","Acinetobacter_baumannii","Streptococcus_pyogenes","Streptococcus_agalactiae","Streptococcus_pneumoniae","Enterococcus_faecium","Pseudomonas_aeruginosa","Staphylococcus_pseudintermedius","Clostridioides_difficile","Klebsiella","Neisseria","Campylobacter","Salmonella","Escherichia","Staphylococcus_aureus","Burkholderia_pseudomallei","Enterococcus_faecalis"]
 
         self.logger =logging.getLogger(__name__) 
         self.logger.setLevel(logging.INFO)

abritamr/abritamr.py

@@ -75,6 +75,7 @@ def main():
         help="Set if you would like to use point mutations, please provide a valid species.",
         choices= ["Burkholderia_cepacia","Acinetobacter_baumannii","Streptococcus_pyogenes","Streptococcus_agalactiae","Streptococcus_pneumoniae","Enterococcus_faecium","Pseudomonas_aeruginosa","Staphylococcus_pseudintermedius","Clostridioides_difficile","Klebsiella","Neisseria","Campylobacter","Salmonella","Escherichia","Staphylococcus_aureus","Burkholderia_pseudomallei","Enterococcus_faecalis"]
     )
+
     parser_mdu = subparsers.add_parser('report', help='Generate report for use at MDU', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
     parser_mdu.add_argument(

abritamr/version.py

@@ -1,2 +1,2 @@
-__version__ = "1.0.13"
+__version__ = "1.0.14"
 db = "2022-08-09.1"

setup.py

@@ -19,7 +19,7 @@
 
 setup(
     name="abritamr",
-    version="1.0.12",
+    version="1.0.14",
     description="Running AMRFinderPlus for MDU",
     long_description=long_description,
     long_description_content_type="text/markdown",

tests/test_abritamr.py

@@ -94,6 +94,20 @@ def test_setup_contigs():
         input_data = T('assembly', amr_obj.contigs, amr_obj.prefix, amr_obj.jobs, amr_obj.species, amr_obj.identity, amr_obj.amrfinder_db)
         assert amr_obj.setup() == input_data
 
+def test_species():
+    with patch.object(SetupAMR, "__init__", lambda x: None):
+        amr_obj = SetupAMR()
+        amr_obj.contigs = f"{CONTROLS / 'contigs.fa'}"
+        amr_obj.prefix = 'somename'
+        amr_obj.jobs  = 16
+        amr_obj.species = 'Neiserria'
+        amr_obj.identity = ''
+        amr_obj.amrfinder_db = f"{pathlib.Path(__file__).parent.parent /'abritamr' /'db' / 'amrfinderplus'/ 'data'/ '2022-08-09.1'}"
+        amr_obj.logger = logging.getLogger(__name__)
+        T = collections.namedtuple('T', ['run_type', 'input', 'prefix', 'jobs', 'organism', 'identity','amrfinder_db'])
+        input_data = T('assembly', amr_obj.contigs, amr_obj.prefix, amr_obj.jobs, amr_obj.species, amr_obj.identity, amr_obj.amrfinder_db)
+        assert amr_obj.setup() == input_data
+
 
 def test_setup_batch():
     with patch.object(SetupAMR, "__init__", lambda x: None):
@@ -215,6 +229,24 @@ def test_batch_cmd_with_org():
         amr_obj.logger = logging.getLogger(__name__)
         assert amr_obj._batch_cmd() == cmd
 
+def test_batch_cmd_with_neiserria():
+    """
+    assert True when non-empty string is given
+    """
+    with patch.object(RunFinder, "__init__", lambda x: None):
+        args = Data("batch", 'tests/batch.txt', '', 9, 'Neiserria')
+        amr_obj = RunFinder()
+        amr_obj.organism = args.organism
+        amr_obj.run_type = args.run_type
+        amr_obj.prefix = args.prefix
+        amr_obj.jobs = args.jobs
+        amr_obj.input = args.input
+        amr_obj.amrfinder_db = "2021-06-01.1"
+        amr_obj.identity = ''
+        cmd = f"parallel -j {args.jobs} --colsep '\\t' 'mkdir -p {{1}} && amrfinder -n {{2}} -o {{1}}/amrfinder.out --plus --organism {args.organism} --threads 1 -d {amr_obj.amrfinder_db}' :::: {args.input}"
+        amr_obj.logger = logging.getLogger(__name__)
+        assert amr_obj._batch_cmd() == cmd
+
 def test_single_cmd_with_org():
     """
     assert True when non-empty string is given