Merge pull request #93 from phac-nml/database_downgrade

Downgraded Database version

.travis.yml

@@ -6,7 +6,7 @@ python:
 
 env:
   matrix:
-    - "DATABASE_COMMITS='--resfinder-commit 25ee4cd5bc9a9ff519b2fc7e53384aceb5fa942d --pointfinder-commit 7fdb7f4cddfb06932e1ae0c6d3b23a0f297d7922 --plasmidfinder-commit 81919954cbedaff39056610ab584ab4c06011ed8'"
+    - "DATABASE_COMMITS='--resfinder-commit e8f1eb2585cd9610c4034a54ce7fc4f93aa95535 --pointfinder-commit 8706a6363bb29e47e0e398c53043b037c24b99a7 --plasmidfinder-commit 81919954cbedaff39056610ab584ab4c06011ed8'"
 
 install:
   - sudo apt-get update -qq

CHANGELOG.md

@@ -1,6 +1,5 @@
-# Version 1.0.0
+# Version 0.6.0
 
-* Add support for *Enterococcus faecalis* and *Enterococcus faecium* from Pointfinder database.
 * Added [coloredlogs](https://pypi.org/project/coloredlogs/) library to format the output
 * Added support for [MLST](https://github.com/tseemann/mlst)
 

README.md

@@ -423,7 +423,7 @@ Restores the default database for `staramr`.
 
 # Caveats
 
-This software is still a work-in-progress.  In particular, not all organisms stored in the PointFinder database are supported (only *salmonella*, *campylobacter*, *enterococcus faecalis* and *enterococcus faecium* are currently supported). Additionally, the predicted phenotypes are for microbiological resistance and *not* clinical resistance. Phenotype/drug resistance predictions are an experimental feature which is continually being improved.
+This software is still a work-in-progress.  In particular, not all organisms stored in the PointFinder database are supported (only *salmonella*, *campylobacter* are currently supported). Additionally, the predicted phenotypes are for microbiological resistance and *not* clinical resistance. Phenotype/drug resistance predictions are an experimental feature which is continually being improved.
 
 `staramr` only works on assembled genomes and not directly on reads. A quick genome assembler you could use is [Shovill][shovill]. Or, you may also wish to try out the [ResFinder webservice][resfinder-web],  or the command-line tools [rgi][] or [ariba][] which will work on sequence reads as well as genome assemblies.  You may also wish to check out the [CARD webservice][card-web]. 
 

staramr/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.0.dev0'
+__version__ = '0.6.0'

staramr/blast/pointfinder/PointfinderBlastDatabase.py

@@ -80,7 +80,7 @@ def get_available_organisms(cls):
         A Class Method to get a list of organisms that are currently supported by staramr.
         :return: The list of organisms currently supported by staramr.
         """
-        return ['salmonella', 'campylobacter', 'enterococcus_faecalis', 'enterococcus_faecium']
+        return ['salmonella', 'campylobacter']
 
     @classmethod
     def get_organisms(cls, database_dir):

staramr/databases/AMRDatabasesManager.py

@@ -12,8 +12,8 @@
 
 class AMRDatabasesManager:
     DEFAULT_COMMITS = {
-        'resfinder': '25ee4cd5bc9a9ff519b2fc7e53384aceb5fa942d',
-        'pointfinder': '7fdb7f4cddfb06932e1ae0c6d3b23a0f297d7922',
+        'resfinder': 'e8f1eb2585cd9610c4034a54ce7fc4f93aa95535',
+        'pointfinder': '8706a6363bb29e47e0e398c53043b037c24b99a7',
         'plasmidfinder': '81919954cbedaff39056610ab584ab4c06011ed8'
     }
 

staramr/tests/integration/databases/test_AMRDatabasesManager.py

@@ -7,8 +7,8 @@
 
 
 class AMRDatabasesManagerIT(unittest.TestCase):
-    RESFINDER_DEFAULT_COMMIT = '25ee4cd5bc9a9ff519b2fc7e53384aceb5fa942d'
-    POINTFINDER_DEFAULT_COMMIT = '7fdb7f4cddfb06932e1ae0c6d3b23a0f297d7922'
+    RESFINDER_DEFAULT_COMMIT = 'e8f1eb2585cd9610c4034a54ce7fc4f93aa95535'
+    POINTFINDER_DEFAULT_COMMIT = '8706a6363bb29e47e0e398c53043b037c24b99a7'
     PLASMIDFINDER_DEFAULT_COMMIT = '81919954cbedaff39056610ab584ab4c06011ed8'
 
     def setUp(self):

staramr/tests/integration/detection/test_AMRDetection.py

@@ -909,6 +909,7 @@ def testPointfinderCampylobacterA2075GSuccess(self):
         expected_records = SeqIO.to_dict(SeqIO.parse(file, 'fasta'))
         self.assertEqual(expected_records['23S'].seq.upper(), records['23S'].seq.upper(), "records don't match")
 
+    """
     def testPointfinderEFaecalisS97NSuccess(self):
         pointfinder_database = PointfinderBlastDatabase(self.pointfinder_dir, 'enterococcus_faecalis')
         blast_handler = JobHandler({'resfinder': self.resfinder_database, 'pointfinder': pointfinder_database}, 2,
@@ -1011,7 +1012,7 @@ def testPointfinderEFaeciumIns466Success(self):
 
         expected_records = SeqIO.to_dict(SeqIO.parse(file, 'fasta'))
         self.assertEqual(expected_records['pbp5'].seq.upper(), records['pbp5'].seq.upper(), "records don't match")
-
+    """
 
 if __name__ == '__main__':
     unittest.main()