Merge pull request #224 from martinghunt/remove_spades_warnings

Remove spades warnings

ariba/assembly.py

@@ -59,7 +59,7 @@ def __init__(self,
         self.threads = threads
 
         if extern_progs is None:
-            self.extern_progs = external_progs.ExternalProgs()
+            self.extern_progs = external_progs.ExternalProgs(using_spades=self.assembler == 'spades')
         else:
             self.extern_progs = extern_progs
 

ariba/cdhit.py

@@ -27,7 +27,7 @@ def __init__(
         self.length_diff_cutoff = length_diff_cutoff
         self.verbose = verbose
         self.min_cluster_number = min_cluster_number
-        extern_progs = external_progs.ExternalProgs(fail_on_error=True)
+        extern_progs = external_progs.ExternalProgs(fail_on_error=True, using_spades=False)
         self.cd_hit_est = extern_progs.exe('cdhit')
 
 

ariba/cluster.py

@@ -130,7 +130,7 @@ def __init__(self,
             self.log_fh = None
 
         if extern_progs is None:
-            self.extern_progs = external_progs.ExternalProgs()
+            self.extern_progs = external_progs.ExternalProgs(using_spades=self.assembler == 'spades')
         else:
             self.extern_progs = extern_progs
 

ariba/external_progs.py

@@ -49,11 +49,12 @@ class Error (Exception): pass
 ])
 
 class ExternalProgs:
-    def __init__(self, verbose=False, fail_on_error=True):
+    def __init__(self, verbose=False, fail_on_error=True, using_spades=False):
         self.progs = {}
         self.version_report = []
         self.all_deps_ok = True
         self.versions = {}
+        self.using_spades = using_spades
 
         if verbose:
             print('{:_^79}'.format(' Checking dependencies and their versions '))
@@ -62,6 +63,9 @@ def __init__(self, verbose=False, fail_on_error=True):
         warnings = []
 
         for prog in sorted(prog_to_default):
+            if prog == 'spades' and not self.using_spades:
+                continue
+
             msg_sink = errors
             if prog in prog_optional:
                 msg_sink = warnings

ariba/read_filter.py

@@ -20,7 +20,7 @@ def __init__(self,
         self.log_fh = log_fh
 
         if extern_progs is None:
-            self.extern_progs = external_progs.ExternalProgs()
+            self.extern_progs = external_progs.ExternalProgs(using_spades=False)
         else:
             self.extern_progs = extern_progs
 

ariba/tasks/prepareref.py

@@ -6,7 +6,7 @@ def run(options):
     if options.no_cdhit and options.cdhit_clusters is not None:
         sys.exit('Cannot use both --no_cdhit and --cdhit_clusters. Neither or exactly one of those options must be used')
 
-    extern_progs, version_report_lines = versions.get_all_versions()
+    extern_progs, version_report_lines = versions.get_all_versions(using_spades=False)
     if options.verbose:
         print(*version_report_lines, sep='\n')
 

ariba/tasks/run.py

@@ -35,7 +35,7 @@ def run(options):
         print('Output directory already exists. ARIBA makes the output directory. Cannot continue.', file=sys.stderr)
         sys.exit(1)
 
-    extern_progs, version_report_lines = ariba.versions.get_all_versions()
+    extern_progs, version_report_lines = ariba.versions.get_all_versions(using_spades=options.assembler == 'spades')
     if options.verbose:
         print(*version_report_lines, sep='\n')
 

ariba/tests/assembly_test.py

@@ -9,7 +9,7 @@
 
 modules_dir = os.path.dirname(os.path.abspath(assembly.__file__))
 data_dir = os.path.join(modules_dir, 'tests', 'data')
-extern_progs = external_progs.ExternalProgs()
+extern_progs = external_progs.ExternalProgs(using_spades=True)
 
 class TestAssembly(unittest.TestCase):
     def test_run_fermilite(self):

ariba/versions.py

@@ -17,8 +17,8 @@
 }
 
 
-def get_all_versions(raise_error=True):
-    extern_progs = external_progs.ExternalProgs(fail_on_error=False)
+def get_all_versions(raise_error=True, using_spades=True):
+    extern_progs = external_progs.ExternalProgs(fail_on_error=False, using_spades=using_spades)
 
     report_lines = [
         'ARIBA version: ' + ariba_version,

setup.py

@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.11.2',
+    version='2.12.0',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},