update 1.4.6

config/MANTIS.cfg

@@ -5,7 +5,8 @@
 #default_ref_folder=
 #####<custom_ref_folder> defines the folder where Mantis will look for MULTIPLE custom HMMs or DMND. Each HMM should be contained within a folder, such that the path will look something like this: /path/to/custom_ref_folder/custom1/custom1.hmm
 #custom_ref_folder=
-nog_ref=dmnd # dmnd or hmm
+# dmnd or hmm
+nog_ref=dmnd
 #nog_ref_folder=
 #pfam_ref_folder=
 #kofam_ref_folder=

mantis/Assembler.py

@@ -48,7 +48,6 @@ def __init__(self, verbose=True, redirect_verbose=None,no_taxonomy=False, mantis
             self.hmm_chunk_size = hmm_chunk_size
         self.read_config_file()
 
-        #self.requirements_met()
         # I use manager instead of queue since I need to be able to add records to the end and start of the 'queue' (actually a list) which is not possible with the multiprocessing.Queue
         # we need manager.list because a normal list cant communicate during multiprocessing
         self.manager = Manager()
@@ -91,29 +90,6 @@ def __str__(self):
 
         return res
 
-    def requirements_met(self):
-        for f in [self.is_conda_available(), self.is_hmmer_available()]:
-            if not f:
-                kill_switch(RequirementsNotMet)
-
-    def is_conda_available(self):
-        process = run_command('conda -V', get_output=True)
-        check = re.search('conda', str(process.stdout))
-        if not check:
-            print_cyan('Conda dependency not met!')
-            print_cyan('Install Conda on your system by following the instructions at: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html')
-        return check
-
-    def is_hmmer_available(self):
-        check_command = ' conda list hmmer '
-        process = run_command(check_command, get_output=True)
-        check = re.search('hmmer', str(process.stdout))
-        if not check:
-            print_cyan('HMMER dependency not met!')
-            print_cyan('Install HMMER on your conda environment by doing the following:')
-            print_cyan('conda activate <conda_environment>')
-            print_cyan('conda install -c bioconda hmmer')
-        return check
 
 
     def check_internet_connection(self):
@@ -222,10 +198,11 @@ def read_config_file(self):
             self.config_file = self.mantis_config
         else:
             if not os.path.isdir(MANTIS_FOLDER):
-                print('Make sure you are calling the folder to run this package, like so:\n python mantis/ <command>\n ',
-                    flush=True, file=self.redirect_verbose)
+                print('Make sure you are calling the folder to run this package, like so:\n python mantis/ <command>\n ',flush=True, file=self.redirect_verbose)
                 raise FileNotFoundError
             self.config_file =f'{MANTIS_FOLDER}config{SPLITTER}MANTIS.cfg'
+            print(f'Using default MANTIS.cfg: {self.mantis_config}', flush=True, file=self.redirect_verbose)
+
         try:
             open(self.config_file, 'r')
         except:
@@ -319,7 +296,6 @@ def check_reference_exists(self, database, taxon_id=None):
                 return True
         elif database == 'taxonomy':
             taxonomy_db=self.mantis_paths['resources'] + 'Taxonomy.db'
-            gtdb_resources = add_slash(self.mantis_paths['resources'] + 'GTDB')
             if file_exists(taxonomy_db):
                 return True
         elif database == 'NOGSQL':
@@ -511,6 +487,7 @@ def check_sql_databases(self,ref_dbs):
             red('------------------------------------------', flush=True, file=self.redirect_verbose)
             red('-------------SQL CHECK FAILED-------------', flush=True, file=self.redirect_verbose)
             red('------------------------------------------', flush=True, file=self.redirect_verbose)
+            raise SQLCheckNotPassed
 
 
     def check_installation(self, verbose=True,check_sql=False):
@@ -589,6 +566,7 @@ def check_installation(self, verbose=True,check_sql=False):
                 yellow('------------------------------------------', flush=True, file=self.redirect_verbose)
             else:
                 print_cyan('Installation check failed', flush=True, file=self.redirect_verbose)
+            raise InstallationCheckNotPassed
         if check_sql: self.check_sql_databases(ref_dbs)
 
 

mantis/Database_generator.py

@@ -1267,7 +1267,7 @@ def compile_NOG_DMND(self):
             eggnog_proteins_path = f'{folder_path}eggnog_seqs.faa'
             extract_seqs_command = f'diamond getseq -d {diamond_db} > {eggnog_proteins_path}'
             if not file_exists(eggnog_proteins_path):
-                print('Extracting sequences from Diamond database',flush=True,file=self.redirect_verbose)
+                print('Extracting sequences from NOG Diamond database',flush=True,file=self.redirect_verbose)
                 run_command(extract_seqs_command,join_command=True,shell=True)
             return self.create_fastas_NOG_DMND()
 

mantis/Exceptions.py

@@ -1,29 +1,31 @@
-RequirementsNotMet='Installation check not passed! Make sure you\'ve setup the databases and your system meets all the requirements!'
 NoValidFiles='No valid files to annotate'
 TargetFileNotFound='Target file does not exist!\n'
 InvalidTargetFile='You did not insert a valid target file!\n'
 InvalidFastaFormat='Fasta format is not valid!\n'
 InstallationCheckNotPassed='Installation check not passed! Make sure you\'ve setup the databases and your system meets all the requirements!'
+SQLCheckNotPassed='SQL check not passed! Make sure you\'ve setup the databases and your system meets all the requirements!'
 CythonNotCompiled= 'Cython has not been correctly compiled! Please run:\n'
 BadNumberWorkers='You should not be seeing this, please contact the developer. Invalid number of workers in '
 ConnectionError='Could not connect to url:\n'
 InvalidTranslation='Invalid residues for translation. Please make sure you provided a CDS of DNA or RNA in the target file:\n'
 InvalidGFFVersion='No valid GFF version found!'
 InvalidNOGType='Your config file does not contain a valid database type for NOG (i.e. <dmnd> or <hmm>)!'
 
-class RequirementsNotMet(Exception):
-    def __init__(self, *args):
-        if args:
-            self.message = args
-        else:
-            self.message = None
 
+
+
+class SQLCheckNotPassed(Exception):
+    def __init__(self):
+        self.message = 'SQL check not passed!'
+    def __str__(self):
+        return self.message
+
+
+
+class InstallationCheckNotPassed(Exception):
+    def __init__(self):
+        self.message = 'Installation check not passed! Make sure you\'ve setup the databases'
     def __str__(self):
-        if self.message:
-            res = 'Requirements not met:\n'
-            res += '\n'.join(i for i in self.message)
-            return res
-        else:
-            return 'Requirements not met'
+        return self.message