added resources path to config file

config/MANTIS.cfg

@@ -3,6 +3,7 @@
 #######DEFAULT PATHS#######
 #You can add custom paths here, otherwise they will be set to default values
 #default_ref_folder=
+#resources_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=
 # dmnd or hmm

mantis/Assembler.py

@@ -67,6 +67,7 @@ def __str__(self):
  if hasattr(self, 'output_folder'):
  res.append(f'Output folder:\nself.output_folder')
  res.append(f'Default references folder:\n{self.mantis_paths["default"]}')
+ res.append(f'Resources folder:\n{self.mantis_paths["resources"]}')
  res.append(f'Custom references folder:\n{self.mantis_paths["custom"]}')
  if self.mantis_paths['NOG'][0:2] != 'NA':
  res.append(f'TAX NOG references folder:\n{self.mantis_paths["NOG"]}')
@@ -100,20 +101,6 @@ def check_internet_connection(self):
  print("Could not connect to internet!\nIf you would like to run offline make sure you introduce organism NCBI IDs instead of synonyms!")
  return False
 
- def get_default_ref_path(self):
- file = open(self.config_file, 'r')
- line = file.readline()
- while line:
- line = line.strip('\n')
- if '#' not in line:
- # data sources configuration
- if 'default_ref_folder=' in line:
- line_path = add_slash(line.replace('default_ref_folder=', ''))
- if line_path:
- default_ref_path = line_path
- return default_ref_path
- line = file.readline()
- file.close()
 
  def set_nogt_line(self, line_path):
  if line_path:
@@ -134,55 +121,100 @@ def set_nogt_line(self, line_path):
  self.mantis_nogt_tax.add(str(i))
 
  def setup_paths_config_file(self):
+ self.mantis_paths = {'default': None,
+ 'resources': None,
+ 'custom': None,
+ 'NOG': None,
+ 'pfam': None,
+ 'kofam': None,
+ 'NCBI': None,
+ 'tcdb': None,
+ }
+
+
  self.nog_db = 'dmnd'
- file = open(self.config_file, 'r')
- line = file.readline()
  nogt_line=None
- while line:
- line = line.strip('\n')
- if not line.startswith('#') and line:
- # data sources configuration
- if line.startswith('custom_ref_folder='):
- line_path = add_slash(line.replace('custom_ref_folder=', ''))
- if line_path: self.mantis_paths['custom'] = line_path
-
- elif line.startswith('nog_ref_folder='):
- line_path = add_slash(line.replace('nog_ref_folder=', ''))
- if line_path: self.mantis_paths['NOG'] = line_path
-
- # taxa ids list for only downloading nogt specific to lineage
- elif line.startswith('nog_tax='):
- nogt_line = line.replace('nog_tax=', '')
-
- elif line.startswith('pfam_ref_folder='):
- line_path = add_slash(line.replace('pfam_ref_folder=', ''))
- if line_path: self.mantis_paths['pfam'] = line_path
-
- elif line.startswith('kofam_ref_folder='):
- line_path = add_slash(line.replace('kofam_ref_folder=', ''))
- if line_path: self.mantis_paths['kofam'] = line_path
-
- elif line.startswith('ncbi_ref_folder='):
- line_path = add_slash(line.replace('ncbi_ref_folder=', ''))
- if line_path: self.mantis_paths['NCBI'] = line_path
-
- elif line.startswith('tcdb_ref_folder='):
- line_path = add_slash(line.replace('tcdb_ref_folder=', ''))
- if line_path: self.mantis_paths['tcdb'] = line_path
-
-
- elif '_weight=' in line:
- ref_source, weight = line.split('_weight=')
- self.mantis_ref_weights[ref_source] = float(weight)
-
- elif line.startswith('nog_ref='):
- nog_db = line.replace('nog_ref=', '').split()[0]
- if nog_db.lower() not in ['dmnd','hmm']:
- kill_switch(InvalidNOGType)
- else:
- self.nog_db=nog_db
- line = file.readline()
- file.close()
+ with open(self.config_file) as file:
+ for line in file:
+ line = line.strip('\n')
+ if not line.startswith('#') and line:
+ # data sources configuration
+ if line.startswith('default_ref_folder='):
+ line_path = add_slash(line.replace('default_ref_folder=', ''))
+ if line_path: self.mantis_paths['default'] = line_path
+
+ elif line.startswith('resources_folder='):
+ line_path = add_slash(line.replace('resources_folder=', ''))
+ if line_path: self.mantis_paths['resources'] = line_path
+
+ elif line.startswith('custom_ref_folder='):
+ line_path = add_slash(line.replace('custom_ref_folder=', ''))
+ if line_path: self.mantis_paths['custom'] = line_path
+
+ elif line.startswith('nog_ref_folder='):
+ line_path = add_slash(line.replace('nog_ref_folder=', ''))
+ if line_path: self.mantis_paths['NOG'] = line_path
+
+ # taxa ids list for only downloading nogt specific to lineage
+ elif line.startswith('nog_tax='):
+ nogt_line = line.replace('nog_tax=', '')
+
+ elif line.startswith('pfam_ref_folder='):
+ line_path = add_slash(line.replace('pfam_ref_folder=', ''))
+ if line_path: self.mantis_paths['pfam'] = line_path
+
+ elif line.startswith('kofam_ref_folder='):
+ line_path = add_slash(line.replace('kofam_ref_folder=', ''))
+ if line_path: self.mantis_paths['kofam'] = line_path
+
+ elif line.startswith('ncbi_ref_folder='):
+ line_path = add_slash(line.replace('ncbi_ref_folder=', ''))
+ if line_path: self.mantis_paths['NCBI'] = line_path
+
+ elif line.startswith('tcdb_ref_folder='):
+ line_path = add_slash(line.replace('tcdb_ref_folder=', ''))
+ if line_path: self.mantis_paths['tcdb'] = line_path
+
+ elif '_weight=' in line:
+ ref_source, weight = line.split('_weight=')
+ self.mantis_ref_weights[ref_source] = float(weight)
+
+ elif line.startswith('nog_ref='):
+ nog_db = line.replace('nog_ref=', '').split()[0]
+ if nog_db.lower() not in ['dmnd','hmm']:
+ kill_switch(InvalidNOGType)
+ else:
+ self.nog_db=nog_db
+ if not self.mantis_paths['default']:
+ self.mantis_paths['default']=add_slash(MANTIS_FOLDER + 'References')
+ default_ref_path=self.mantis_paths['default']
+
+ if not self.mantis_paths['resources']:
+ self.mantis_paths['resources']=add_slash(MANTIS_FOLDER + 'Resources')
+
+ if not self.mantis_paths['custom']:
+ self.mantis_paths['custom']= add_slash(default_ref_path + 'Custom_references')
+
+ if not self.mantis_paths['NOG']:
+ self.mantis_paths['NOG']= add_slash(default_ref_path + 'NOG')
+
+ if not self.mantis_paths['pfam']:
+ self.mantis_paths['pfam']= add_slash(default_ref_path + 'pfam')
+
+ if not self.mantis_paths['kofam']:
+ self.mantis_paths['kofam']= add_slash(default_ref_path + 'kofam')
+
+ if not self.mantis_paths['NCBI']:
+ self.mantis_paths['NCBI']= add_slash(default_ref_path + 'NCBI')
+
+ if not self.mantis_paths['tcdb']:
+ self.mantis_paths['tcdb']= add_slash(default_ref_path + 'tcdb')
+
+
+
+
+ #setting up which taxa we need to have references for
+ Taxonomy_SQLITE_Connector.__init__(self,resources_folder=self.mantis_paths['resources'])
  if self.use_taxonomy:
  if nogt_line:
  if self.launch_taxonomy_connector():
@@ -210,22 +242,6 @@ def read_config_file(self):
  flush=True, file=self.redirect_verbose)
  raise FileNotFoundError
 
- default_ref_path = self.get_default_ref_path()
-
- # if there's no path, we just assume its in the default folder
- if not default_ref_path: default_ref_path = add_slash(MANTIS_FOLDER + 'References')
- resources_path = add_slash(MANTIS_FOLDER + 'Resources')
-
- self.mantis_paths = {'default': default_ref_path,
- 'resources': resources_path,
- 'custom': add_slash(default_ref_path + 'Custom_references'),
- 'NOG': add_slash(default_ref_path + 'NOG'),
- 'pfam': add_slash(default_ref_path + 'pfam'),
- 'kofam': add_slash(default_ref_path + 'kofam'),
- 'NCBI': add_slash(default_ref_path + 'NCBI'),
- 'tcdb': add_slash(default_ref_path + 'tcdb'),
- }
- Taxonomy_SQLITE_Connector.__init__(self,resources_folder=self.mantis_paths['resources'])
 
  self.setup_paths_config_file()
  if not self.use_taxonomy: