Removed *Runner from class name, expanded top-level docs

bactria/blastdb_aliastool_runner.py

@@ -3,9 +3,18 @@
 from bactria.config import Config
 
 
-class BlastdbAliastoolRunner(ToolRunner):
+class BlastdbAliastool(ToolRunner):
     """
     A subclass of ToolRunner specifically for running blastdb_aliastool.
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> aliastool_runner = BlastdbAliastoolRunner(config)
+        >>> aliastool_runner.set_db('my_blast_db')
+        >>> aliastool_runner.set_out('my_alias_db')
+        >>> aliastool_runner.set_gilist('my_gi_list.txt')
+        >>> return_code = aliastool_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -193,12 +202,3 @@ def run(self) -> int:
         """
         self.validate_parameters()
         return super().run()
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# aliastool_runner = BlastdbAliastoolRunner(config)
-# aliastool_runner.set_db('my_blast_db')
-# aliastool_runner.set_out('my_alias_db')
-# aliastool_runner.set_gilist('my_gi_list.txt')
-# return_code = aliastool_runner.run()

bactria/blastdbcmd_runner.py

@@ -3,9 +3,18 @@
 from bactria.config import Config
 
 
-class BlastdbcommandRunner(ToolRunner):
+class Blastdbcommand(ToolRunner):
     """
     A subclass of ToolRunner specifically for running blastdbcmd.
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> blastdbcmd_runner = Blastdbcommand(config)
+        >>> blastdbcmd_runner.set_db('nr')
+        >>> blastdbcmd_runner.set_entry(['NP_000508.1', 'NP_001018081.2'])
+        >>> blastdbcmd_runner.set_outfmt('%f')
+        >>> return_code = blastdbcmd_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -281,12 +290,3 @@ def run(self) -> int:
         """
         self.validate_parameters()
         return super().run()
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# blastdbcmd_runner = BlastdbcommandRunner(config)
-# blastdbcmd_runner.set_db('nr')
-# blastdbcmd_runner.set_entry(['NP_000508.1', 'NP_001018081.2'])
-# blastdbcmd_runner.set_outfmt('%f')
-# return_code = blastdbcmd_runner.run()

bactria/blastn_runner.py

@@ -3,9 +3,22 @@
 from bactria.config import Config
 
 
-class BLASTNRunner(ToolRunner):
+class BLASTN(ToolRunner):
     """
     A subclass of ToolRunner specifically for running BLASTN (Nucleotide-Nucleotide BLAST).
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> blastn_runner = BLASTN(config)
+        >>> blastn_runner.set_query('input.fasta')
+        >>> blastn_runner.set_db('nr')
+        >>> blastn_runner.set_out('output.txt')
+        >>> blastn_runner.set_evalue(1e-5)
+        >>> blastn_runner.set_outfmt(6)
+        >>> blastn_runner.set_num_threads(4)
+        >>> blastn_runner.set_remote(True)
+        >>> return_code = blastn_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -216,16 +229,3 @@ def build_command(self) -> List[str]:
                 command.append(f'-{param}')
 
         return command
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# blastn_runner = BLASTNRunner(config)
-# blastn_runner.set_query('input.fasta')
-# blastn_runner.set_db('nr')
-# blastn_runner.set_out('output.txt')
-# blastn_runner.set_evalue(1e-5)
-# blastn_runner.set_outfmt(6)
-# blastn_runner.set_num_threads(4)
-# blastn_runner.set_remote(True)
-# return_code = blastn_runner.run()

bactria/hmmalign_runner.py

@@ -3,9 +3,19 @@
 from bactria.config import Config
 
 
-class HmmalignRunner(ToolRunner):
+class Hmmalign(ToolRunner):
     """
     A subclass of ToolRunner specifically for running hmmalign.
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> hmmalign_runner = Hmmalign(config)
+        >>> hmmalign_runner.set_hmmfile('model.hmm')
+        >>> hmmalign_runner.set_seqfile('sequences.fasta')
+        >>> hmmalign_runner.set_output('alignment.sto')
+        >>> hmmalign_runner.set_outformat('Stockholm')
+        >>> return_code = hmmalign_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -140,13 +150,3 @@ def run(self) -> int:
         """
         self.validate_parameters()
         return super().run()
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# hmmalign_runner = HmmalignRunner(config)
-# hmmalign_runner.set_hmmfile('model.hmm')
-# hmmalign_runner.set_seqfile('sequences.fasta')
-# hmmalign_runner.set_output('alignment.sto')
-# hmmalign_runner.set_outformat('Stockholm')
-# return_code = hmmalign_runner.run()

bactria/makeblastdb_runner.py

@@ -2,9 +2,19 @@
 from bactria.tool_runner import ToolRunner
 from bactria.config import Config
 
-class MakeblastdbRunner(ToolRunner):
+class Makeblastdb(ToolRunner):
     """
     A subclass of ToolRunner specifically for running makeblastdb.
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> makeblastdb_runner = Makeblastdb(config)
+        >>> makeblastdb_runner.set_in('input_sequences.fasta')
+        >>> makeblastdb_runner.set_dbtype('prot')
+        >>> makeblastdb_runner.set_out('my_blast_db')
+        >>> makeblastdb_runner.set_parse_seqids()
+        >>> return_code = makeblastdb_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -213,13 +223,3 @@ def run(self) -> int:
         """
         self.validate_parameters()
         return super().run()
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# makeblastdb_runner = MakeblastdbRunner(config)
-# makeblastdb_runner.set_in('input_sequences.fasta')
-# makeblastdb_runner.set_dbtype('prot')
-# makeblastdb_runner.set_out('my_blast_db')
-# makeblastdb_runner.set_parse_seqids()
-# return_code = makeblastdb_runner.run()

bactria/megatree_loader_runner.py

@@ -4,9 +4,17 @@
 import logging
 
 
-class MegatreeLoaderRunner(ToolRunner):
+class MegatreeLoader(ToolRunner):
     """
     A subclass of ToolRunner specifically for running megatree-loader.
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> megatree_runner = MegatreeLoaderRunner(config)
+        >>> megatree_runner.set_infile('input_tree.newick')
+        >>> megatree_runner.set_dbfile('output_db.sqlite')
+        >>> return_code = megatree_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -80,11 +88,3 @@ def run(self) -> int:
         """
         self.validate_parameters()
         return super().run()
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# megatree_runner = MegatreeLoaderRunner(config)
-# megatree_runner.set_infile('input_tree.newick')
-# megatree_runner.set_dbfile('output_db.sqlite')
-# return_code = megatree_runner.run()

bactria/megatree_pruner_runner.py

@@ -4,9 +4,19 @@
 import logging
 
 
-class MegatreePrunerRunner(ToolRunner):
+class MegatreePruner(ToolRunner):
     """
     A subclass of ToolRunner specifically for running megatree-pruner.
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> megatree_pruner = MegatreePruner(config)
+        >>> megatree_pruner.set_dbfile('tree_database.sqlite')
+        >>> megatree_pruner.set_infile('taxa_list.txt')
+        >>> megatree_pruner.set_tabular(True)
+        >>> megatree_pruner.set_relabel(True)
+        >>> return_code = megatree_pruner.run()
     """
 
     def __init__(self, config: Config):
@@ -115,13 +125,3 @@ def run(self) -> int:
         """
         self.validate_parameters()
         return super().run()
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# megatree_pruner = MegatreePrunerRunner(config)
-# megatree_pruner.set_dbfile('tree_database.sqlite')
-# megatree_pruner.set_infile('taxa_list.txt')
-# megatree_pruner.set_tabular(True)
-# megatree_pruner.set_relabel(True)
-# return_code = megatree_pruner.run()

bactria/raxml_ng_runner.py

@@ -3,9 +3,20 @@
 from bactria.config import Config
 
 
-class RAXMLNGRunner(ToolRunner):
+class RAXMLNG(ToolRunner):
     """
     A subclass of ToolRunner specifically for running RAxML-NG (Randomized Axelerated Maximum Likelihood - Next Generation).
+
+    Examples:
+        >>> config = Config()
+        >>> config.load_config('path/to/config.yaml')
+        >>> raxml_runner = RAXMLNG(config)
+        >>> raxml_runner.set_msa('alignment.fa')
+        >>> raxml_runner.set_model('GTR+G')
+        >>> raxml_runner.set_prefix('test_run')
+        >>> raxml_runner.set_threads(4)
+        >>> raxml_runner.set_all()
+        >>> return_code = raxml_runner.run()
     """
 
     def __init__(self, config: Config):
@@ -176,14 +187,3 @@ def build_command(self) -> List[str]:
                 command.append(f'--{param}')
 
         return command
-
-# Example usage:
-# config = Config()
-# config.load_config('path/to/config.yaml')
-# raxml_runner = RAXMLNGRunner(config)
-# raxml_runner.set_msa('alignment.fa')
-# raxml_runner.set_model('GTR+G')
-# raxml_runner.set_prefix('test_run')
-# raxml_runner.set_threads(4)
-# raxml_runner.set_all()
-# return_code = raxml_runner.run()