made module, made class names more consistent snake-to-camel

bactria/tools/__init__.py

@@ -0,0 +1,19 @@
+from .blastdb_aliastool import BlastdbAliastool
+from .blastdbcmd import Blastdbcmd
+from .blastn import Blastn
+from .hmmalign import Hmmalign
+from .makeblastdb import Makeblastdb
+from .megatree_loader import MegatreeLoader
+from .megatree_pruner import MegatreePruner
+from .raxml_ng import RaxmlNg
+
+__all__ = [
+    'BlastdbAliastool',
+    'Blastdbcmd',
+    'Blastn',
+    'Hmmalign',
+    'Makeblastdb',
+    'MegatreeLoader',
+    'MegatreePruner',
+    'RaxmlNg',
+]

bactria/blastdb_aliastool.py → bactria/tools/blastdb_aliastool.py

@@ -1,5 +1,5 @@
 from typing import Optional, List
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 

bactria/blastdbcmd.py → bactria/tools/blastdbcmd.py

@@ -1,16 +1,16 @@
 from typing import Optional, List
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
-class Blastdbcommand(ToolRunner):
+class Blastdbcmd(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 = Blastdbcmd(config)
         >>> blastdbcmd_runner.set_db('nr')
         >>> blastdbcmd_runner.set_entry(['NP_000508.1', 'NP_001018081.2'])
         >>> blastdbcmd_runner.set_outfmt('%f')

bactria/blastn.py → bactria/tools/blastn.py

@@ -1,16 +1,16 @@
 from typing import List, Union
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
-class BLASTN(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 = Blastn(config)
         >>> blastn_runner.set_query('input.fasta')
         >>> blastn_runner.set_db('nr')
         >>> blastn_runner.set_out('output.txt')

bactria/hmmalign.py → bactria/tools/hmmalign.py

@@ -1,5 +1,5 @@
 from typing import List
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 

bactria/raxml_ng.py → bactria/tools/raxml_ng.py

@@ -1,16 +1,16 @@
 from typing import Optional, List, Union
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
-class RAXMLNG(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 = RaxmlNg(config)
         >>> raxml_runner.set_msa('alignment.fa')
         >>> raxml_runner.set_model('GTR+G')
         >>> raxml_runner.set_prefix('test_run')