adding wrapper classes for tools used in the pipeline. Note:

- as yet untested
- likely to move to nbitk
- likely to be renamed to nbitk.tools.ToolName
- omits seqmagick (it's just a biopython wrapper)

bactria/blastdb_aliastool_runner.py

@@ -0,0 +1,204 @@
+from typing import Optional, List
+from bactria.tool_runner import ToolRunner
+from bactria.config import Config
+
+
+class BlastdbAliastoolRunner(ToolRunner):
+    """
+    A subclass of ToolRunner specifically for running blastdb_aliastool.
+    """
+
+    def __init__(self, config: Config):
+        """
+        Initialize the BlastdbAliastoolRunner with a configuration object.
+
+        :param config: Configuration object containing tool and logger settings.
+        :type config: Config
+        """
+        super().__init__(config)
+        self.tool_name = 'blastdb_aliastool'
+
+    def set_gi_file_in(self, file_path: str) -> None:
+        """
+        Set the input text file containing GIs to convert.
+
+        :param file_path: Path to the input file.
+        :type file_path: str
+        """
+        self.set_parameter('gi_file_in', file_path)
+
+    def set_gi_file_out(self, file_path: str) -> None:
+        """
+        Set the output file name for the converted GI file.
+
+        :param file_path: Path to the output file.
+        :type file_path: str
+        """
+        self.set_parameter('gi_file_out', file_path)
+
+    def set_db(self, dbname: str) -> None:
+        """
+        Set the BLAST database name.
+
+        :param dbname: Name of the BLAST database.
+        :type dbname: str
+        """
+        self.set_parameter('db', dbname)
+
+    def set_dbtype(self, molecule_type: str) -> None:
+        """
+        Set the molecule type stored in the BLAST database.
+
+        :param molecule_type: Molecule type ('nucl' or 'prot').
+        :type molecule_type: str
+        """
+        self.set_parameter('dbtype', molecule_type)
+
+    def set_title(self, title: str) -> None:
+        """
+        Set the title for the BLAST database.
+
+        :param title: Title for the database.
+        :type title: str
+        """
+        self.set_parameter('title', title)
+
+    def set_gilist(self, file_path: str) -> None:
+        """
+        Set the text or binary gi file to restrict the BLAST database.
+
+        :param file_path: Path to the gi file.
+        :type file_path: str
+        """
+        self.set_parameter('gilist', file_path)
+
+    def set_seqidlist(self, file_path: str) -> None:
+        """
+        Set the text sequence id or accession file to restrict the BLAST database.
+
+        :param file_path: Path to the sequence id file.
+        :type file_path: str
+        """
+        self.set_parameter('seqidlist', file_path)
+
+    def set_taxidlist(self, file_path: str) -> None:
+        """
+        Set the text taxonomy id file to restrict the BLAST database.
+
+        :param file_path: Path to the taxonomy id file.
+        :type file_path: str
+        """
+        self.set_parameter('taxidlist', file_path)
+
+    def set_oid_masks(self, mask_value: int) -> None:
+        """
+        Set the oid masks for creating alias db.
+
+        :param mask_value: Integer value for oid masks.
+        :type mask_value: int
+        """
+        self.set_parameter('oid_masks', str(mask_value))
+
+    def set_out(self, database_name: str) -> None:
+        """
+        Set the name of the BLAST database alias to be created.
+
+        :param database_name: Name of the database alias.
+        :type database_name: str
+        """
+        self.set_parameter('out', database_name)
+
+    def set_dblist(self, database_names: List[str]) -> None:
+        """
+        Set a list of BLAST database names to aggregate.
+
+        :param database_names: List of database names.
+        :type database_names: List[str]
+        """
+        self.set_parameter('dblist', ' '.join(database_names))
+
+    def set_dblist_file(self, file_path: str) -> None:
+        """
+        Set a file containing a list of BLAST database names to aggregate.
+
+        :param file_path: Path to the file containing database names.
+        :type file_path: str
+        """
+        self.set_parameter('dblist_file', file_path)
+
+    def set_vdblist(self, vdb_names: List[str]) -> None:
+        """
+        Set a list of VDB names to aggregate.
+
+        :param vdb_names: List of VDB names.
+        :type vdb_names: List[str]
+        """
+        self.set_parameter('vdblist', ' '.join(vdb_names))
+
+    def set_vdblist_file(self, file_path: str) -> None:
+        """
+        Set a file containing a list of VDB names to aggregate.
+
+        :param file_path: Path to the file containing VDB names.
+        :type file_path: str
+        """
+        self.set_parameter('vdblist_file', file_path)
+
+    def set_num_volumes(self, num: int) -> None:
+        """
+        Set the number of volumes to aggregate.
+
+        :param num: Number of volumes.
+        :type num: int
+        """
+        self.set_parameter('num_volumes', str(num))
+
+    def set_logfile(self, file_path: str) -> None:
+        """
+        Set the file to which the program log should be redirected.
+
+        :param file_path: Path to the log file.
+        :type file_path: str
+        """
+        self.set_parameter('logfile', file_path)
+
+    def set_version(self) -> None:
+        """
+        Set the version flag to print the version number.
+        """
+        self.set_parameter('version', '')
+
+    def validate_parameters(self) -> None:
+        """
+        Validate that required parameters are set and incompatible options are not used together.
+
+        :raises ValueError: If required parameters are missing or incompatible options are set.
+        """
+        # This method should implement validation logic based on the manual page.
+        # For brevity, only a few checks are implemented here.
+        if self.get_parameter('out') and self.get_parameter('gi_file_in'):
+            raise ValueError("'out' and 'gi_file_in' options are incompatible.")
+
+        if self.get_parameter('dblist') and not (
+                self.get_parameter('out') and self.get_parameter('dbtype') and self.get_parameter('title')):
+            raise ValueError("'dblist' requires 'out', 'dbtype', and 'title' to be set.")
+
+    def run(self) -> int:
+        """
+        Run the blastdb_aliastool command after validating parameters.
+
+        :return: The return code of the blastdb_aliastool command.
+        :rtype: int
+        :raises ValueError: If required parameters are missing or incompatible options are set.
+        """
+        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()