Updated initiation of bbconf object (initiaded once for insert option)

bedboss/bedboss.py

@@ -9,6 +9,7 @@
 from eido import validate_project
 import pephubclient
 from pephubclient.helpers import is_registry_path
+import bbconf
 
 from bedboss.bedstat.bedstat import bedstat
 from bedboss.bedmaker.bedmaker import BedMaker
@@ -76,7 +77,7 @@ def run_all(
     input_type: str,
     outfolder: str,
     genome: str,
-    bedbase_config: str,
+    bedbase_config: Union[str, bbconf.BedBaseConf],
     rfg_config: str = None,
     narrowpeak: bool = False,
     check_qc: bool = True,
@@ -103,7 +104,7 @@ def run_all(
     :param input_type: Input type [required] options: (bigwig|bedgraph|bed|bigbed|wig)
     :param outfolder: Folder, where output should be saved  [required]
     :param genome: genome_assembly of the sample. [required] options: (hg19, hg38) #TODO: add more
-    :param bedbase_config: a path to the bedbase configuration file. [required] #TODO: add example
+    :param bedbase_config: The path to the bedbase configuration file, or bbconf object.
     :param open_signal_matrix: a full path to the openSignalMatrix required for the tissue [optional]
     :param rfg_config: file path to the genome config file [optional]
     :param narrowpeak: whether the regions are narrow
@@ -126,8 +127,9 @@ def run_all(
     """
     _LOGGER.warning(f"Unused arguments: {kwargs}")
 
-    if not check_db_connection(bedbase_config=bedbase_config):
-        raise Exception("Database connection failed. Exiting...")
+    if isinstance(bedbase_config, str):
+        if not check_db_connection(bedbase_config=bedbase_config):
+            raise Exception("Database connection failed. Exiting...")
 
     file_name = extract_file_name(input_file)
     genome = standardize_genome_name(genome)
@@ -235,6 +237,8 @@ def insert_pep(
     else:
         raise BedBossException("Incorrect pep type. Exiting...")
 
+    bbc = bbconf.BedBaseConf(config_path=bedbase_config, database_only=True)
+
     validate_project(pep, BEDBOSS_PEP_SCHEMA_PATH)
 
     for i, pep_sample in enumerate(pep.samples):
@@ -251,7 +255,7 @@ def insert_pep(
             cell_type=pep_sample.get("cell_type"),
             treatment=pep_sample.get("treatment"),
             outfolder=output_folder,
-            bedbase_config=bedbase_config,
+            bedbase_config=bbc,
             rfg_config=rfg_config,
             check_qc=check_qc,
             standard_chrom=standard_chrom,
@@ -266,7 +270,7 @@ def insert_pep(
     if create_bedset:
         _LOGGER.info(f"Creating bedset from {pep.name}")
         run_bedbuncher(
-            bedbase_config=bedbase_config,
+            bedbase_config=bbc,
             bedset_pep=pep,
             pephub_registry_path=pephub_registry_path,
         )

bedboss/bedbuncher/bedbuncher.py

@@ -1,3 +1,4 @@
+import bbconf
 from geniml.io import BedSet
 from bbconf import BedBaseConf
 from bbconf.const import CFG_PATH_KEY, CFG_PATH_BEDBUNCHER_DIR_KEY
@@ -230,7 +231,7 @@ def add_bedset_to_database(
 
 
 def run_bedbuncher(
-    bedbase_config: str,
+    bedbase_config: Union[str, bbconf.BedBaseConf],
     bedset_pep: Union[str, peppy.Project],
     bedset_name: str = None,
     pephub_registry_path: str = None,
@@ -253,7 +254,8 @@ def run_bedbuncher(
     :return: None
     """
 
-    bbc = BedBaseConf(bedbase_config)
+    if isinstance(bedbase_config, str):
+        bbc = BedBaseConf(bedbase_config)
     if isinstance(bedset_pep, peppy.Project):
         pep_of_bed = bedset_pep
     elif isinstance(bedset_pep, str):

bedboss/bedstat/bedstat.py

@@ -1,4 +1,4 @@
-from typing import NoReturn
+from typing import Union
 import json
 import yaml
 import os
@@ -34,7 +34,7 @@ def convert_unit(size_in_bytes: int) -> str:
 
 def bedstat(
     bedfile: str,
-    bedbase_config: str,
+    bedbase_config: Union[str, bbconf.BedBaseConf],
     genome: str,
     outfolder: str,
     ensdb: str = None,
@@ -59,7 +59,7 @@ def bedstat(
     :param str bigbed: the full path to the bigbed file. Defaults to None.
         (bigbed won't be created and some producing of some statistics will
         be skipped.)
-    :param str bedbase_config: The path to the bedbase configuration file.
+    :param str bedbase_config: The path to the bedbase configuration file, or bbconf object
     :param str open_signal_matrix: a full path to the openSignalMatrix
         required for the tissue specificity plots
     :param str outfolder: The folder for storing the pipeline results.
@@ -86,7 +86,12 @@ def bedstat(
         os.makedirs(outfolder_stats)
     except FileExistsError:
         pass
-    bbc = bbconf.BedBaseConf(config_path=bedbase_config, database_only=True)
+
+    # if bbconf is a string, create a bbconf object
+    if isinstance(bedbase_config, str):
+        bbc = bbconf.BedBaseConf(config_path=bedbase_config, database_only=True)
+    else:
+        bbc = bedbase_config
 
     bed_digest = RegionSet(bedfile).identifier
     bedfile_name = os.path.split(bedfile)[1]