simplifed import path

akikuno · Dec 15, 2023 · 6e2d172 · 6e2d172
1 parent 52c2158
commit 6e2d172
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Showing 4 changed files with 8 additions and 9 deletions.
diff --git a/docs/ROADMAP.md b/docs/ROADMAP.md
@@ -6,8 +6,8 @@
 
 ## 📝 Documentation
 
-+ [x] Added `ROADMAP.md` to track the progress of the project (https://github.com/akikuno/DAJIN2/commit/cf05d3e5c9b1d3ee806d66c9c1d9f8079863e312)
-+ [x] Added *Prerequisites* section to README.md (https://github.com/akikuno/DAJIN2/commit/7d5a3cd8305f9d414a492f5223d5dbec7399aa46)
++ [x] Added `ROADMAP.md` to track the progress of the project [Commit Detail](https://github.com/akikuno/DAJIN2/commit/cf05d3e5c9b1d3ee806d66c9c1d9f8079863e312)
++ [x] Added *Prerequisites* section to README.md [Commit Detail](https://github.com/akikuno/DAJIN2/commit/7d5a3cd8305f9d414a492f5223d5dbec7399aa46)
 
 ## 🚀 Features
 
@@ -19,7 +19,7 @@
 
 ## 🔧 Maintenance
 
-+ [x] Modified batch processing to run on a single CPU thread per process. (https://github.com/akikuno/DAJIN2/commit/7b43e36b9482cceabe79f47814f62f69d46b7d3e)
++ [x] Modified batch processing to run on a single CPU thread per process [Commit Detail](https://github.com/akikuno/DAJIN2/commit/7b43e36b9482cceabe79f47814f62f69d46b7d3e)
 
 + [x] Simplifed import path:
   + `preprocess.midsv_caller.execute` to `preprocess.generate_midsv`

diff --git a/src/DAJIN2/core/core.py b/src/DAJIN2/core/core.py
@@ -146,12 +146,12 @@ def execute_control(arguments: dict):
     # Mapping using mappy
     # ============================================================
     paths_fasta = Path(ARGS.tempdir, ARGS.control_name, "fasta").glob("*.fasta")
-    preprocess.mapping.generate_sam(ARGS, paths_fasta, is_control=True, is_insertion=False)
+    preprocess.generate_sam(ARGS, paths_fasta, is_control=True, is_insertion=False)
 
     ###########################################################
     # MIDSV conversion
     ###########################################################
-    preprocess.midsv_caller.execute(ARGS, is_control=True, is_insertion=False)
+    preprocess.generate_midsv(ARGS, is_control=True, is_insertion=False)
 
     ###########################################################
     # Prepare data to `extract mutaion loci`

diff --git a/src/DAJIN2/core/preprocess/__init__.py b/src/DAJIN2/core/preprocess/__init__.py
@@ -3,11 +3,10 @@
     genome_fetcher,
     cache_checker,
     directories,
-    mapping,
-    midsv_caller,
 )
 
-
+from DAJIN2.core.preprocess.mapping import generate_sam
+from DAJIN2.core.preprocess.midsv_caller import generate_midsv
 from DAJIN2.core.preprocess.knockin_handler import extract_knockin_loci
 from DAJIN2.core.preprocess.mutation_extractor import cache_mutation_loci
 from DAJIN2.core.preprocess.insertions_to_fasta import generate_insertion_fasta
diff --git a/src/DAJIN2/core/preprocess/midsv_caller.py b/src/DAJIN2/core/preprocess/midsv_caller.py
@@ -122,7 +122,7 @@ def filter_samples_by_n_proportion(midsv_sample: Generator[dict], threshold: int
 ###########################################################
 
 
-def execute(ARGS, is_control: bool = False, is_insertion: bool = False) -> None:
+def generate_midsv(ARGS, is_control: bool = False, is_insertion: bool = False) -> None:
     name = ARGS.control_name if is_control else ARGS.sample_name
 
     for allele, sequence in ARGS.fasta_alleles.items():