fixes

configs/data_task/fimo/pre_fimo.yaml

@@ -2,5 +2,7 @@ name: pre_fimo
 type: fimo
 
 input_csv: dpacman/data_files/processed/remap/remap2022_crm_macs2_hg38_v1_0_clean.tsv
-output_csv: dpacman/data_files/processed/fimo/remap2022_crm_fimo_input.tsv
-window_total: 500
+output_csv: dpacman/data_files/processed/fimo/remap2022_crm_fimo_input.csv
+window_total: 500
+
+save_example_files: true

configs/data_task/fimo/run_fimo.yaml

@@ -1,6 +1,8 @@
 name: post_fimo
 type: fimo
 
+debug: false
+
 paths:
   input_csv: dpacman/data_files/processed/fimo/remap2022_crm_fimo_input.tsv
   output_csv: dpacman/data_files/processed/fimo/remap2022_crm_fimo_output.csv

dpacman/data_tasks/fimo/pre_fimo.py

@@ -10,7 +10,6 @@ from pathlib import Path
 root = rootutils.setup_root(__file__, indicator=".project-root", pythonpath=True)
 logger = logging.getLogger(__name__)
 
-
 def main(cfg: DictConfig):
     # 1) load
     input_path = Path(root) / cfg.data_task.input_csv
@@ -48,7 +47,7 @@ def main(cfg: DictConfig):
             "chromEnd",  # original ChIPEnd
             "contextEnd",
             "score",  # original score column
-            "TF",
+            "TR",
         ]
     ].rename(
         columns={
@@ -63,9 +62,26 @@ def main(cfg: DictConfig):
     output_path = Path(root) / cfg.data_task.output_csv
     os.makedirs(output_path.parent, exist_ok=True)
 
-    # 8) write tsv
-    out.to_csv(output_path, sep="\t", index=False)
-    print(f"Wrote {len(out)} rows to {output_path}")
+    # 8) write csv
+    out.to_csv(output_path, index=False)
+    logger.info(f"Wrote {len(out)} rows to {output_path}")
+    
+    # 9) write example csv if necessary
+    if cfg.data_task.save_example_files:
+        example_dir = output_path.parent / "examples"
+        os.makedirs(example_dir, exist_ok=True)
+        output_csv_name = cfg.data_task.output_csv.split("/")[-1]
+        example_savepath = os.path.join(
+            example_dir, "example500_" + output_csv_name
+        )
+
+        if not (os.path.exists(example_savepath)):
+            out.sample(n=500, random_state=42).reset_index(drop=True).to_csv(
+                example_savepath, sep="\t", index=False
+            )
+            logger.info(
+                f"Saved example FIMO input file with 500 rows to: {example_savepath}"
+            )
 
 
 if __name__ == "__main__":

environment.yaml

@@ -25,7 +25,7 @@ dependencies:
   - dask[complete]
   - pip>=23
   - pip:
-    - rootutils
+    - rootutils==1.0.7
     - hydra-core==1.3.2         # Hydra for config management
     - hydra-colorlog==1.2.0     # Allow colorful logging in Hydra
     - omegaconf==2.3.0          # Required by hydra-core
@@ -34,5 +34,6 @@ dependencies:
     - pymex==0.9.31
     - gitpython==3.1.44
     - black==25.1.0   # code formatter
+    - tqdm==4.67.1
     - matplotlib==3.10.3
     - -e .