smftools 0.3.1__py3-none-any.whl → 0.3.2__py3-none-any.whl

smftools/cli/helpers.py

@@ -5,7 +5,16 @@ from pathlib import Path
 
 import anndata as ad
 
-from smftools.constants import H5_DIR, HMM_DIR, LATENT_DIR, LOAD_DIR, PREPROCESS_DIR, SPATIAL_DIR
+from smftools.constants import (
+    CHIMERIC_DIR,
+    H5_DIR,
+    HMM_DIR,
+    LATENT_DIR,
+    LOAD_DIR,
+    PREPROCESS_DIR,
+    SPATIAL_DIR,
+    VARIANT_DIR,
+)
 
 from ..metadata import write_runtime_schema_yaml
 from ..readwrite import safe_write_h5ad
@@ -19,6 +28,8 @@ class AdataPaths:
     spatial: Path
     hmm: Path
     latent: Path
+    variant: Path
+    chimeric: Path
 
 
 def get_adata_paths(cfg) -> AdataPaths:
@@ -27,8 +38,8 @@ def get_adata_paths(cfg) -> AdataPaths:
     """
     output_directory = Path(cfg.output_directory)
 
+    # Raw and Preprocessed adata file pathes will have set names.
     raw = output_directory / LOAD_DIR / H5_DIR / f"{cfg.experiment_name}.h5ad.gz"
-
     pp = output_directory / PREPROCESS_DIR / H5_DIR / f"{cfg.experiment_name}_preprocessed.h5ad.gz"
 
     if cfg.smf_modality == "direct":
@@ -44,9 +55,12 @@ def get_adata_paths(cfg) -> AdataPaths:
 
     pp_dedup_base = pp_dedup.name.removesuffix(".h5ad.gz")
 
+    # All of the following just append a new suffix to the preprocessesed_deduplicated base name
     spatial = output_directory / SPATIAL_DIR / H5_DIR / f"{pp_dedup_base}_spatial.h5ad.gz"
     hmm = output_directory / HMM_DIR / H5_DIR / f"{pp_dedup_base}_hmm.h5ad.gz"
     latent = output_directory / LATENT_DIR / H5_DIR / f"{pp_dedup_base}_latent.h5ad.gz"
+    variant = output_directory / VARIANT_DIR / H5_DIR / f"{pp_dedup_base}_variant.h5ad.gz"
+    chimeric = output_directory / CHIMERIC_DIR / H5_DIR / f"{pp_dedup_base}_chimeric.h5ad.gz"
 
     return AdataPaths(
         raw=raw,
@@ -55,6 +69,8 @@ def get_adata_paths(cfg) -> AdataPaths:
         spatial=spatial,
         hmm=hmm,
         latent=latent,
+        variant=variant,
+        chimeric=chimeric,
     )
 
 

smftools/cli/hmm_adata.py

@@ -18,7 +18,7 @@ from ..hmm.HMM import _safe_int_coords, _to_dense_np, create_hmm, normalize_hmm_
 logger = get_logger(__name__)
 
 if TYPE_CHECKING:
-    import torch as torch_types
+    import torch
 
 torch = require("torch", extra="torch", purpose="HMM CLI")
 mpl = require("matplotlib", extra="plotting", purpose="HMM plotting")
@@ -586,9 +586,18 @@ def hmm_adata(config_path: str):
     if paths.hmm.exists():
         adata, _ = safe_read_h5ad(paths.hmm)
         source_path = paths.hmm
+    elif paths.latent.exists():
+        adata, _ = safe_read_h5ad(paths.latent)
+        source_path = paths.latent
     elif paths.spatial.exists():
         adata, _ = safe_read_h5ad(paths.spatial)
         source_path = paths.spatial
+    elif paths.chimeric.exists():
+        adata, _ = safe_read_h5ad(paths.chimeric)
+        source_path = paths.chimeric
+    elif paths.variant.exists():
+        adata, _ = safe_read_h5ad(paths.variant)
+        source_path = paths.variant
     elif paths.pp_dedup.exists():
         adata, _ = safe_read_h5ad(paths.pp_dedup)
         source_path = paths.pp_dedup
@@ -1080,6 +1089,10 @@ def hmm_adata_core(
                 deaminase=deaminase,
                 min_signal=0,
                 index_col_suffix=cfg.reindexed_var_suffix,
+                overlay_variant_calls=getattr(cfg, "overlay_variant_calls", False),
+                variant_overlay_seq1_color=getattr(cfg, "variant_overlay_seq1_color", "white"),
+                variant_overlay_seq2_color=getattr(cfg, "variant_overlay_seq2_color", "black"),
+                variant_overlay_marker_size=getattr(cfg, "variant_overlay_marker_size", 4.0),
             )
 
     hmm_length_dir = hmm_directory / "12b_hmm_length_clustermaps"
@@ -1136,6 +1149,10 @@ def hmm_adata_core(
                 min_signal=0,
                 index_col_suffix=cfg.reindexed_var_suffix,
                 length_feature_ranges=length_feature_ranges,
+                overlay_variant_calls=getattr(cfg, "overlay_variant_calls", False),
+                variant_overlay_seq1_color=getattr(cfg, "variant_overlay_seq1_color", "white"),
+                variant_overlay_seq2_color=getattr(cfg, "variant_overlay_seq2_color", "black"),
+                variant_overlay_marker_size=getattr(cfg, "variant_overlay_marker_size", 4.0),
             )
 
     hmm_dir = hmm_directory / "13_hmm_bulk_traces"