Support baysor>=0.7.0 (#125)

gustaveroussy · Sep 25, 2024 · ff9ff66 · ff9ff66
1 parent 02cf901
commit ff9ff66
Show file tree

Hide file tree

Showing 16 changed files with 14 additions and 29 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,9 @@
+## [1.x.x] - 2024-xx-xx
+
+### Fix
+- Support `baysor>=0.7.0` (#125, @lguerard).
+  - NB: For Snakemake, please remove the `new_component_*` arguments from the Baysor config.
+
 ## [1.1.5] - 2024-09-17
 
 ### Fix

diff --git a/docs/tutorials/cli_usage.md b/docs/tutorials/cli_usage.md
@@ -165,8 +165,6 @@ iters = 500
 n_cells_init = 0
 nuclei_genes = ""
 cyto_genes = ""
-new_component_weight = 0.2
-new_component_fraction = 0.3
 ```
 
 Then, we generate the bounding boxes of the patches on which Baysor will be run. Here, the patches have a width and height of 1200 microns and an overlap of 50 microns. We advise bigger sizes for real datasets (see our default parameters in one of our [config files](https://github.com/gustaveroussy/sopa/tree/master/workflow/config)). On the toy dataset, this will generate **4** patches.

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -113,7 +113,6 @@ rule patch_segmentation_baysor:
         patches_file = paths.smk_patches_file_baysor,
         baysor_patch = paths.smk_baysor_temp_dir / "{index}",
     output:
-        paths.smk_baysor_temp_dir / "{index}" / "segmentation_polygons.json",
         paths.smk_baysor_temp_dir / "{index}" / "segmentation_counts.loom",
     params:
         args_baysor_prior_seg = args.baysor_prior_seg,
@@ -126,7 +125,13 @@ rule patch_segmentation_baysor:
         fi
 
         cd {input.baysor_patch}
-        {config[executables][baysor]} run --save-polygons GeoJSON -c config.toml transcripts.csv {params.args_baysor_prior_seg}
+
+        help_output=$({config[executables][baysor]} run --help 2>&1) # check if the polygon-format option is available
+        if [[ $help_output == *"polygon-format"* ]]; then
+            {config[executables][baysor]} run --polygon-format GeometryCollection -c config.toml transcripts.csv {params.args_baysor_prior_seg}
+        else
+            {config[executables][baysor]} run --save-polygons GeoJSON -c config.toml transcripts.csv {params.args_baysor_prior_seg}
+        fi
         """
 
 rule patch_segmentation_comseg:

diff --git a/workflow/config/cosmx/baysor.yaml b/workflow/config/cosmx/baysor.yaml
@@ -34,8 +34,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/cosmx/cellpose_baysor.yaml b/workflow/config/cosmx/cellpose_baysor.yaml
@@ -41,8 +41,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/example_commented.yaml b/workflow/config/example_commented.yaml
@@ -63,8 +63,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 
 aggregate:

diff --git a/workflow/config/merscope/baysor_cellpose.yaml b/workflow/config/merscope/baysor_cellpose.yaml
@@ -42,8 +42,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/merscope/baysor_vizgen.yaml b/workflow/config/merscope/baysor_vizgen.yaml
@@ -37,8 +37,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/toy/uniform_baysor.yaml b/workflow/config/toy/uniform_baysor.yaml
@@ -34,8 +34,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/toy/uniform_baysor_overlaps.yaml b/workflow/config/toy/uniform_baysor_overlaps.yaml
@@ -34,8 +34,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/toy/uniform_baysor_vizgen.yaml b/workflow/config/toy/uniform_baysor_vizgen.yaml
@@ -38,8 +38,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/toy/uniform_cellpose_baysor.yaml b/workflow/config/toy/uniform_cellpose_baysor.yaml
@@ -41,8 +41,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/xenium/baysor.yaml b/workflow/config/xenium/baysor.yaml
@@ -32,8 +32,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/xenium/baysor_multimodal.yaml b/workflow/config/xenium/baysor_multimodal.yaml
@@ -36,8 +36,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/config/xenium/cellpose_baysor.yaml b/workflow/config/xenium/cellpose_baysor.yaml
@@ -41,8 +41,6 @@ segmentation:
         n_cells_init: 0
         nuclei_genes: ""
         cyto_genes: ""
-        new_component_weight: 0.2
-        new_component_fraction: 0.3
 
 aggregate:
   average_intensities: true

diff --git a/workflow/utils.py b/workflow/utils.py
@@ -98,7 +98,7 @@ def cells_paths(self, file_content: str, name, dirs: bool = False):
             return [str(self.smk_cellpose_temp_dir / f"{i}.parquet") for i in range(int(file_content))]
         if name == "baysor":
             indices = map(int, file_content.split())
-            BAYSOR_FILES = ["segmentation_polygons.json", "segmentation_counts.loom"]
+            BAYSOR_FILES = ["segmentation_counts.loom"]
 
             if dirs:
                 return [str(self.smk_baysor_temp_dir / str(i)) for i in indices]