Reinstating gff default values

Author: Jon Brenas

malariagen_data/adar1.py

@@ -123,6 +123,9 @@ def __init__(
             gcs_region_urls=GCS_REGION_URLS,
             major_version_number=MAJOR_VERSION_NUMBER,
             major_version_path=MAJOR_VERSION_PATH,
+            gff_gene_type="gene",
+            gff_gene_name_attribute="Note",
+            gff_default_attributes=("ID", "Parent", "Note", "description"),
             storage_options=storage_options,
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,

malariagen_data/adir1.py

@@ -123,6 +123,9 @@ def __init__(
             gcs_region_urls=GCS_REGION_URLS,
             major_version_number=MAJOR_VERSION_NUMBER,
             major_version_path=MAJOR_VERSION_PATH,
+            gff_gene_type="protein_coding_gene",
+            gff_gene_name_attribute="Note",
+            gff_default_attributes=("ID", "Parent", "Note", "description"),
             storage_options=storage_options,
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,

malariagen_data/af1.py

@@ -125,6 +125,9 @@ def __init__(
             gcs_region_urls=GCS_REGION_URLS,
             major_version_number=MAJOR_VERSION_NUMBER,
             major_version_path=MAJOR_VERSION_PATH,
+            gff_gene_type="protein_coding_gene",
+            gff_gene_name_attribute="Note",
+            gff_default_attributes=("ID", "Parent", "Note", "description"),
             storage_options=storage_options,
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,

malariagen_data/ag3.py

@@ -204,6 +204,9 @@ def __init__(
             gcs_region_urls=GCS_REGION_URLS,
             major_version_number=MAJOR_VERSION_NUMBER,
             major_version_path=MAJOR_VERSION_PATH,
+            gff_gene_type="gene",
+            gff_gene_name_attribute="Name",
+            gff_default_attributes=("ID", "Parent", "Name", "description"),
             storage_options=storage_options,
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,

malariagen_data/amin1.py

@@ -123,6 +123,9 @@ def __init__(
             gcs_region_urls=GCS_REGION_URLS,
             major_version_number=MAJOR_VERSION_NUMBER,
             major_version_path=MAJOR_VERSION_PATH,
+            gff_gene_type="protein_coding_gene",
+            gff_gene_name_attribute="Note",
+            gff_default_attributes=("ID", "Parent", "Note", "description"),
             storage_options=storage_options,  # used by fsspec via init_filesystem()
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,

malariagen_data/anopheles.py

@@ -128,6 +128,9 @@ def __init__(
         gcs_region_urls: Mapping[str, str],
         major_version_number: int,
         major_version_path: str,
+        gff_gene_type: str,
+        gff_gene_name_attribute: str,
+        gff_default_attributes: Tuple[str, ...],
         tqdm_class,
         storage_options: Mapping,
         taxon_colors: Optional[Mapping[str, str]] = None,
@@ -152,6 +155,9 @@ def __init__(
             major_version_number=major_version_number,
             major_version_path=major_version_path,
             storage_options=storage_options,
+            gff_gene_type=gff_gene_type,
+            gff_gene_name_attribute=gff_gene_name_attribute,
+            gff_default_attributes=gff_default_attributes,
             cohorts_analysis=cohorts_analysis,
             aim_analysis=aim_analysis,
             aim_metadata_dtype=aim_metadata_dtype,