:wq

Merge remote-tracking branch 'upstream/master' into fix/issue-1206-surveillance-flags-graceful-fallback

Author: khushthecoder

malariagen_data/adar1.py

@@ -105,6 +105,8 @@ def __init__(
             cohorts_analysis=cohorts_analysis,
             aim_analysis=None,
             aim_metadata_dtype=None,
+            aim_ids=None,
+            aim_palettes=None,
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask="darlingi",
@@ -121,6 +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

@@ -105,6 +105,8 @@ def __init__(
             cohorts_analysis=cohorts_analysis,
             aim_analysis=None,
             aim_metadata_dtype=None,
+            aim_ids=None,
+            aim_palettes=None,
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask="dirus",
@@ -121,6 +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

@@ -107,6 +107,8 @@ def __init__(
             cohorts_analysis=cohorts_analysis,
             aim_analysis=None,
             aim_metadata_dtype=None,
+            aim_ids=None,
+            aim_palettes=None,
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask="funestus",
@@ -123,6 +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

@@ -186,6 +186,8 @@ def __init__(
             cohorts_analysis=cohorts_analysis,
             aim_analysis=aim_analysis,
             aim_metadata_dtype=AIM_METADATA_DTYPE,
+            aim_ids=("gambcolu_vs_arab", "gamb_vs_colu"),
+            aim_palettes=AIM_PALETTES,
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask="gamb_colu_arab",
@@ -202,6 +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

@@ -105,6 +105,8 @@ def __init__(
             cohorts_analysis=cohorts_analysis,
             aim_analysis=None,
             aim_metadata_dtype=None,
+            aim_ids=None,
+            aim_palettes=None,
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask="minimus",
@@ -121,6 +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

@@ -14,6 +14,7 @@
 
 
 from .anoph import (
+    aim_params,
     base_params,
     dash_params,
     gplt_params,
@@ -109,6 +110,8 @@ def __init__(
         cohorts_analysis: Optional[str],
         aim_analysis: Optional[str],
         aim_metadata_dtype: Optional[Mapping[str, Any]],
+        aim_ids: Optional[aim_params.aim_ids],
+        aim_palettes: Optional[aim_params.aim_palettes],
         site_filters_analysis: Optional[str],
         discordant_read_calls_analysis: Optional[str],
         default_site_mask: Optional[str],
@@ -125,6 +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,
@@ -149,9 +155,14 @@ 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,
+            aim_ids=aim_ids,
+            aim_palettes=aim_palettes,
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask=default_site_mask,