Merge branch 'master' into GH716_add_constructor_params

Author: leehart

README.md

@@ -128,6 +128,17 @@ the documentation via GitHub Actions.
 The version switcher for the documentation can then be updated by
 modifying the `docs/source/_static/switcher.json` file accordingly.
 
+## Citation
+
+If you use the `malariagen_data` package in a publication
+or include any of its functions or code in other materials (_e.g._ training resources),
+please cite: [doi.org/10.5281/zenodo.11173411](doi.org/10.5281/zenodo.11173411)
+
+Some functions may require additional citations to acknowledge specific contributions. These are indicated in the description for each relevant function.
+
+For any questions, please feel free to contact us at: [support@malariagen.net](mailto:support@malariagen.net)
+
+
 ## Sponsorship
 
 This project is currently supported by the following grants:

malariagen_data/af1.py

@@ -9,6 +9,7 @@
 MAJOR_VERSION_PATH = "v1.0"
 CONFIG_PATH = "v1.0-config.json"
 GCS_DEFAULT_URL = "gs://vo_afun_release_master_us_central1/"
+GCS_DEFAULT_PUBLIC_URL = "gs://vo_anoph_temp_us_central1/vo_agam_release/"
 GCS_REGION_URLS = {
     "us-central1": "gs://vo_afun_release_master_us_central1",
 }
@@ -78,6 +79,7 @@ class Af1(AnophelesDataResource):
     def __init__(
         self,
         url=None,
+        public_url=GCS_DEFAULT_PUBLIC_URL,
         bokeh_output_notebook=True,
         results_cache=None,
         log=sys.stdout,
@@ -95,6 +97,7 @@ def __init__(
     ):
         super().__init__(
             url=url,
+            public_url=public_url,
             config_path=CONFIG_PATH,
             cohorts_analysis=cohorts_analysis,
             aim_analysis=None,

malariagen_data/ag3.py

@@ -15,6 +15,7 @@
 MAJOR_VERSION_PATH = "v3"
 CONFIG_PATH = "v3-config.json"
 GCS_DEFAULT_URL = "gs://vo_agam_release_master_us_central1/"
+GCS_DEFAULT_PUBLIC_URL = "gs://vo_anoph_temp_us_central1/vo_agam_release/"
 GCS_REGION_URLS = {
     "us-central1": "gs://vo_agam_release_master_us_central1",
 }
@@ -138,6 +139,7 @@ class Ag3(AnophelesDataResource):
     def __init__(
         self,
         url=None,
+        public_url=GCS_DEFAULT_PUBLIC_URL,
         bokeh_output_notebook=True,
         results_cache=None,
         log=sys.stdout,
@@ -156,6 +158,7 @@ def __init__(
     ):
         super().__init__(
             url=url,
+            public_url=public_url,
             config_path=CONFIG_PATH,
             cohorts_analysis=cohorts_analysis,
             aim_analysis=aim_analysis,

malariagen_data/anoph/base.py

@@ -47,6 +47,7 @@ def __init__(
         self,
         *,
         url: str,
+        public_url: str,
         config_path: str,
         pre: bool,
         major_version_number: int,
@@ -121,6 +122,8 @@ def __init__(
             raise ValueError("A value for the `url` parameter must be provided.")
         del url
 
+        self._public_url = public_url
+
         # Set up fsspec filesystem. N.B., we use fsspec here to allow for
         # accessing different types of storage - fsspec will automatically
         # detect which type of storage to use based on the URL provided.

malariagen_data/anoph/dipclust.py

@@ -47,7 +47,7 @@ def __init__(
         summary=""""
         Hierarchically cluster diplotypes in region and produce an interactive plot.
 
-        If you use this function in a publication, please cite the original manuscript: doi.org/10.1093/molbev/msae140
+        If you use this function in a publication, please cite both this package and the original manuscript: doi.org/10.1093/molbev/msae140
         """,
     )
     def plot_diplotype_clustering(
@@ -602,7 +602,7 @@ def _insert_dipclust_snp_trace(
         summary=""""
         Perform diplotype clustering, annotated with heterozygosity, gene copy number and amino acid variants.
 
-        If you use this function in a publication, please cite the original manuscript: doi.org/10.1093/molbev/msae140
+        If you use this function in a publication, please cite both this package and the original manuscript: doi.org/10.1093/molbev/msae140
         """,
         parameters=dict(
             heterozygosity="Plot heterozygosity track.",

malariagen_data/anoph/igv.py

@@ -31,20 +31,21 @@ def _igv_config(
             "reference": {
                 "id": self._genome_ref_id,
                 "name": self._genome_ref_name,
-                "fastaURL": f"{self._url}{self._genome_fasta_path}",
-                "indexURL": f"{self._url}{self._genome_fai_path}",
+                "fastaURL": f"{self._public_url}{self._genome_fasta_path}",
+                "indexURL": f"{self._public_url}{self._genome_fai_path}",
                 "tracks": [
                     {
                         "name": "Genes",
                         "type": "annotation",
                         "format": "gff3",
-                        "url": f"{self._url}{self._geneset_gff3_path}",
+                        "url": f"{self._public_url}{self._geneset_gff3_path}",
                         "indexed": False,
                     }
                 ],
             },
             "locus": str(region),
         }
+
         if tracks:
             config["tracks"] = tracks
 
@@ -58,7 +59,7 @@ def _igv_site_filters_tracks(
     ):
         tracks = []
         for site_mask in self.site_mask_ids:
-            site_filters_vcf_url = f"{self._url}{self._major_version_path}/site_filters/{self._site_filters_analysis}/vcf/{site_mask}/{contig}_sitefilters.vcf.gz"  # noqa
+            site_filters_vcf_url = f"{self._public_url}{self._major_version_path}/site_filters/{self._site_filters_analysis}/vcf/{site_mask}/{contig}_sitefilters.vcf.gz"  # f"{self._url}{self._major_version_path}/site_filters/{self._site_filters_analysis}/vcf/{site_mask}/{contig}_sitefilters.vcf.gz"  # noqa
             track_config = {
                 "name": f"Filters - {site_mask}",
                 "url": site_filters_vcf_url,

malariagen_data/anopheles.py

@@ -101,6 +101,7 @@ class AnophelesDataResource(
     def __init__(
         self,
         url,
+        public_url,
         config_path,
         cohorts_analysis: Optional[str],
         aim_analysis: Optional[str],
@@ -137,6 +138,7 @@ def __init__(
     ):
         super().__init__(
             url=url,
+            public_url=public_url,
             config_path=config_path,
             bokeh_output_notebook=bokeh_output_notebook,
             log=log,

malariagen_data/pf8_config.json

@@ -1,5 +1,5 @@
 {
-    "default_url": "gs://pf8-release/",
+    "default_url": "s3://pf8-release/" ,
     "metadata_path": "metadata/Pf8_samples.txt",
     "reference_path": "reference/PlasmoDB-54-Pfalciparum3D7-Genome.zarr/",
     "reference_contigs": [