vaquita annotations.py

small changes

md5sums updated

stdpopsim/catalog/PhoSin/__init__.py

@@ -3,3 +3,4 @@
 """
 from . import species  # noqa: F401
 from . import demographic_models  # noqa: F401
+from . import annotations  # noqa: F401

stdpopsim/catalog/PhoSin/annotations.py

@@ -0,0 +1,60 @@
+import stdpopsim
+
+_species = stdpopsim.get_species("PhoSin")
+
+_an = stdpopsim.Annotation(
+    species=_species,
+    id="Phocoena_sinus.mPhoSin1.pri.110_exons",
+    description="Vaquita exon annotations from Morin et al 2020 using NCBI's pipeline",
+    url=(
+        "https://ftp.ensembl.org/pub/release-110/"
+        "gff3/phocoena_sinus/Phocoena_sinus.mPhoSin1.pri.110.chr.gff3.gz"
+    ),
+    gff_sha256="dbc8640f8f2e046d063c45f160f39edcf729fc39549726603e389cb7b6ce542e",
+    intervals_url=(
+        "https://stdpopsim.s3-us-west-2.amazonaws.com/"
+        "annotations/PhoSin/Phocoena_sinus.mPhoSin1.pri.110_exons.tar.gz"
+    ),
+    intervals_sha256="12e767581efc46c5494f800e17011d3e80eb000950f51a98308249afdeb68f87",
+    citations=[
+        stdpopsim.Citation(
+            year=2020,
+            author="Morin et al",
+            doi="https://doi.org/10.1111/1755-0998.13284",
+            reasons={stdpopsim.CiteReason.ANNOTATION},
+        )
+    ],
+    file_pattern="Phocoena_sinus.mPhoSin1.pri.110_exon_{id}.txt",
+    annotation_source="ensembl",
+    annotation_type="exon",
+)
+_species.add_annotations(_an)
+
+# add CDS
+_an2 = stdpopsim.Annotation(
+    species=_species,
+    id="Phocoena_sinus.mPhoSin1.pri.110_CDS",
+    description="Vaquita CDS annotations from Morin et al 2020 using NCBI's pipeline",
+    url=(
+        "https://ftp.ensembl.org/pub/release-110/"
+        "gff3/phocoena_sinus/Phocoena_sinus.mPhoSin1.pri.110.chr.gff3.gz"
+    ),
+    gff_sha256="dbc8640f8f2e046d063c45f160f39edcf729fc39549726603e389cb7b6ce542e",
+    intervals_url=(
+        "https://stdpopsim.s3-us-west-2.amazonaws.com/"
+        "annotations/PhoSin/Phocoena_sinus.mPhoSin1.pri.110_CDS.tar.gz"
+    ),
+    intervals_sha256="f44859c4ce99e93f1bacce1da1e620ed41eb2fe1bd75aafe8ac99d54cb6e7a7a",
+    citations=[
+        stdpopsim.Citation(
+            year=2020,
+            author="Morin et al",
+            doi="https://doi.org/10.1111/1755-0998.13284",
+            reasons={stdpopsim.CiteReason.ANNOTATION},
+        )
+    ],
+    file_pattern="Phocoena_sinus.mPhoSin1.pri.110_CDS_{id}.txt",
+    annotation_source="ensembl",
+    annotation_type="CDS",
+)
+_species.add_annotations(_an2)