flu: check in data from current season (#239)

Check in influenza data from current season

Also ran new version of black

figures/counts-by-pathogen-and-study.py

@@ -86,9 +86,9 @@ def start():
                 matching_reads = mgs_data.viral_reads(bioproject, taxids)
                 viral_samples = mgs_data.sample_attributes(
                     bioproject,
-                    enrichment=None
-                    if study == "brinch"
-                    else mgs.Enrichment.VIRAL,
+                    enrichment=(
+                        None if study == "brinch" else mgs.Enrichment.VIRAL
+                    ),
                 )
                 n_samples += len(viral_samples)
                 counts = [

mgs.py

@@ -106,9 +106,11 @@ def make_count_tree(
     taxtree: Tree[TaxID], sample_counts: SampleCounts
 ) -> Tree[tuple[TaxID, Counter[Sample]]]:
     return taxtree.map(
-        lambda taxid: (taxid, Counter(sample_counts[taxid]))
-        if taxid in sample_counts
-        else (taxid, Counter()),
+        lambda taxid: (
+            (taxid, Counter(sample_counts[taxid]))
+            if taxid in sample_counts
+            else (taxid, Counter())
+        ),
     )
 
 

pathogen_properties.py

@@ -301,8 +301,7 @@ def average(in1: "Scalar", in2: "Scalar"):
 
 class Predictor(abc.ABC, Variable):
     @abc.abstractmethod
-    def get_data(self) -> float:
-        ...
+    def get_data(self) -> float: ...
 
 
 @dataclass(kw_only=True, eq=True, frozen=True)

pathogens/aav2.py

@@ -29,7 +29,7 @@
     # (93K%2C%20docx)-,Supplemental%20data%3A,-Click%20here%20to
     date="2022",
     active=Active.LATENT,
-    source="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9063149/#:~:text=Seropositivity%20for%20(A)%20the%20global%20population"
+    source="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9063149/#:~:text=Seropositivity%20for%20(A)%20the%20global%20population",
     # This number matches AAV-2 seroprevalence in a study of 101 males with
     # Duchenne Muscular Dystrophy, showing a seroprevalence of 56%:
     # "https://pubmed.ncbi.nlm.nih.gov/36324212/#:~:text=We%20prospectively%20enrolled,and%20AAV8%20(47%25)."

pathogens/bkv.py

@@ -61,7 +61,7 @@
     date="2007",
     # Study is from 2009, sera are from 2007
     active=Active.LATENT,
-    source="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000363#:~:text=We%20found%20the%20seroprevalence%20(%2B/%E2%88%92%201%25)%20in%20healthy%20adult%20blood%20donors%20(1501)%20was%20SV40%20(9%25)%2C%20BKV%20(82%25)%2C%20JCV%20(39%25)%2C%20LPV"
+    source="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000363#:~:text=We%20found%20the%20seroprevalence%20(%2B/%E2%88%92%201%25)%20in%20healthy%20adult%20blood%20donors%20(1501)%20was%20SV40%20(9%25)%2C%20BKV%20(82%25)%2C%20JCV%20(39%25)%2C%20LPV",
     # A tabular breakdown can be found here: "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000363#:~:text=original%20image-,Table%201.,-Seroprevalence%20of%20polyomaviruses"
 )
 

pathogens/hcv.py

@@ -25,7 +25,7 @@
     date="2020",
     country="United States",
     state="Ohio",
-    source="https://odh.ohio.gov/wps/wcm/connect/gov/ec0dec22-1eea-4d17-a86a-ac4bc35be4d3/HCV+5+Year+Report+2021.pdf?MOD=AJPERES&CONVERT_TO=url&CACHEID=ROOTWORKSPACE.Z18_M1HGGIK0N0JO00QO9DDDDM3000-ec0dec22-1eea-4d17-a86a-ac4bc35be4d3-oqU9kQ8"
+    source="https://odh.ohio.gov/wps/wcm/connect/gov/ec0dec22-1eea-4d17-a86a-ac4bc35be4d3/HCV+5+Year+Report+2021.pdf?MOD=AJPERES&CONVERT_TO=url&CACHEID=ROOTWORKSPACE.Z18_M1HGGIK0N0JO00QO9DDDDM3000-ec0dec22-1eea-4d17-a86a-ac4bc35be4d3-oqU9kQ8",
     # Page 1 of 8
 )
 

pathogens/hiv.py

@@ -89,7 +89,7 @@
     people=652_221,
     country="Denmark",
     date="2022",
-    source="https://kk.statistikbank.dk/statbank5a/SelectVarVal/Define.asp?MainTable=KKBEF1"
+    source="https://kk.statistikbank.dk/statbank5a/SelectVarVal/Define.asp?MainTable=KKBEF1",
     # Search variables: Copenhagen in total, Gender in general, Age in total,
     # 2022 Q4
 )

pathogens/jcv.py

@@ -57,7 +57,7 @@
     date="2007",
     # Study is from 2009, sera are from 2007
     active=Active.LATENT,
-    source="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000363#:~:text=We%20found%20the%20seroprevalence%20(%2B/%E2%88%92%201%25)%20in%20healthy%20adult%20blood%20donors%20(1501)%20was%20SV40%20(9%25)%2C%20BKV%20(82%25)%2C%20JCV%20(39%25)%2C%20LPV"
+    source="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000363#:~:text=We%20found%20the%20seroprevalence%20(%2B/%E2%88%92%201%25)%20in%20healthy%20adult%20blood%20donors%20(1501)%20was%20SV40%20(9%25)%2C%20BKV%20(82%25)%2C%20JCV%20(39%25)%2C%20LPV",
     # A tabular breakdown can be found here: "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000363#:~:text=original%20image-,Table%201.,-Seroprevalence%20of%20polyomaviruses"
 )
 

pathogens/mcv.py

@@ -38,7 +38,7 @@
     country="United States",
     date="2009",
     active=Active.LATENT,
-    source="https://academic.oup.com/jnci/article/101/21/1510/963538#:~:text=A%20cut%20point%20of%2015%E2%80%89000%20median%20fluorescent%20intensity%20units%20was%20chosen%20as%20described%20above%20and%20used%20to%20identify%20268%20(59.4%25)%20of%20the%20451%20control%20subjects%20as%20seropositive%20for%20MCPyV%20VP1%3B%20this%20percentage%20was%20similar%20to%20that%20among%20women%20in%20control%20group%201%20(ie%2C%2053%25)."
+    source="https://academic.oup.com/jnci/article/101/21/1510/963538#:~:text=A%20cut%20point%20of%2015%E2%80%89000%20median%20fluorescent%20intensity%20units%20was%20chosen%20as%20described%20above%20and%20used%20to%20identify%20268%20(59.4%25)%20of%20the%20451%20control%20subjects%20as%20seropositive%20for%20MCPyV%20VP1%3B%20this%20percentage%20was%20similar%20to%20that%20among%20women%20in%20control%20group%201%20(ie%2C%2053%25).",
     # Other studies give numbers that are up to 20 percentage points smaller
     # or larger:
     # "In an early study from the United States (US), MCPyV seroprevalence in