Merge pull request #349 from apriltuesday/update-variant-types

Update clinvar variant types diagrams
EBIvariation · Oct 27, 2022 · cc005e5 · cc005e5
2 parents 1246419 + 7b855d2
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diff --git a/data-exploration/clinvar-variant-types/README.md b/data-exploration/clinvar-variant-types/README.md
@@ -2,7 +2,7 @@
 
 The script in this directory parses the ClinVar XML data dump and constructs several diagrams and tables which illustrate how variation and disease data are represented. This helps guide the design of the pipeline and its output structure.
 
-The data was last updated on **2021-05-27.** Graphs can be enlarged by clicking on them.
+The data was last updated on **2022-10-24.** Graphs can be enlarged by clicking on them.
 
 
 
@@ -70,15 +70,6 @@ These fields reflect the strength of evidence supporting the assertion of varian
 
 ![](diagrams/star-rating.png)
 
-### Distribution of records by star rating
-Star rating|Count
-:--|:--
-☆☆☆☆|167118
-★☆☆☆|1022556
-★★☆☆|72589
-★★★☆|12226
-★★★★|42
-
 
 
 ## Mode of inheritance

diff --git a/data-exploration/clinvar-variant-types/clinvar-variant-types.py b/data-exploration/clinvar-variant-types/clinvar-variant-types.py
@@ -4,7 +4,7 @@
 from collections import Counter
 import logging
 
-import eva_cttv_pipeline.clinvar_xml_io.clinvar_xml_io as clinvar_xml_utils
+from eva_cttv_pipeline.clinvar_xml_io import clinvar_xml_io
 
 logging.basicConfig()
 logger = logging.getLogger(__name__)

diff --git a/data-exploration/clinvar-variant-types/diagrams/allele-origin.png b/data-exploration/clinvar-variant-types/diagrams/allele-origin.png
diff --git a/data-exploration/clinvar-variant-types/diagrams/clinical-significance.png b/data-exploration/clinvar-variant-types/diagrams/clinical-significance.png
diff --git a/data-exploration/clinvar-variant-types/diagrams/inheritance-origin.png b/data-exploration/clinvar-variant-types/diagrams/inheritance-origin.png
diff --git a/data-exploration/clinvar-variant-types/diagrams/mode-of-inheritance.png b/data-exploration/clinvar-variant-types/diagrams/mode-of-inheritance.png
diff --git a/data-exploration/clinvar-variant-types/diagrams/star-rating.png b/data-exploration/clinvar-variant-types/diagrams/star-rating.png
diff --git a/data-exploration/clinvar-variant-types/diagrams/traits.png b/data-exploration/clinvar-variant-types/diagrams/traits.png
diff --git a/data-exploration/clinvar-variant-types/diagrams/variant-types.png b/data-exploration/clinvar-variant-types/diagrams/variant-types.png
diff --git a/data-exploration/clinvar-variant-types/supplementary-tables.md b/data-exploration/clinvar-variant-types/supplementary-tables.md