Add io validation for step 3

broadinstitute · Sep 21, 2023 · aed81ab · aed81ab
1 parent eabf55b
commit aed81ab
Show file tree

Hide file tree

Showing 12 changed files with 1,278 additions and 24 deletions.
diff --git a/data-pipeline/poetry.lock b/data-pipeline/poetry.lock
diff --git a/data-pipeline/pyproject.toml b/data-pipeline/pyproject.toml
@@ -18,10 +18,30 @@ cattrs = "^23.1.2"
 hail = "^0.2.122"
 pytest = "^7.4.2"
 ipython = "^8.15.0"
+pylint = "^2.17.5"
 
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.black]
 line-length = 120
+
+[tool.pylint.basic]
+# ds: frequently used name for a variable containing a Hail table
+good-names = [
+  "ds",
+]
+
+[tool.pylint.messages_control]
+disable = [
+  # Ignore refactor and convention categories
+  "R",
+  "C",
+]
+
+[tool.pylint.miscellaneous]
+notes = [
+  "FIXME",
+  "TODO",
+]
diff --git a/..._v4_exome_transcript_consequences/mane_transcripts_path/mane_select_transcripts.ht.schema b/..._v4_exome_transcript_consequences/mane_transcripts_path/mane_select_transcripts.ht.schema
@@ -0,0 +1,14 @@
+----------------------------------------
+Global fields:
+    'version': str 
+----------------------------------------
+Row fields:
+    'gene_id': str 
+    'matched_gene_version': str 
+    'ensembl_id': str 
+    'ensembl_version': str 
+    'refseq_id': str 
+    'refseq_version': str 
+----------------------------------------
+Key: ['gene_id']
+----------------------------------------