Merge branch 'master' into development

usnistgov · Mar 16, 2022 · 6a14e79 · 6a14e79
2 parents 3a1a8b6 + d877d80
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diff --git a/.gitattributes b/.gitattributes
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+*.pt filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitignore b/.gitignore
@@ -8,4 +8,5 @@ __pycache__/
 docs/examples
 docs/*.pt
 docs/*.csv
-docs/_build/
+docs/_build/
+manuscript/experiments/
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -67,6 +67,15 @@ tensor([1., 0., 1., 0., 0.])
 '+c:+e'
 
 
+An alternative data format is supported, comparing the full sequence
+for each variant against the wild-type (see :meth:`~lantern.dataset.Dataset.from_sequences`).
+
+>>> df = pd.DataFrame({"phenotype": [0]*3, "sequence": ["AAA", "ATC", "CGA"]})
+>>> ds = lantern.dataset.Dataset.from_sequences(df, wildtype="AAA", sequence_col="sequence")
+>>> ds.tokenizer.tokens
+['A1C', 'A2G', 'A2T', 'A3C']
+
+
 
 
 Building a LANTERN model