varcode 2.3.0__tar.gz → 2.3.1__tar.gz

{varcode-2.3.0/varcode.egg-info → varcode-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 2.3.0
+Version: 2.3.1
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode
@@ -106,7 +106,22 @@ print(premature_stop_effect.gene.name)
 ### 'TP53'
 ```
 
-If you are looking for a quick start guide, you can check out [this iPython book](./examples/varcode-quick_start.ipynb) that demonstrates simple use cases of Varcode
+If you are looking for a quick start guide, you can check out [this iPython book](./examples/varcode-quick_start.ipynb) that demonstrates simple use cases of Varcode.
+
+## Further reading
+
+Feature guides live in [`docs/`](./docs/):
+
+- [**Genotypes and sample-aware queries**](./docs/genotype.md) — per-sample
+  zygosity on multi-sample VCFs (`Genotype`, `Zygosity`, `VariantCollection.for_sample`,
+  `.heterozygous_in`, `.homozygous_alt_in`). New in 2.3.
+- [**CSV round-trip and metadata headers**](./docs/csv.md) — `to_csv` /
+  `from_csv` on both collection types, with `#`-prefixed provenance
+  headers. New in 2.1, refined in 2.2.
+- [**Error handling**](./docs/errors.md) — `ReferenceMismatchError`,
+  `SampleNotFoundError`, and the `raise_on_error=False` escape hatch.
+
+See [`CHANGELOG.md`](./CHANGELOG.md) for the release history.
 
 ## Effect Types
 

{varcode-2.3.0 → varcode-2.3.1}/README.md

@@ -79,7 +79,22 @@ print(premature_stop_effect.gene.name)
 ### 'TP53'
 ```
 
-If you are looking for a quick start guide, you can check out [this iPython book](./examples/varcode-quick_start.ipynb) that demonstrates simple use cases of Varcode
+If you are looking for a quick start guide, you can check out [this iPython book](./examples/varcode-quick_start.ipynb) that demonstrates simple use cases of Varcode.
+
+## Further reading
+
+Feature guides live in [`docs/`](./docs/):
+
+- [**Genotypes and sample-aware queries**](./docs/genotype.md) — per-sample
+  zygosity on multi-sample VCFs (`Genotype`, `Zygosity`, `VariantCollection.for_sample`,
+  `.heterozygous_in`, `.homozygous_alt_in`). New in 2.3.
+- [**CSV round-trip and metadata headers**](./docs/csv.md) — `to_csv` /
+  `from_csv` on both collection types, with `#`-prefixed provenance
+  headers. New in 2.1, refined in 2.2.
+- [**Error handling**](./docs/errors.md) — `ReferenceMismatchError`,
+  `SampleNotFoundError`, and the `raise_on_error=False` escape hatch.
+
+See [`CHANGELOG.md`](./CHANGELOG.md) for the release history.
 
 ## Effect Types
 

{varcode-2.3.0 → varcode-2.3.1}/varcode/effects/effect_collection.py

@@ -260,9 +260,12 @@ class EffectCollection(Collection):
             Dictionary mapping transcript IDs to length-normalized expression
             levels (either FPKM or TPM)
 
-        Returns dictionary mapping each transcript effect to an expression
-        quantity. Effects that don't have an associated transcript
-        (e.g. Intergenic) will not be included.
+        Returns
+        -------
+        OrderedDict
+            Mapping from each transcript effect to an expression quantity.
+            Effects that don't have an associated transcript (e.g. Intergenic)
+            are excluded.
         """
         return OrderedDict(
             (effect, expression_levels.get(effect.transcript.id, 0.0))

varcode-2.3.1/varcode/version.py

@@ -0,0 +1 @@
+__version__ = "2.3.1"

{varcode-2.3.0 → varcode-2.3.1/varcode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 2.3.0
+Version: 2.3.1
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode
@@ -106,7 +106,22 @@ print(premature_stop_effect.gene.name)
 ### 'TP53'
 ```
 
-If you are looking for a quick start guide, you can check out [this iPython book](./examples/varcode-quick_start.ipynb) that demonstrates simple use cases of Varcode
+If you are looking for a quick start guide, you can check out [this iPython book](./examples/varcode-quick_start.ipynb) that demonstrates simple use cases of Varcode.
+
+## Further reading
+
+Feature guides live in [`docs/`](./docs/):
+
+- [**Genotypes and sample-aware queries**](./docs/genotype.md) — per-sample
+  zygosity on multi-sample VCFs (`Genotype`, `Zygosity`, `VariantCollection.for_sample`,
+  `.heterozygous_in`, `.homozygous_alt_in`). New in 2.3.
+- [**CSV round-trip and metadata headers**](./docs/csv.md) — `to_csv` /
+  `from_csv` on both collection types, with `#`-prefixed provenance
+  headers. New in 2.1, refined in 2.2.
+- [**Error handling**](./docs/errors.md) — `ReferenceMismatchError`,
+  `SampleNotFoundError`, and the `raise_on_error=False` escape hatch.
+
+See [`CHANGELOG.md`](./CHANGELOG.md) for the release history.
 
 ## Effect Types
 

varcode-2.3.0/varcode/version.py

@@ -1 +0,0 @@
-__version__ = "2.3.0"