orfdata 0.43.0__tar.gz → 0.43.1__tar.gz

{orfdata-0.43.0/orfdata.egg-info → orfdata-0.43.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.43.0
+Version: 0.43.1
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0

{orfdata-0.43.0 → orfdata-0.43.1}/docs/catalogs.md

@@ -605,22 +605,26 @@ and its [coordinate discrepancy](https://github.com/openvax/orfdata/issues/55)
 remain separate from this data-management API.
 
 The pinned files contain transcript/protein sequences, not chromosome DNA.
-For intronic sequence and structural products, explicitly install the consortium's
-[CHM13v2.0 chromosome FASTA](https://github.com/marbl/CHM13):
+For intronic sequence and structural products, explicitly install the matching
+[Ensembl CHM13v2.0 chromosome FASTA](https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/genome/):
 
 ```bash
-orfdata genomes install t2t-chm13 --genome-fasta https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz
+orfdata genomes install t2t-chm13 --genome-fasta https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/genome/Homo_sapiens-GCA_009914755.4-unmasked.fa.gz
 ```
 
 ```python
 from orfdata import load_genome
 
-dna = "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz"
+dna = "https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/genome/Homo_sapiens-GCA_009914755.4-unmasked.fa.gz"
 genome = load_genome("t2t-chm13", genome_fasta_path_or_url=dna)
 sequence = genome.sequence("1", 1, 100)  # 1-based inclusive; offline after install
 ```
 
 A local chromosome FASTA path works too. Supply the same source when loading;
+contig names must match the annotation (`1` ... `22`, `X`, `Y`). The consortium
+analysis FASTA uses `chr1` etc. and requires explicit contig-name remapping before
+use with this annotation. Renaming contigs is not coordinate liftover.
+
 DNA is optional and is not silently added to annotation-only loads. This DNA
 source is caller-selected, separate from the checksum-pinned annotation assets.
 Allow roughly 1 GB for the compressed download and several GB for installed DNA

orfdata-0.43.1/orfdata/version.py

@@ -0,0 +1 @@
+__version__ = "0.43.1"

{orfdata-0.43.0 → orfdata-0.43.1/orfdata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.43.0
+Version: 0.43.1
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0

orfdata-0.43.0/orfdata/version.py

@@ -1 +0,0 @@
-__version__ = "0.43.0"