orfdata 0.42.1__tar.gz → 0.42.2__tar.gz

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Files changed (385) hide show
  1. {orfdata-0.42.1/orfdata.egg-info → orfdata-0.42.2}/PKG-INFO +1 -1
  2. {orfdata-0.42.1 → orfdata-0.42.2}/docs/catalogs.md +13 -4
  3. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/catalogs.json +8 -2
  4. orfdata-0.42.2/orfdata/version.py +1 -0
  5. {orfdata-0.42.1 → orfdata-0.42.2/orfdata.egg-info}/PKG-INFO +1 -1
  6. orfdata-0.42.1/orfdata/version.py +0 -1
  7. {orfdata-0.42.1 → orfdata-0.42.2}/LICENSE +0 -0
  8. {orfdata-0.42.1 → orfdata-0.42.2}/MANIFEST.in +0 -0
  9. {orfdata-0.42.1 → orfdata-0.42.2}/README.md +0 -0
  10. {orfdata-0.42.1 → orfdata-0.42.2}/deploy.sh +0 -0
  11. {orfdata-0.42.1 → orfdata-0.42.2}/docs/copy-yeast.md +0 -0
  12. {orfdata-0.42.1 → orfdata-0.42.2}/docs/coverage.md +0 -0
  13. {orfdata-0.42.1 → orfdata-0.42.2}/docs/dog-data-sources.md +0 -0
  14. {orfdata-0.42.1 → orfdata-0.42.2}/docs/dog-peptides.md +0 -0
  15. {orfdata-0.42.1 → orfdata-0.42.2}/docs/downloads.md +0 -0
  16. {orfdata-0.42.1 → orfdata-0.42.2}/docs/downstream.md +0 -0
  17. {orfdata-0.42.1 → orfdata-0.42.2}/docs/examples.md +0 -0
  18. {orfdata-0.42.1 → orfdata-0.42.2}/docs/human-tissue.md +0 -0
  19. {orfdata-0.42.1 → orfdata-0.42.2}/docs/index.md +0 -0
  20. {orfdata-0.42.1 → orfdata-0.42.2}/docs/ingolia-yeast.md +0 -0
  21. {orfdata-0.42.1 → orfdata-0.42.2}/docs/measurements.md +0 -0
  22. {orfdata-0.42.1 → orfdata-0.42.2}/docs/pairing.md +0 -0
  23. {orfdata-0.42.1 → orfdata-0.42.2}/docs/pfizer-peptides.md +0 -0
  24. {orfdata-0.42.1 → orfdata-0.42.2}/docs/pfizer-protein.md +0 -0
  25. {orfdata-0.42.1 → orfdata-0.42.2}/docs/pfizer-rna.md +0 -0
  26. {orfdata-0.42.1 → orfdata-0.42.2}/docs/proteome.md +0 -0
  27. {orfdata-0.42.1 → orfdata-0.42.2}/docs/reference.md +0 -0
  28. {orfdata-0.42.1 → orfdata-0.42.2}/docs/search-references.md +0 -0
  29. {orfdata-0.42.1 → orfdata-0.42.2}/docs/source-references.md +0 -0
  30. {orfdata-0.42.1 → orfdata-0.42.2}/docs/species.md +0 -0
  31. {orfdata-0.42.1 → orfdata-0.42.2}/docs/storage.md +0 -0
  32. {orfdata-0.42.1 → orfdata-0.42.2}/docs/stylesheets/docs.css +0 -0
  33. {orfdata-0.42.1 → orfdata-0.42.2}/docs/viral.md +0 -0
  34. {orfdata-0.42.1 → orfdata-0.42.2}/docs.sh +0 -0
  35. {orfdata-0.42.1 → orfdata-0.42.2}/lint.sh +0 -0
  36. {orfdata-0.42.1 → orfdata-0.42.2}/mkdocs.yml +0 -0
  37. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/__init__.py +0 -0
  38. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/_pinned_genome.py +0 -0
  39. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/_structure.py +0 -0
  40. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/artifact_archives.py +0 -0
  41. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/build.py +0 -0
  42. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/catalog.py +0 -0
  43. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/catalog_cli.py +0 -0
  44. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/catalog_manifest.py +0 -0
  45. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/catalogs.py +0 -0
  46. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/cli.py +0 -0
  47. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/cli_output.py +0 -0
  48. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/chains.json +0 -0
  49. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/datasets.json +0 -0
  50. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/genomes.json +0 -0
  51. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/ires/rfam-15.1-human-ires.json +0 -0
  52. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/orf-evidence/AUTHOR-LICENSE.txt +0 -0
  53. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/orf-evidence/NOTICE.txt +0 -0
  54. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/orf-evidence/catalog.json.gz +0 -0
  55. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/orf-evidence/manifest.json +0 -0
  56. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/uorf-evidence/AUTHOR-LICENSE.txt +0 -0
  57. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/uorf-evidence/NOTICE.txt +0 -0
  58. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/uorf-evidence/catalog.json.gz +0 -0
  59. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/uorf-evidence/manifest.json +0 -0
  60. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/viral/NOTICE.md +0 -0
  61. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/viral/gdc-grch38-d1-vd1-coverage.tsv +0 -0
  62. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/viral/gdc-grch38-d1-vd1-genbank.tsv +0 -0
  63. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/viral/gdc-grch38-d1-vd1-pave.tsv +0 -0
  64. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/viral/hpv16-refseq-CDS.json.gz +0 -0
  65. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/viral/subsets.yaml +0 -0
  66. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data_resources.py +0 -0
  67. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/dataset.py +0 -0
  68. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/dataset_cli.py +0 -0
  69. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/datasets.py +0 -0
  70. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/download_cli.py +0 -0
  71. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/downloads.py +0 -0
  72. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/evidence.py +0 -0
  73. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/evidence_summary.py +0 -0
  74. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/fasta.py +0 -0
  75. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/genbank.py +0 -0
  76. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/genomes.py +0 -0
  77. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/genomes_cli.py +0 -0
  78. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/gtf.py +0 -0
  79. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/initiation_context.py +0 -0
  80. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/install.py +0 -0
  81. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/liftover.py +0 -0
  82. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/liftover_cli.py +0 -0
  83. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/measurements.py +0 -0
  84. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/model.py +0 -0
  85. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/net.py +0 -0
  86. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/numeric_vector.py +0 -0
  87. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/pairing.py +0 -0
  88. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/proteome.py +0 -0
  89. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/proteome_cli.py +0 -0
  90. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/record_sources.py +0 -0
  91. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/reference.py +0 -0
  92. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/reference_ledger.py +0 -0
  93. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/reference_mapping.py +0 -0
  94. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/reference_table.py +0 -0
  95. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/refseq.py +0 -0
  96. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/rna.py +0 -0
  97. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/search_reference.py +0 -0
  98. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sequence.py +0 -0
  99. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/__init__.py +0 -0
  100. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/copy.py +0 -0
  101. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/ingolia.py +0 -0
  102. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/kaabinejadian.py +0 -0
  103. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/ncorf_mammals.py +0 -0
  104. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/openprot.py +0 -0
  105. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/peptideatlas.py +0 -0
  106. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer.py +0 -0
  107. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_attribution.py +0 -0
  108. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_dataset.py +0 -0
  109. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_definitions.py +0 -0
  110. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_evidence.py +0 -0
  111. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_lineage.py +0 -0
  112. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_native.py +0 -0
  113. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_queries.py +0 -0
  114. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_rna.py +0 -0
  115. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/pfizer_vendor.py +0 -0
  116. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/riborf.py +0 -0
  117. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/sources/wang.py +0 -0
  118. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral.py +0 -0
  119. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral_annotation.py +0 -0
  120. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral_cli.py +0 -0
  121. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral_coverage.py +0 -0
  122. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral_panel.py +0 -0
  123. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral_registry.py +0 -0
  124. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata/viral_subsets.py +0 -0
  125. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata.egg-info/SOURCES.txt +0 -0
  126. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata.egg-info/dependency_links.txt +0 -0
  127. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata.egg-info/entry_points.txt +0 -0
  128. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata.egg-info/requires.txt +0 -0
  129. {orfdata-0.42.1 → orfdata-0.42.2}/orfdata.egg-info/top_level.txt +0 -0
  130. {orfdata-0.42.1 → orfdata-0.42.2}/pyproject.toml +0 -0
  131. {orfdata-0.42.1 → orfdata-0.42.2}/setup.cfg +0 -0
  132. {orfdata-0.42.1 → orfdata-0.42.2}/test.sh +0 -0
  133. {orfdata-0.42.1 → orfdata-0.42.2}/tests/conftest.py +0 -0
  134. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/aggregate_evidence.json +0 -0
  135. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905474.soft +0 -0
  136. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905474_KL9_fpkm.txt.gz +0 -0
  137. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905476.soft +0 -0
  138. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905476_KL10_fpkm.txt.gz +0 -0
  139. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905478.soft +0 -0
  140. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905478_KL11_fpkm.txt.gz +0 -0
  141. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905479.soft +0 -0
  142. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/GSM1905479_KL12_fpkm.txt.gz +0 -0
  143. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/NOTICE.md +0 -0
  144. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/expected.json +0 -0
  145. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/geo-series.soft +0 -0
  146. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/manifest.json +0 -0
  147. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/methods.pdf +0 -0
  148. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/paper.xml +0 -0
  149. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/pmc-metadata.json +0 -0
  150. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/qconcat.fasta +0 -0
  151. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/copy/workbook.xlsx +0 -0
  152. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346111.metadata.txt +0 -0
  153. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346111.quant.txt.gz +0 -0
  154. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346114.metadata.txt +0 -0
  155. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346114.quant.txt.gz +0 -0
  156. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346115.metadata.txt +0 -0
  157. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346115.quant.txt.gz +0 -0
  158. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346116.metadata.txt +0 -0
  159. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346116.quant.txt.gz +0 -0
  160. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346117.metadata.txt +0 -0
  161. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346117.quant.txt.gz +0 -0
  162. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346118.metadata.txt +0 -0
  163. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346118.quant.txt.gz +0 -0
  164. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346120.metadata.txt +0 -0
  165. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346120.quant.txt.gz +0 -0
  166. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346122.metadata.txt +0 -0
  167. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/GSM346122.quant.txt.gz +0 -0
  168. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/NOTICE.md +0 -0
  169. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/expected.json +0 -0
  170. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/manifest.json +0 -0
  171. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ingolia/readMe.txt.gz +0 -0
  172. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/kaabinejadian/README.md +0 -0
  173. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/kaabinejadian/Results.zip +0 -0
  174. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/kaabinejadian/manifest-v1.json +0 -0
  175. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/kaabinejadian/manifest.json +0 -0
  176. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/kaabinejadian/sdrf.tsv +0 -0
  177. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/README.md +0 -0
  178. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/S3.xlsx +0 -0
  179. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/ensembl107.cdna.fa.gz +0 -0
  180. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/ensembl107.gtf.gz +0 -0
  181. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/human-ensembl107.gtf.gz +0 -0
  182. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/human.bed +0 -0
  183. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/human.pep.fa +0 -0
  184. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/mouse.bed +0 -0
  185. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/ncorf_mammals/mouse.pep.fa +0 -0
  186. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/openprot/README.md +0 -0
  187. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/openprot/ensembl106.cdna.fa.gz +0 -0
  188. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/openprot/ensembl106.gtf.gz +0 -0
  189. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.bed.zip +0 -0
  190. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.fasta.zip +0 -0
  191. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.tsv.zip +0 -0
  192. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/peptideatlas/README.md +0 -0
  193. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/peptideatlas/atlas_build.tsv.zip +0 -0
  194. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/peptideatlas/ensembl.pep.fa.gz +0 -0
  195. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/peptideatlas/manifest.json +0 -0
  196. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/pfizer/NOTICE.md +0 -0
  197. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/pfizer/dog/expected.json +0 -0
  198. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/pfizer/dog/manifest.json +0 -0
  199. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/pfizer/dog/protein.tsv +0 -0
  200. {orfdata-0.42.1 → orfdata-0.42.2}/tests/data/pfizer/dog/search.fasta +0 -0
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{orfdata-0.42.1/orfdata.egg-info → orfdata-0.42.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: orfdata
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- Version: 0.42.1
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+ Version: 0.42.2
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  Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
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  Author: OpenVax
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  License-Expression: Apache-2.0
{orfdata-0.42.1 → orfdata-0.42.2}/docs/catalogs.md RENAMED
@@ -17,7 +17,8 @@ original PyEnsembl transcript through `ReferenceORF`. To use several catalogues
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  for one species together, see
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  [merging catalogues](proteome.md#merging-catalogues).
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- The packaged registry builds each catalogue from its sources' own files:
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+ The packaged registry supplies catalogues as pinned downloads or builds from
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  | Species | Catalogues | ORFs |
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  | --- | --- | ---: |
@@ -78,11 +79,11 @@ existing standalone local-file workflow.
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  ```sh
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  pip install "orfdata"
81
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+ orfdata setup --species mouse --accept-terms # Three catalogues and the chains
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  ```
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84
- `orfdata setup` builds each registered mouse catalogue from its pinned sources
85
- and downloads the chain files (`--accept-terms` for UCSC's non-commercial
85
+ `orfdata setup` downloads the published Chang et al. catalogue, builds the other
86
+ registered mouse catalogues from their pinned sources, and downloads the chain files (`--accept-terms` for UCSC's non-commercial
86
87
  GRCm38/GRCm39 chains). It prints what it did with each: built, downloaded,
87
88
  already installed, repaired or skipped. If one fails, the rest are still
88
89
  installed and it exits with status 1, naming each failure; in Python,
@@ -115,6 +116,14 @@ least two callers find it in a library, in at least two libraries, starting at
115
116
  ATG, CTG, GTG or TTG. Its types are uORF (8,294), lncORF (3,576), uoORF
116
117
  (1,950), iORF (1,749), dORF (741) and doORF (174).
117
118
 
119
+ - **Download.** `orfdata data fetch ncorf-mammals-mouse` installs the
120
+ checksum-pinned 2.22 MB catalogue. `orfdata data path ncorf-mammals-mouse`
121
+ returns its local path for offline use. Python callers use
122
+ `fetch_data("ncorf-mammals-mouse")` and `CatalogRegistry().open("ncorf-mammals-mouse")`.
123
+ The [data release](https://github.com/openvax/orfdata/releases/tag/data-ncorf-mammals-mouse-1)
124
+ includes the manifest, source access terms and acceptance receipt.
125
+ `orfdata catalogs build ncorf-mammals-mouse` still explicitly rebuilds from
126
+ the original inputs; `catalogs query ncorf-mammals-mouse --built` selects that result.
118
127
  - **Sources.** The authors' BED and protein FASTA (MIT, pinned commit), the
119
128
  paper's Table S3 (CC BY 4.0) and Ensembl 107's GTF; about 40 MB.
120
129
  - **Coding paths.** The BED garbles multi-exon block sizes, so each ORF's
{orfdata-0.42.1 → orfdata-0.42.2}/orfdata/data/catalogs.json RENAMED
@@ -190,10 +190,16 @@
190
190
  "schema": "orfdata.catalog-manifest.v1"
191
191
  },
192
192
  "distribution": {
193
- "access_terms": "Built locally from the pinned source files: the authors' ncORF files (MIT), the paper's Table S3 (CC BY 4.0) and Ensembl 107's GTF. Cite Chang et al., eLife 2025 (doi:10.7554/eLife.109128).",
193
+ "access_terms": "Redistributed from the pinned authors' ncORF files (MIT), Table S3 (CC BY 4.0) and Ensembl 107 GTF (unrestricted). Includes source provenance and one unresolved row. Cite Chang et al., eLife 2025 (doi:10.7554/eLife.109128).",
194
194
  "redistributable": true
195
195
  },
196
- "assets": {}
196
+ "assets": {
197
+ "catalog.json.gz": {
198
+ "url": "https://github.com/openvax/orfdata/releases/download/data-ncorf-mammals-mouse-1/catalog.json.gz",
199
+ "sha256": "255f1d089b1eaa88a0bed53006c05ec78350626659461086fa11164947f151f1",
200
+ "size": 2219659
201
+ }
202
+ }
197
203
  }
198
204
  },
199
205
  "priority": 20
orfdata-0.42.2/orfdata/version.py ADDED
@@ -0,0 +1 @@
1
+ __version__ = "0.42.2"
{orfdata-0.42.1 → orfdata-0.42.2/orfdata.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: orfdata
3
- Version: 0.42.1
3
+ Version: 0.42.2
4
4
  Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
5
5
  Author: OpenVax
6
6
  License-Expression: Apache-2.0
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@@ -1 +0,0 @@
1
- __version__ = "0.42.1"
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