openvax / pyensembl

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LAST BUILD ON BRANCH v2.9.5

branch: v2.9.5

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Build # 25768006282

Build Type

push

github

Committed by web-flow

Commit Message

Add Xenopus + soybean species and tighten maize/tomato release ranges (#349)

Follow-up to PR #334 (which would have collided with the maize/tomato
entries shipped in v2.9.0). Picks up the parts of #334 that aren't
duplicates and fixes the remaining issues:

* Adds soybean (glycine_max) with division="plants",
  ensembl_genomes=True, range (43, MAX_ENSEMBL_GENOMES_RELEASE).
* Adds xenopus_tropicalis to main Ensembl with two assemblies:
  Xenopus_tropicalis_v9.1 (98-106) and UCB_Xtro_10.0 (107..current).
  PR #334's proposed lower bound of 100 was wrong - UCB_Xtro_10.0
  doesn't appear on the Ensembl FTP until release 107 (releases 100-106
  still serve the older v9.1 assembly).
* Tightens maize from (40, MAX_ENSEMBL_GENOMES_RELEASE) to
  (54, MAX_ENSEMBL_GENOMES_RELEASE) - the Zm-B73-REFERENCE-NAM-5.0
  assembly only exists on the Ensembl Plants FTP from release 54.
* Tightens tomato from (40, ...) to (42, ...) for the same reason.

All seven of the new generated GTF URLs (maize r54, tomato r42, soybean
r43, xenopus r98/r106 for v9.1 + r107/r115 for UCB_Xtro_10.0) verified
to return HTTP 200 from the Ensembl / Ensembl Genomes FTP.

Bump version to 2.9.5.

Coverage Stats

3 of 3 new or added lines in 2 files covered. (100.0%)

1592 of 1875 relevant lines covered (84.91%)

3.4 hits per line