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v0.7.0
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@HajkD HajkD released this 17 Jan 10:58
· 840 commits to master since this release
v0.7.0
89d4c90

Function changes:

  • the function meta.retrieval() will now pick up the download at the organism where it left off and will report which species have already been retrieved

  • all get*() functions and the meta.retrieval() function receive a new argument reference which allows users to retrieve not-reference or not-representative genome versions when downloading from NCBI RefSeq or NCBI Genbank

  • the argument order in meta.retrieval() changed from meta.retrieval(kingdom, group, db, ...) to meta.retrieval(db,kingdom, group, ...) to make the argument order more consistent with the get*() functions

  • the argument order in getGroups() changed from getGroups(kingdom, db) to getGroups(db, kingdom) to make the argument order more consistent with the get*() and meta.retrieval() functions

New Functions:

  • new internal functions existingOrganisms() and existingOrganisms_ensembl() which check the organisms that have already been downloaded
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