Ingest extra sources #35
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The default line endings for `csv.DictWriter` are CRLF (amazingly) <https://docs.python.org/3/library/csv.html#csv.Dialect.lineterminator>
in preparation for the subsequent commit which will add another ingest source
This adds a new ingest "source", namely hardcoded source-data which is not yet available from the existing two sources. The point of this is to produce up-to-date whole genome builds, so we tailor the ingest for this purpose. From internal discussion¹² we are aiming to keep this data separate to the fauna-derived (and S3 uploaded) dataset. ¹ <https://bedfordlab.slack.com/archives/CD84ELG0N/p1715729994271819> ² <https://bedfordlab.slack.com/archives/CD84ELG0N/p1715731530506199>
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With addition of NCBI ingest in PR #40, we now grab this milk sequence directly from GenBank. We can close this PR unmerged. Thank you so much @jameshadfield for the putting in the speedy work on this when it was needed. |
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See commit messages for more. This PR was used to update the live cattle-flu genome build.
I'm not thrilled with the complexity added here, and we're scheduled to discuss this tomorrow (internally) so let's wait until after that to merge.