introduce bakta_io output file reconstruction #339
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
oschwengers
added a commit
that referenced
this pull request
Oct 30, 2024
oschwengers
added a commit
that referenced
this pull request
Oct 30, 2024
# for free
to join this conversation on GitHub.
Already have an account?
# to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
As requested in #300 and #304, this PR introduces the new
bakta_iofunction to reconstruct all output files from theJSONresult file (optionally gzipped).bakta_io --output <output-path> result.json[.gz]is able to reconstruct the following output files:<prefix>.fna<prefix>.faa<prefix>.ffn<prefix>.gff3<prefix>.gbff<prefix>.embl<prefix>.hypotheticals.faa<prefix>.hypotheticals.tsv<prefix>.inference.tsv<prefix>.png<prefix>.svg<prefix>.tsv<prefix>.txtAnd, in addition, it writes its own
<prefix>.reconstruction.logfile.Hence, to backup and store all information, the original
<prefix>.logfile should be stored along with the<prefix>.jsonfile, if required.