introduce bakta_io output file reconstruction #339
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oschwengers
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oschwengers
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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.