As requested in #300 and #304, this PR introduces the new bakta_io function to reconstruct all output files from the JSON result 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>.txt
And, in addition, it writes its own <prefix>.reconstruction.log file.
Hence, to backup and store all information, the original <prefix>.log file should be stored along with the <prefix>.json file, if required.
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.