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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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could one "opt out" of Genbank submission #469

Open phiweger opened 4 years ago

phiweger commented 4 years ago

hi Torsten,

several issues relate to prokka trying to create records than can be uploaded to Genbank w/o further postprocessing (looking at you tbl2asn and the "contig-name-too-long issue"). I often use prokka as part of some pipeline, w/o intending to submit the annotation.

could you add a --relax flag that simply does not perform the Genbank submission formalities?

kind regards, Adrian

tseemann commented 4 years ago

Removing tbl2asn would mean NO .gbk file would be created.

The simplest thing to do for now is to just comment out or delete these lines. Maybe make a copy first and call it prokka-nogbk or similar.

runcmd(
  "tbl2asn -V b -a r10k -l paired-ends $tbl2asn_opt -N $accver -y 'Annotated using $EXE $VERSION from $URL'".
  " -Z \Q$outdir/$prefix.err\E -i \Q$outdir/$prefix.fsa\E 2> /dev/null"
);
delfile("$outdir/errorsummary.val");
delfile( map { "$outdir/$prefix.$_" } qw(dr fixedproducts ecn val) );

msg("Repairing broken .GBK output that tbl2asn produces...");
runcmd("sed 's/COORDINATES: profile/COORDINATES:profile/' < \Q$outdir/$prefix.gbf\E > \Q$outdir/$prefix.gbk\E")