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Add an option to turn off tbl2asn #386

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1 change: 1 addition & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -219,6 +219,7 @@ $HOME/prokka/bin/prokka --setupdb
--rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
--norrna Don't run rRNA search (default OFF)
--notrna Don't run tRNA search (default OFF)
--notbl2asn Don't run tbl2asn (default OFF)
--rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)

### Option: --proteins
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42 changes: 24 additions & 18 deletions bin/prokka
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Expand Up @@ -229,7 +229,7 @@ my(@Options, $quiet, $debug, $kingdom, $fast, $force, $outdir, $prefix, $cpus, $
$gcode, $gram, $gffver, $locustag, $increment, $mincontiglen, $evalue, $coverage,
$genus, $species, $strain, $plasmid,
$usegenus, $proteins, $hmms, $centre, $scaffolds,
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
$rfam, $norrna, $notrna, $notbl2asn, $rnammer, $rawproduct, $noanno, $accver,
$metagenome, $compliant, $listdb, $citation);

$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
Expand Down Expand Up @@ -1352,26 +1352,31 @@ close $txtFh;
# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# Use tbl2asn tool to make .gbk and .sqn for us

# NOTE: the -A and -N fake accession and version needed for Mauve!
# BUT: -A xxx has a bug where it uses xxx as the LOCUS (contig) ID for 1st contig
# SO: *sigh*
if (!$notbl2asn) {
# NOTE: the -A and -N fake accession and version needed for Mauve!
# BUT: -A xxx has a bug where it uses xxx as the LOCUS (contig) ID for 1st contig
# SO: *sigh*

my $tbl2asn_opt = @seq > 10_000 ? '-M b' : '-M n'; # Issue 93 - big assemblies
my $tbl2asn_opt = @seq > 10_000 ? '-M b' : '-M n'; # Issue 93 - big assemblies

msg("Generating Genbank and Sequin files");
#runcmd("tbl2asn -a s -q F -A $prefix -N 1 -y 'Annotated using $EXE $VERSION from $URL' -Z $outdir/$prefix.err -M n -V b -i $outdir/$prefix.fsa -f $outdir/$prefix.tbl 2> /dev/null");
#runcmd("tbl2asn -V b -a s -A $prefix -N 1 -y 'Annotated using $EXE $VERSION from $URL' -Z $outdir/$prefix.err -i $outdir/$prefix.fsa");
#runcmd("tbl2asn -V b -a s -N 1 -y 'Annotated using $EXE $VERSION from $URL' -Z $outdir/$prefix.err -i $outdir/$prefix.fsa 2> /dev/null");
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("Generating Genbank and Sequin files");
#runcmd("tbl2asn -a s -q F -A $prefix -N 1 -y 'Annotated using $EXE $VERSION from $URL' -Z $outdir/$prefix.err -M n -V b -i $outdir/$prefix.fsa -f $outdir/$prefix.tbl 2> /dev/null");
#runcmd("tbl2asn -V b -a s -A $prefix -N 1 -y 'Annotated using $EXE $VERSION from $URL' -Z $outdir/$prefix.err -i $outdir/$prefix.fsa");
#runcmd("tbl2asn -V b -a s -N 1 -y 'Annotated using $EXE $VERSION from $URL' -Z $outdir/$prefix.err -i $outdir/$prefix.fsa 2> /dev/null");
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");
delfile("$outdir/$prefix.gbf");
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");
delfile("$outdir/$prefix.gbf");
}
else {
msg("Disabling tbl2asn");
}

# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# Some final log output
Expand Down Expand Up @@ -1740,6 +1745,7 @@ sub setOptions {
{OPT=>"rfam", VAR=>\$rfam, DEFAULT=>0, DESC=>"Enable searching for ncRNAs with Infernal+Rfam (SLOW!)"},
{OPT=>"norrna!", VAR=>\$norrna, DEFAULT=>0, DESC=>"Don't run rRNA search"},
{OPT=>"notrna!", VAR=>\$notrna, DEFAULT=>0, DESC=>"Don't run tRNA search"},
{OPT=>"notbl2asn!", VAR=>\$notbl2asn, DEFAULT=>0, DESC=>"Don't run tbl2asn"},
{OPT=>"rnammer!", VAR=>\$rnammer, DEFAULT=>0, DESC=>"Prefer RNAmmer over Barrnap for rRNA prediction"},
);

Expand Down