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tbl2asn disable by default #475

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tbl2asn disable by default #475

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58 changes: 33 additions & 25 deletions bin/prokka
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ my %tools = (
GETVER => "tbl2asn - | grep '^tbl2asn'",
REGEXP => qr/tbl2asn\s+($BIDEC)/,
MINVER => "24.3",
NEEDED => 1,
NEEDED => 0,
},
# now just the standard unix tools we need
'grep' => { NEEDED=>1 }, # yes, we need this before we can test versions :-/
Expand Down Expand Up @@ -232,7 +232,7 @@ my(@Options, $quiet, $debug, $kingdom, $fast, $force, $outdir, $prefix, $cpus, $
$gcode, $gram, $gffver, $locustag, $increment, $mincontiglen, $evalue, $coverage,
$genus, $species, $strain, $plasmid, $prodigaltf,
$usegenus, $proteins, $hmms, $centre, $scaffolds,
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
$rfam, $norrna, $notrna, $rnammer, $tbl2asn, $rawproduct, $noanno, $accver,
$metagenome, $compliant, $listdb, $citation);

$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
Expand Down Expand Up @@ -400,6 +400,9 @@ if ($rnammer and $tools{'rnammer'}->{HAVE}) {
if ($proteins and ! $tools{'makeblastdb'}->{HAVE}) {
err("You need to install 'makeblastdb' to use the --proteins option.");
}
if ($tbl2asn and ! $tools{'tbl2asn'}->{HAVE}) {
err("You need to install 'tbl2asn' to use the --tbl2asn option.");
}
if ($rfam and ! $tools{'cmscan'}->{HAVE}) {
err("You need to install 'cmscan' to use the --rfam option.");
}
Expand Down Expand Up @@ -1402,33 +1405,37 @@ close $txtFh;
# NOTE: the -A and -N fake accession and version needed for Mauve!
# BUT: -A xxx has a bug where it uses xxx as the LOCUS (contig) ID for 1st contig
# SO: *sigh*
if ($tbl2asn) {
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) );

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("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");

# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# Some final log output
# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# Some final log output

msg("Output files:");
foreach (qx(find \Q$outdir\E -type f -name "$prefix.*")) {
chomp;
msg($_);
msg("Output files:");
foreach (qx(find \Q$outdir\E -type f -name "$prefix.*")) {
chomp;
msg($_);
}
msg("Annotation finished successfully.");
}
else {
msg("Disabling tbl2asn");
}
msg("Annotation finished successfully.");
my $endtime = localtime;
my $walltime = $endtime - $starttime;
#msg("Walltime used:", $walltime->pretty); # Heikki says this method only came with 1.20
Expand Down Expand Up @@ -1780,6 +1787,7 @@ 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=>"tbl2asn!", VAR=>\$tbl2asn, DEFAULT=>0, DESC=>"Run tbl2asn tool"},
{OPT=>"rnammer!", VAR=>\$rnammer, DEFAULT=>0, DESC=>"Prefer RNAmmer over Barrnap for rRNA prediction"},
);

Expand Down