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check RepeatMasker results in case no repeat is identified
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@oushujun
oushujun committed Jun 22, 2022
1 parent 9150329 commit c86d6db
Showing 1 changed file with 8 additions and 4 deletions.
12 changes: 8 additions & 4 deletions EDTA.pl
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if (-s "$genome.RM.consensi.fa"){
`${TEsorter}TEsorter $genome.RM.consensi.fa -p $threads`;
`perl $rename_RM $genome.RM.consensi.fa.rexdb.cls.lib > $genome.RepeatModeler.raw.fa`;
`${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -lib $genome.LTR.TIR.Helitron.fa.stg1 $genome.RepeatModeler.raw.fa 2>/dev/null`;
my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -lib $genome.LTR.TIR.Helitron.fa.stg1 $genome.RepeatModeler.raw.fa 2>/dev/null`;
`cp $genome.RepeatModeler.raw.fa $genome.RepeatModeler.raw.fa.masked` if $rm_status =~ /No repetitive sequences were detected/i;
`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.RepeatModeler.raw.fa.masked > $genome.RepeatModeler.fa.stg1`;
`cat $genome.LTR.TIR.Helitron.fa.stg1 $genome.RepeatModeler.fa.stg1 > $genome.LTR.TIR.Helitron.others.fa.stg2`;

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# remove cds-related sequences in the EDTA library
print "\t\t\t\tRemove CDS-related sequences in the EDTA library:\n\n";
if (-s "$cds"){
`${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -cutoff 225 -lib $cds $genome.EDTA.raw.fa 2>/dev/null`;
`${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -cutoff 225 -lib $cds $genome.EDTA.intact.fa.raw 2>/dev/null`;
my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -cutoff 225 -lib $cds $genome.EDTA.raw.fa 2>/dev/null`;
`cp $genome.EDTA.raw.fa $genome.EDTA.raw.fa.masked` if $rm_status =~ /No repetitive sequences were detected/i;
my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -cutoff 225 -lib $cds $genome.EDTA.intact.fa.raw 2>/dev/null`;
`cp $genome.EDTA.intact.fa.raw $genome.EDTA.intact.fa.raw.masked` if $rm_status =~ /No repetitive sequences were detected/i;
`perl $cleanup_tandem -misschar N -Nscreen 1 -nc 1000 -nr 0.3 -minlen 80 -maxlen 5000000 -trf 0 -cleanN 1 -cleanT 1 -f $genome.EDTA.raw.fa.masked > $genome.EDTA.raw.fa.cln`;
`perl $cleanup_tandem -misschar N -Nscreen 1 -nc 1000 -nr 0.8 -minlen 80 -maxlen 5000000 -trf 0 -cleanN 0 -f $genome.EDTA.intact.fa.raw.masked > $genome.EDTA.intact.fa.rmCDS`;

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print "$date\tCombine the high-quality TE library $HQlib with the EDTA library:\n\n";

# remove known TEs in the EDTA library
`${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -lib $HQlib $genome.EDTA.TElib.fa 2>/dev/null`;
my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -lib $HQlib $genome.EDTA.TElib.fa 2>/dev/null`;
`cp $genome.EDTA.TElib.fa $genome.EDTA.TElib.fa.masked` if $rm_status =~ /No repetitive sequences were detected/i;
`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 0 -cleanN 1 -cleanT 0 -f $genome.EDTA.TElib.fa.masked > $genome.EDTA.TElib.novel.fa`;
`mv $genome.EDTA.TElib.fa $genome.EDTA.TElib.ori.fa`;
`cat $HQlib $genome.EDTA.TElib.novel.fa > $genome.EDTA.TElib.fa`;
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