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Converts Tandem Repeat Finder .dat file output into GFF3 format.
TRF2GFF requires Python >= v3.8
Install directly from this git repository.
pip install git+https://github.com/Adamtaranto/TRF2GFF.git
Or clone and install locally.
git clone https://github.com/Adamtaranto/TRF2GFF.git && cd TRF2GFF pip install -e .
trf genome.fa 2 6 6 80 10 50 2000 -h # Where args are Match, Mismatch, Delta, PM, PI, Minscore, MaxPeriod, [options] # Output: genome.fa.2.6.6.80.10.50.2000.dat
Here are three examples of how you can use trf2gff to process a trf .dat file
# Option 1: # Read from infile and write gff to default outfile trf2gff -i genome.fa.2.6.6.80.10.50.2000.dat # Output: genome.fa.2.6.6.80.10.50.2000.gff3 # Option 2: # Read input from stdin and write to stdout trf2gff -o - < genome.fa.2.6.6.80.10.50.2000.dat > genome.gff3 # Output: genome.gff3 # Option 3: # Read from stdin and write to file trf2gff -o genome.gff3 < genome.fa.2.6.6.80.10.50.2000.dat # Output: genome.gff3
Use bedtools getfasta to extract trf features from genome.
bedtools getfasta -fi genome.fa -bed genome.gff3