TRF2GFF

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Converts Tandem Repeat Finder .dat file output into GFF3 format.

Installation

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 .

Usage

Run trf

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

Convert .dat file to gff3

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

Extract annotated tandem-repeat features

Use bedtools getfasta to extract trf features from genome.

bedtools getfasta -fi genome.fa -bed genome.gff3