Created
March 7, 2024 20:51
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Run tandem repeat finder and convert the output to TSV
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| ln -s $assembly ${strain}.fasta | |
| $trf_cmd ${strain}.fasta 2 7 7 80 10 50 2000 -f -h -d -m | |
| rm ${strain}.fasta | |
| mv ${strain}.fasta.2.7.7.80.10.50.2000.dat ${strain}.trf.dat | |
| mv ${strain}.fasta.2.7.7.80.10.50.2000.mask ${strain}.trf.mask | |
| grep -P '^[S0-9]' ${strain}.trf.dat | cut -d ' ' -f 1,2,3,4,6,7,8,13,14 | awk '{if(\$1 ~ /Sequence/){chr=\$2} else {print chr, \$0}}' | tr [:blank:] '\t' > ${strain}.trf.tsv | |
| rm ${strain}.fasta |
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