1. # TEannogff=../../23.EDTA/Aly/genome.fa.mod.EDTA.TEanno.gff3
    2. TEannogff=/pfs/proj/nobackup/fs/projnb10/hpc2nstor2024-021/shwzhao/01_research/02_T89/06_evaluate3/edta/genome.all.polished.fa.mod.EDTA.TEanno.gff3
    3. ref=genome.fa
    5. awk '{if($3 ~ "LTR_retrotransposon")print}' ${TEannogff} \
    6.   | grep "Method=structural" > intact.LTR.gff3
    8. awk '{if($3 ~ "LTR_retrotransposon" && $9 ~ /Method=structural/)print}' ${TEannogff} > intact.LTR.gff3
    11. # 无strand 信息的使用 +
    12. awk 'BEGIN{OFS="\t"}
    13.      {gsub(/;.*/, "", $9);
    14.       gsub(/ID=/, "", $9);
    15.       if($7 != "?")
    16.         {print $1, $4-1, $5, $9, ".", $7}
    17.       else
    18.         {print $1, $4-1, $5, $9, ".", "+"}
    19.       }' intact.LTR.gff3 \
    20.   > intact.LTR.bed
    23. # 根据 gff 提取序列
    24. bedtools getfasta \
    25.   -fi ${ref} \
    26.   -bed intact.LTR.bed \
    27.   -fo - -name -s \
    28.   | awk -F '::' '{print $1}' \
    29.   | seqtk seq -l 60 \
    30.   > intact.LTR.fa
    1. TEsorter -db rexdb intact.LTR.fa