gff3转为bed12格式

gff3转为bed12格式：

用法：bash xx.sh gff3 gff3.bed
注意：最后生成的结果需要做细微的调整

#!/bin/bash

# 检查输入参数
if [ "$#" -ne 2 ]; then
    echo "Usage: $0 input.gff3 output.bed"
    exit 1
fi

input_gff3=$1
output_bed=$2
# 转换 GFF3 到 BED12 格式
awk 'BEGIN {OFS="\t"}
$3 == "exon" {
    # 初始化变量
    id = ""; parent = "";
    # 解析第九列的属性
    if (split($9, attr, ";") > 0) {
        for (i in attr) {
            split(attr[i], a, "=");
            if (a[1] == "ID") id = a[2];
            else if (a[1] == "Parent") parent = a[2];
        }
    }
    # 设置 BED12 字段
    chrom = $1;
    start = $4 - 1;
    end = $5;
    name = (parent != "") ? parent : id;
    score = 0;
    strand = $7;
    thickStart = start;
    thickEnd = end;
    itemRgb = "0,0,0";
    blockCount = 1;
    blockSizes = end - start;
    blockStarts = 0;
    # 输出 BED12 格式
    print chrom, start, end, name, score, strand, thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts;
}' $input_gff3 > $output_bed

echo "Conversion complete: $output_bed"