bedtools intersect -a lfmm.bed -b fst.bed 
##将文件转为为bed格式：
cat -e lfmm.bed
cat lfmm.bed | tr -d '\r' > lfmm-clean.bed
cat lfmm-clean.bed
cat -e lfmm-clean.bed
cat -e fst.bed
cat fst.bed | tr -d '\r' > fst-clean.bed
cat fst-clean.bed
cat -e fst-clean.bed
cat -e xpehh.bed
cat xpehh.bed | tr -d '\r' > xpehh-clean.bed
cat xpehh-clean.bed
cat -e xpehh-clean.bed
cat -e sam.bed
cat sam.bed | tr -d '\r' > sam-clean.bed
cat sam-clean.bed
cat -e sam-clean.bed

bedtools intersect -a lfmm-clean.bed -b fst-clean.bed  xpehh-clean.bed sam-clean.bed >over2
bedtools intersect -a t2.gff -b over2 -wa >re1
##处理山羊GFF注释文件
awk -F "\t" 'BEGIN {OFS="\t"}$3=="gene" {print $1,$4,$5,$9}' t2.gff> ARS1-gene
sed 替换命令：
sed 's/word1/word2/g' ARS1-gene > 1
 用word2替换word1,g参数会在word1出现的所有位置替换
sed 's/NC_030808.1/chr1/g' ARS1-gene.gff > chr1
sed 's/NC_030809.1/chr2/g'  chr1 > chr2
sed 's/NC_030810.1/chr3/g'  chr2 > chr3
sed 's/NC_030811.1/chr4/g'  chr3 > chr4
sed 's/NC_030812.1/chr5/g'  chr4 > chr5
sed 's/NC_030813.1/chr6/g'  chr5 > chr6
sed 's/NC_030814.1/chr7/g'  chr6 > chr7
sed 's/NC_030815.1/chr8/g'  chr7 > chr8
sed 's/NC_030816.1/chr9/g'  chr8 > chr9
sed 's/NC_030817.1/chr10/g'  chr9 > chr10
sed 's/NC_030818.1/chr11/g'  chr10 > chr11
sed 's/NC_030819.1/chr12/g'  chr11 > chr12
sed 's/NC_030820.1/chr13/g'  chr12 > chr13
sed 's/NC_030821.1/chr14/g'  chr13 > chr14
sed 's/NC_030822.1/chr15/g'  chr14 > chr15
sed 's/NC_030823.1/chr16/g'  chr15 > chr16
sed 's/NC_030824.1/chr17/g'  chr16 > chr17
sed 's/NC_030825.1/chr18/g'  chr17 > chr18
sed 's/NC_030826.1/chr19/g'  chr18 > chr19
sed 's/NC_030827.1/chr20/g'  chr19 > chr20
sed 's/NC_030828.1/chr21/g'  chr20 > chr21
sed 's/NC_030829.1/chr22/g'  chr21 > chr22
sed 's/NC_030830.1/chr23/g'  chr22 > chr23
sed 's/NC_030831.1/chr24/g'  chr23 > chr24
sed 's/NC_030832.1/chr25/g'  chr24 > chr25
sed 's/NC_030833.1/chr26/g'  chr25 > chr26
sed 's/NC_030834.1/chr27/g'  chr26 > chr27
sed 's/NC_030835.1/chr28/g'  chr27 > chr28
sed 's/NC_030836.1/chr29/g'  chr28 > chr29
bedtools intersect -a ARS1-gene-chr.gff -b over2 -wa >gene1
bedtools intersect -a ARS1-gene-chr.gff -b lfmm-clean.bed -wa >lfmm-gene
bedtools intersect -a ARS1-gene-chr.gff -b fst-clean.bed -wa >fst-gene
bedtools intersect -a ARS1-gene-chr.gff -b xpehh-clean.bed -wa >xpehh-gene
bedtools intersect -a ARS1-gene-chr.gff -b sam-clean.bed -wa >sam-gene