于师兄提取特定基因环境优化

cat ./res_sum.txt | awk '$6=="CmeB" {print $1,$2,$3,$4}' | cat > ./id.txt ; split -l 1 ./id.txt -d ./roll

for i in ` ls ./roll* `
do
        id=$(cat $i |awk '{print $1}')
        contig=$(cat $i | awk '{print $2}')
        start=$(cat $i | awk '{print $3}')
        cat $i |awk -v OFS="\t" '{print $2,$3,$4}' | cat > ./$id.id.txt ;seqkit subseq --bed ./$id.id.txt ../206_fa/$id -o ./CmeB_${id}_${contig}_${start}.fa
done

rm roll*
rm *.id.txt

cat ./res_sum.txt | awk '$6=="RECmeB" {print $1,$2,$3,$4}' | cat > ./id.txt ; split -l 1 ./id.txt -d ./roll

for i in ` ls ./roll* `
do 
	id=$(cat $i |awk '{print $1}')
	contig=$(cat $i | awk '{print $2}')
	start=$(cat $i | awk '{print $3}')
	cat $i |awk -v OFS="\t" '{print $2,$3,$4}' | cat > ./$id.id.txt ;seqkit subseq --bed ./$id.id.txt ../206_fa/$id -o ./RECmeB_${id}_${contig}_${start}.fa
done

rm roll*
rm *.id.txt

#!/bin/bash

mkdir -p general_ab_anno ; mkdir -p general_ab_anno/ncbi general_ab_anno/resfinder general_ab_anno/plasmidfinder general_ab_anno/vfdb

for id in ` ls *.fa `

do

abricate --threads 32 --db ncbi ${id} > general_ab_anno/ncbi/${id}.txt ; abricate --threads 40 --db resfinder ${id} > general_ab_anno/resfinder/${id}.txt ; abricate --threads 40 --db plasmidfinder ${id} > general_ab_anno/plasmidfinder/${id}.txt ; abricate --threads 40 --db vfdb ${id} > general_ab_anno/vfdb/${id}.txt

done

abricate --summary general_ab_anno/ncbi/*.txt > general_ab_anno/ncbi.summary.txt ; abricate --summary general_ab_anno/plasmidfinder/*.txt > general_ab_anno/plasmidfinder.summary.txt ; abricate --summary general_ab_anno/resfinder/*.txt > general_ab_anno/resfinder.summary.txt ; abricate --summary general_ab_anno/vfdb/*.txt > general_ab_anno/vfdb.summary.txt


mkdir -p ncbi_exc ; cat general_ab_anno/ncbi/*.fa.txt >ncbi_exc/res_sum.txt ;cat ncbi_exc/res_sum.txt |grep -v "#" |awk '{print $1,$6,$2,$3-1,$4}' | sed 's#/#_#g' | cat > ncbi_exc/id.txt ; split -l 1 ncbi_exc/id.txt -d ncbi_exc/roll
for i in ` ls ncbi_exc/roll* |sed 's#ncbi_exc/##g' `
do
	str=$(cat ncbi_exc/$i |awk '{print $1}' |sed 's/.fa//g')
	res=$(cat ncbi_exc/$i |awk '{print $2}')
	mkdir -p ncbi_exc/$str ;cat ncbi_exc/$i |awk -v OFS="\t" '{print $3,$4,$5}' |cat >ncbi_exc/${str}_${res}_id.txt ;cp ncbi_exc/${str}_* ncbi_exc/${str}/ ; seqkit subseq --bed ncbi_exc/${str}/${str}_${res}_id.txt $str.fa -o ncbi_exc/$str/$res.fa
done

mkdir -p vfdb_exc ; cat general_ab_anno/vfdb/*.fa.txt >vfdb_exc/vir_sum.txt ;cat vfdb_exc/vir_sum.txt |grep -v "#" |awk '{print $1,$6,$2,$3-1,$4}' | sed 's#/#_#g' |cat > vfdb_exc/id.txt ; split -l 1 vfdb_exc/id.txt -d vfdb_exc/roll
for i in ` ls vfdb_exc/roll* |sed 's#vfdb_exc/##g' `
do
        str=$(cat vfdb_exc/$i |awk '{print $1}' |sed 's/.fa//g')
        vir=$(cat vfdb_exc/$i |awk '{print $2}')
        mkdir -p vfdb_exc/$str ;cat vfdb_exc/$i |awk -v OFS="\t" '{print $3,$4,$5}' |cat >vfdb_exc/${str}_${vir}_id.txt