run_line.last.bwa.screen-ngs-pipeline

最新推荐文章于 2024-06-17 10:26:55 发布

lj_learn

最新推荐文章于 2024-06-17 10:26:55 发布

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文章标签：数据库服务器

本文链接：https://blog.csdn.net/m0_50542529/article/details/135156932

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## step 1
path=/data/lijing/data
outpath=/data/lijing/result

#ls ${path}/*.gz |while read id; do echo $(basename $id)>>${outpath}/name.txt;done
#cut -d'.' -f 1 ${outpath}/name.txt |sort|uniq > ${outpath}/name.uniq.txt
cd /data/lijing/FFPE_16S 
ls *.gz|awk '{split($0,a,"_");print a[1]"_"a[2]"_"a[3]}' |sort|uniq > ${outpath}/name.uniq.txt

## step 2
# for item in `cat ${outpath}/name.uniq.txt`; do echo $item; done
for item in `cat ${outpath}/name.uniq.txt`; do /home/biosoft/fastp/fastp \
        --thread 20 -W 4 -q 20 -l 150 -y 30 --detect_adapter_for_pe -x \
        -i ${path}/${item}_R1_001.fastq.gz \
        -I ${path}/${item}_R2_001.fastq.gz \
        -o ${outpath}/${item}.R1.out.fq.gz \
        -O ${outpath}/${item}.R2.out.fq.gz \
        -j ${outpath}/${item}.json \
        -h ${outpath}/${item}.html && \
        /usr/bin/python3 /data/lijing/download/20230329_estimate_qc.py \
        -i ${outpath}/${item}.json \
        -o ${outpath}/${item}.qc.xls; done

## step 3 assemble not good (optional)
for j in `cat ${outpath}/name.uniq.txt`
do
/data/lijing/download_software/MEGAHIT-1.2.9-Linux-x86_64-static/bin/megahit \
        -1 ${outpath}/${j}.R1.out.fq.gz \
        -2 ${outpath}/${j}.R2.out.fq.gz \
        -o ${outpath}/${j}
done

## step 4 ### judge contig good/bad (optional)
for j in `cat ${outpath}/name.uniq.txt`
do
python /data/lijing/download_software/quast/quast-5.0.2/quast.py \
        ${outpath}/${j}/final.contigs.fa \
        -t 15 -o ${outpath}/${j}
done

for j in `cat ${outpath}/name.uniq.txt`
do
/data/lijing/download_software/ncbi-blast/bin/blastn \
	-db /data/lijing/assemble_capture_test/silva_database/SILVA_138.1_SSURef_NR99_tax_silva.fa \
	-query ${outpath}/${j}/final.contigs.fa \
	-out ${outpath}/${j}.blastn.xls \
	-outfmt 6 -num_threads 20 && \
	/usr/bin/python3 /data/lijing/assemble_capture_test/last_step1.py \
	-ip1 ${outpath}/${j}.blastn.xls \
	-r /data/lijing/assemble_capture_test/silva_database/taxmap_slv_ssu_ref_nr_138.1.xls \
	-op1 ${outpath}/${j}.blastn.result.xls && \
	/usr/bin/python3 /data/lijing/assemble_capture_test/last_step2.py \
	-ip1 ${outpath}/${j}/final.contigs.fa \
	-ip2 ${outpath}/${j}.blastn.result.xls \
	-op1 ${outpath}/${j}/${j}.final.contigs.fa
done

#for j in `cat ${outpath}/name.uniq.txt`
#do
#/home/biosoft/bwa-0.7.17/bwa index -a is ${outpath}/${j}/${j}.final.contigs.fa -p ${outpath}/${j}/${j}.final.contigs.fa
#done

#for j in `cat ${outpath}/name.uniq.txt`
#do
#/home/biosoft/bwa-0.7.17/bwa mem -t 20 ${outpath}/${j}/${j}.final.contigs.fa 
for item in `cat ${outpath}/name.uniq.txt`; do /home/biosoft/bwa-0.7.17/bwa mem -t 20 \
        /data/lijing/assemble_capture_test/silva_database/SILVA_138.1_SSURef_NR99_tax_silva.fa \
        ${outpath}/${item}.R1.out.fq.gz \
        ${outpath}/${item}.R2.out.fq.gz > \
        ${outpath}/${item}.out.sam && \
       /usr/bin/samtools view -@ 20 -F 4 ${outpath}/${item}.out.sam > \
        ${outpath}/${item}.out.mapped.sam ; done

for j in `cat ${outpath}/name.uniq.txt`
do
/usr/bin/python3 /data/lijing/assemble_capture_test/last_step3.py \
	-ip1 ${outpath}/${j}.out.mapped.sam \
	-ip2 ${outpath}/${j}.blastn.result.xls \
	-r /data/lijing/assemble_capture_test/silva_database/taxmap_slv_ssu_ref_nr_138.1.xls \
	-op1 ${outpath}/${j}.genus.count.xls \
	-op2 ${outpath}/${j}.species.count.xls \
	-ml 150
done