2.组装

项目对应参考 /share/nas1/yuj/project/virus/ref.fa

nohup perl /share/nas1/yuj/pipline/genome-assembly-seq/virus-genome-seq/v2.0/assembly/virus.assembly.pip.pl -i ass.cfg &

3.注释

1.下载参考
编辑list_ann文件
down- ann

2.提取cds序列
cd ref_ann && python3 /share/nas1/yuj/script/virus/vi_from_gbk_get_cds.py -i gbk/ -o out  -d && cd -

3.blast
blastn -query ref_ann/out/cds/cds_*.fasta -subject *.fsa -outfmt 6 -out blast.txt

4.使用程序解析表格
python3 /share/nas1/yuj/script/virus/virus_parse_blast_table.py -i blast.txt > gene.annotation.info2

5.查看基因排列,根据参考修改注释
count=0 && for i in $(grep 'CDS' gene.annotation.info2 | awk '{print $3 "_:_" $2}'); do count=$((count+1)) &&  echo "" && echo "###############" $count ":"  $(echo "$i" | awk -F "_:_" '{print $1}') "###############" && mt_add.py  -i *.fsa -p $(echo "$i" | awk -F "_:_" '{print $2}') -n 1;done  > sample_ann.log

count=0 && for i in $(grep 'CDS' gene.annotation.info2 | awk '{print $3 "_:_" $2}'); do count=$((count+1)) && echo "" && echo "###############" $count ":" $(echo "$i" | awk -F "_:_" '{print $1}') "###############" && cp_add.py -i *.fsa -p $(echo "$i" | awk -F "_:_" '{print $2}') ;done > sample_ann.log

count=0 && for i in $(grep 'CDS' *.gbk.ann | awk '{print $3 "_:_" $2}'); do count=$((count+1)) && echo "" && echo "###############" $count ":" $(echo "$i" | awk -F "_:_" '{print $1}') "###############" && mt_add.py -i *.fasta -p $(echo "$i" | awk -F "_:_" '{print $2}') -n 1;done > ref_ann.log


6.没有问题的话,生成gene.annotation.info
mt_move_pos.py -i gene.annotation.info2 -o gene.annotation.info
rename gene.annotation.info_tmp gene.annotation.info gene.annotation.info_tmp

1.配置文件 
20210918]$ python3 /share/nas1/yuj/script/chloroplast/get_ann_cfg.py 
# 在项目编号目录下直接运行 或者cp /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/cp.anno.config.yaml ann.cfg
# 修改配置文件,写参考

2.
perl /share/nas1/yuj/pipline/genome-assembly-seq/virus-genome-seq/v2.0/annotation/virus_annotation_pip.pl -i ann.cfg -g 1 -c
!!!第一遍流程加-c参数!!!!!!好用来修改gbk
!!!注意gbk中不确定起始位置的  
!!!第二遍还要改tbl文件

4.整理结果

perl /share/nas1/yuj/pipline/genome-assembly-seq/virus-genome-seq/v2.0/html_report/virus_pip_dir.pl -i analysis

5.整理报告

cp /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report.cfg ./report.cfg && realpath  report.cfg # 修改

# 标准分析+高级分析 / 标准分析用也行
perl /share/nas1/yuj/pipline/genome-assembly-seq/virus-genome-seq/v2.0/html_report/report2xml.virus.pl  -id complete_dir/ -cfg report.cfg