售后

老师需求：根据二级通路统计注释到各通路上的差异基因个数；

脚本

/TJPROJ6/RNA_SH/personal_dir/yangdan/new/script/level2_cp_count.R --cpname  --anno  --diff  --outdir  --type

--cpname 比较组合名字
--anno  the lev2 anno file ; as 0.SupFile/GOclassification/GO_classification.xls or anno_kegg.xls
--diff 差异文件路径 
--outdir 输出路径
--type go or kegg

1.get anno_kegg.xls

wget "https://www.genome.jp/kegg-bin/download_htext?htext=kpm00001&format=json&filedir=" -O kpm00001.json
/home/zhangxin/get_kegg_abbr_from_json.py kpm00001.json kpm
/home/zhangxin/add_lev12.py kegg.xls kpm_kegg_lev.xls anno_kegg.xls

2.结果展示

result/go/go_lev2.xls  result/kegg/kegg_lev2.xls
result/go/TreatmentvsControl:
  TreatmentvsControl_lev2.xls    TreatmentvsControl_updown.png
  TreatmentvsControl_updown.pdf  TreatmentvsControl_updown.svg
result/kegg/TreatmentvsControl:
  TreatmentvsControl_lev2.xls    TreatmentvsControl_updown.png
  TreatmentvsControl_updown.pdf  TreatmentvsControl_updown.svg
  

*_lev2.xls : 第二层级注释gene_id统计

cp/cp_lev2.xls : 第二层及差异基因注释统计

*_updown.* : 第二层及差异基因注释统计展示