刷GSEA脚本
  用fpkm输入的老流程
  /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/get_gsea_old.py

  用差异矫正后的readcount输入的新流程
  /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/get_gsea.py


----

参数说明
  fpkm输入
  Usage
  -T TYPE, --type TYPE  type of analysis, go or kegg, default is both(go,kegg), 分析类型<go or kegg or both>
  -O OUTDIR, --outdir OUTDIR
                        Output directory of script and result
  -D DEGDIR, --degdir DEGDIR
                        deglist directory, used to get compare groups. 非必需，有差异deglist路径时可填，默认读取所有比较组
  -C COMPARE, --compare COMPARE
                        Compare group <AvsB,CvsD>, default is all compare in
                        degdir. 
  -c CONDITION, --condition CONDITION
                        The group condition file.
  -G GO, --go GO        go.xls, if go.gmt file is provided, then go.xls is not
                        required. 生成gmt用，有gmt就不填
  -K KEGG, --kegg KEGG  kegg.xls, if kegg.gmt file is provided, then kegg.xls
                        is not required. 生成gmt用，有gmt就不填
  -P PJCODE, --pjcode PJCODE
                        project code
  -g GENE, --gene GENE  gene.xls, if gmt file is provided, then gene.xls is
                        not required
  -X GMT, --gmt GMT     gmt file <go.gmt,kegg.gmt>, gmt filename must end with
                        "go.gmt" or "kegg.gmt", if projcet type is med, then
                        use hsa/mmu gmt in db: /TJPROJ6/GB_TR/reference_data/n
                        ew_pip/Animal/Homo_sapiens/Homo_sapiens_Ensemble_94/Ho
                        mo_sapiens_Ensemble_94_go.gmt ; /TJPROJ6/GB_TR/referen
                        ce_data/new_pip/Animal/Homo_sapiens/Homo_sapiens_Ensem
                        ble_94/Homo_sapiens_Ensemble_94_hsa_kegg.gmt ; /TJPROJ
                        6/GB_TR/reference_data/new_pip/Animal/Mus_musculus/Mus
                        _musculus_Ensemble_94/Mus_musculus_Ensemble_94_go.gmt
                        ; /TJPROJ6/GB_TR/reference_data/new_pip/Animal/Mus_mus
                        culus/Mus_musculus_Ensemble_94/Mus_musculus_Ensemble_9
                        4_mmu_kegg.gmt
  -F FPKM, --fpkm FPKM  gene_fpkm.xls file
  --pjtype PJTYPE       project type, med or ref, default is ref
  -N PLOT_NUM, --plot_num PLOT_NUM
                        plot number, default is 50 , 画图个数，默认50
  -S SVG2PDF, --svg2pdf SVG2PDF
                        output svg and pdf format picture, <true or false> , 输出svg与pdf的图片

运行
  python /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/get_gsea_old.py \
  --outdir /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/gsea_test \
  --condition /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/gsea_test/condition.xls \
  --pjcode X101SC21110453-Z01-J001 \
  --gmt /TJPROJ6/GB_TR/reference_data/new_pip/Animal/Homo_sapiens/Homo_sapiens_Ensemble_94/Homo_sapiens_Ensem\
  ble_94_go.gmt,/TJPROJ6/GB_TR/reference_data/new_pip/Animal/Homo_sapiens/Homo_sapiens_Ensemble_94/Homo_sapien\
  s_Ensemble_94_hsa_kegg.gmt \  # 数据库中人的gmt
  --gene /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/gsea_test/gene.xls \
  --compare HNK_20uMvsControl,HNK_100uMvsControl \
  --fpkm /TJPROJ6/RNA_SH/personal_dir/wangjun/person_script/gsea_test/ch_gene_fpkm.xls \
  --pjtype med \
  --N 100 \
  --svg2pdf true


注释：gsea默认输出的svg是gz压缩的，会链接到html中，解压转pdf后就是svg格式的了，不会在报告中链接，有需要再优化，正常结果是png,svg,pdf的文件，html报告中链接的只有png。