新增新的程序

• xxxxxxxxxx20240816 /share/nas1/yuj/script/Genome/1plot_genome_structure.py

• xxxxxxxxxx/share/nas2/zhangwanruo001/project/2024/chloroplast_genomics/GP-20231122-7371-1_xizangzangyiyaodaxue_mimapanduo_1sample_ximalayadahuang_yelvti/ref_adv/02_IR.py

• 遗传多样性structureHarvester /share/nas2/zhouxy/pipline/marker/snp/current/snp-diversity.pl中structureHarvester这一步用到的在线网站打不开,换成本地r语言绘图/share/nas1/yuj/script/diversity/deltaK_plot.r

• 20240113 /share/nas1/yuj/script/chloroplast/advance/kaks/merged.py增加kaks的汇总程序，用于绘制柱状图

• 20240529 增加/share/nas1/yuj/script/chloroplast/advance/calculate_pi.py all.fasta.line滑窗计算全基因组的pi

• 20240531 增加/share/nas1/yuj/script/chloroplast/advance/pi/full_genome_pi_plot.py绘制全基因组pi值折线图

• 20240628 /share新增查找反向重复区的脚本，兼顾速度和准确率

• 20240718 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_genome_pi_plot.py新增叶绿体全基因组pi分析的绘图

• 20240718 /share/nas1/yuj/script/chloroplast/advance/pi/mt_full_genome_pi_plot.py新增动物线粒体全基因组pi分析的绘图

• 20240718 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_gene_pi_plot.py显示大于阈值的基因

• 20240723 /share/nas1/yuj/script/Genome/ensembl_data/downfasta.py&/share/nas1/yuj/script/Genome/ensembl_data/downgff.pyensembl数据库批量获取链接

• 20240725 /share/nas1/yuj/script/Genome/split_chromosome_arms.py根据着丝粒分割染色体

• 20240730 /share/nas1/yuj/script/Genome/extract_gff_annotations.sh提取指定区间的gff

• 20240807 /share/nas1/yuj/script/chloroplast/advance/pi/mt_full_gene_pi_plot.pypi显示动物线粒体基因

• 20240816 /share/nas2/yuj/project/2024/re-sequencing/GP-20240708-8721_20240726/T-DNA/pipline/ZH310-2/find.py从gff中寻找插入位点附近的基因

• 20240829 /share/nas1/yuj/script/chloroplast/annotation/repeats_ssr_lsr_plot/plot_ssr.py新增单样品的ssr柱状图

• 20240903 /share/nas1/yuj/script/chloroplast/advance/pi/position_mapping.py新增程序，获取比对前后位置对应关系，以及比对后基因所处位置

• 20240905 /share/nas1/yuj/script/chloroplast/advance/kaks/boxplot_kaks.R新增动物线粒体kaks的箱线图

• 20240906 /share/nas1/yuj/script/chloroplast/annotation/repeats_ssr_lsr_plot/repeat_plot_bar.py与perl程序原版对比，去掉多余线段，拆分为两张图

• 0906 /share/nas1/yuj/program/mt2/annotation/pipline/src/plot_RNAedit_nu.R

• 0906 /share/nas1/yuj/script/chloroplast/advance/pi/plmt_plot.pi.no.ir.py新增植物线粒体pi图，对比原版修改部分参数

• 0911 /share/nas1/yuj/script/fungi/annotation/fungi_parse_info_table.py新增真菌解析mitos2结果程序

• 0914 /share/nas1/yuj/script/fungi/advance/pi/fu_plot.pi.no.ir.py新增真菌线粒体基因pi折线图绘制，考虑取同一基因最大值绘图

修改已有程序

• 202403 当重测序流程中，富集分析因为前后ID不一致（缺少gene-前缀）没有生成图时，使用sh /share/nas1/yuj/pipline/reseq/v1.2/script/variant_gene.sh该命令解决
• 202404 修改/share/nas1/yuj/pipline/pop-pip/v1.1/html_report/pop_report2html.pl，当群体指标统计目录不存在时，跳过该部分
• 20240426 当染色体结构变异文件夹不存在时去除报告相关内容/share/nas1/yuj/pipline/reseq/v1.2/re-report_html_for_lumpy_sv.pl
• 20240508 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl当存在3代覆盖度就用3代图片，否则用2代
• 20240508 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.3dai.pl修改对应文本描述
• 20240508 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/annotation/mt_annotation_pip.pl 将repeat命令部分写入文件
• 20240508 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl优化高级分析目录生成的代码逻辑
• 20240528 修改ir.py程序，考虑比对中有gap时的序列长度获取
• 20240531 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl修改cgview的判断方式
• 20240531 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.pl增加pi分析的报告内容，重新添加snp、indel
• 20240531 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl增加全基因组的pi分析
• 20240605 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/phytree/raxml_phytree.pl增加-automated1参数，使trimal生效
• 20240617 /share/nas1/yuj/pipline/reseq/v1.2/script/03vcf/VariationDraw_kb.pl修改显示单位，以Kb计算
• 20240625 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/assembly/cp.assembly.pip.pl修改组装软件为getorganelle
• 20240626 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti.pl修改报告对应的组装描述
• 20240627 /share/nas1/yuj/pipline/reseq/v1.2/re-report_html_for_lumpy_sv.pl恢复报告中结构变异的部分
• 20240718 ``叶绿体报告增加全基因组pi分析的图片及说明
• 20240722 /share/nas1/yuj/program/chloroplast/assembly/draw_line_depth.pl设置y轴最大值为max depth+200
• 20240812 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_advance.pl完善进化树枝长的描述，增加tmp文件夹的删除
• 20240814 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_gene_pi_plot.py新增一些绘图参数
• 20240822 删除原/share/nas1/yuj/script/chloroplast/advance/pi/cp_full_genome_pi_plot.py程序，将功能合并入/share/nas1/yuj/script/chloroplast/advance/pi/cp_full_gene_pi_plot.py程序并重命名为cp_full_genome_pi_plot.py
• 20240828 /share/nas1/yuj/script/chloroplast/phytree/cp_extract_and_mafft_V2.0.py完善修改cds列表，去除错误的基因名
• 20240828 /share/nas1/yuj/script/chloroplast/phytree/cp_from_gbk_get_cds_V4.0.py更正输出的CDS名，增加rrna的输出
• 20240828 /share/nas1/yuj/program/chloroplast/kaks/boxplot_kaks.R对比原版，修改长宽，加上最大值横线
• 20240830 /share/nas1/yuj/script/chloroplast/phytree/cp_from_gbk_get_cds_V4.0.py增加寄生植物的处理
• 20240830 /share/nas1/yuj/script/chloroplast/advance/pi/mt_full_genome_pi_plot.py调整动物线粒体pi绘图参数
• 20240830 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.pl去除报告生成后的tmp文件夹
• 20240830 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.3dai.pl修改线粒体全基因组pi分析的描述
• 20240903 /share/nas1/yuj/script/chloroplast/advance/pi/mt_full_gene_pi_plot.py修改曲线为折线，修改基因标签的样式，修改图片标题名
• 20240905 /share/nas1/yuj/script/chloroplast/advance/kaks/merged.py修改kaks的汇总程序，根据不同参数输出不同的文件，以便于绘图
• 20240909 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/cp_pip_dir.pl叶绿体增加kaks箱线图到结果目录
• 20240909 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti.pl叶绿体报告增加kaks箱线图及其描述
• 20240909 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_advance.pl高级分析报告新增内容同上
• 20240909 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/cp_pip_dir_only_advance.pl叶绿体仅高级分析目录增加kaks箱线图
• 0912 /share/nas1/yuj/program/mt2/coline/src/draw_collinearity.pl修改植物线粒体共线性图的颜色
• 0913 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/annotation/etc/plot_ogdraw_cpgenome_genbank/conf/OGDraw_chondriom_set.xml增加真菌线粒体rps3基因的绘图参数
• 0914 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.pl增加线粒体同源基因pi值及kaks箱线图描述
• 0914 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl增加线粒体kaks箱线图和基因pi值