2024流程更改记录

产品部<marketing@genepioneer.com>
客户部<caretaker@genepioneer.com>

项目管理<run@genepioneer.com>
信息部-周向阳<zhouxy@genepioneer.com>
信息部-徐雷<xul@genepioneer.com>
信息部-于杰<yuj@genepioneer.com>

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
20240520 增加/share/nas1/yuj/script/chloroplast/annotation/draw_line_depth_v2.py版本2，用于一个深度文件里有多个基因组的绘制
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
1011 for i in *; do python /share/nas1/yuj/project/re-sequencing/GP-20230327-5799_20230519/202307-second/i1/analysis_dir/v3.py $i/analysis_dir/vcf_filter/samples.pop.snp.filter.recode.vcf > $i.region.txt && python /share/nas1/yuj/project/re-sequencing/GP-20230327-5799_20230519/202307-second/i1/analysis_dir/filter.py -r $i.region.txt -g $i/data/*.gff -o $i.matched_output.txt && grep "ID=gene-" $i.matched_output.txt > $i.filter_gene.txt & done重测序答疑
1030 /share/nas1/yuj/script/chloroplast/advance/kaks/scatter_plot_kaks_values.py新增kaks的散点图绘制

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
0920 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/annotation/bin/chloroplast_annotaion.pl.v2.1.pl修改样式2深度线性图的程序路径，为v1版本
0925 /share/nas1/yuj/script/chloroplast/advance/pi/plmt_plot.pi.no.ir.py按客户要求修改字体以及字号大小
0926 /share/nas1/yuj/script/chloroplast/advance/pi/plmt_plot.pi.no.ir.py根据pi最大值自动设定Y轴刻度，且Y轴线段终止于最后刻度
0927 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.pl1.修改为“当箱线图存在时，生成对应部分”；2.修改共有cds构建进化树的方法描述
0927 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_sandai.pl1.修改叶绿体2+3代数据组装方法描述；2.增加3代覆盖度图片；3.运行结束删除tmp文件夹
0927 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/cp_pip_dir.pl增加3代覆盖度图片整理
0930 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti.pl1.修改为“当箱线图存在时，生成对应部分”；2.修改全基因组最大似然法进化树的方法描述
0930 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_advance.pl1.修改为“当箱线图存在时，生成对应部分”；2.修改全基因组最大似然法进化树的方法描述；3.修改kaks的统计表生成
0930 /share/nas1/yuj/pipline/marker/snp/v1.0/Web_Report/snp_Web_Report.pl1.修改为当GenAlEx结果存在时，生成对应部分；2.去除指纹图谱

202410

1017 /share/nas1/yuj/program/mt2/annotation_for_multi_seq/pipline/repeat/mt2_repeat.pl修改mt重复序列圈图的ssr参数以供叶绿体分析用
1022 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl补全四种进化树的整理结果
1022 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.pl补全四种进化树的方法描述
1023 /share/nas1/yuj/script/chloroplast/get_ass_cfg.py提供样品名映射文件，自动将送样编号替换为拉丁名
1023 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/assembly/cp.assembly.pip.pl移除组装完成后的其他步骤，缩短流程时间
1028 /share/nas1/yuj/pipline/reseq/v1.2/re-report_html_for_lumpy_sv.pl参考基因组无gff时，跳过未生成结果部分的报告描述
1028 /share/nas1/yuj/pipline/reseq/v1.2/script/02variant/snp_ver.stat.pl考虑颠换为0时，Ti/Tv赋值为null，避免程序出错
1029 /share/nas1/yuj/pipline/genetic_diversity_pip/v1.0/script/10pts/pca/drawPCA_gtca.R按客户要求，增加PCA图字体大小

202411

1101 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/asmqc/src/cp2circos.pl修改叶绿体覆盖度的统计，使最大值可以显示
1105 /share/nas1/yuj/script/chloroplast/annotation/cp_add_gene_seq.py解决一些特殊基因的序列获取顺序，如rps12