2024流程更改记录

######2024年######

一.新增

202401

0113 /share/nas1/yuj/script/chloroplast/advance/kaks/merged.py增加kaks的汇总程序，用于绘制柱状图

202402

0221 /share/nas1/yuj/script/diversity/deltaK_plot.r新增遗传多样性中structureHarvester的r语言绘图脚本，替换/share/nas2/zhouxy/pipline/marker/snp/current/snp-diversity.pl中这一步用到的在线网站

202405

0520 /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
0529 /share/nas1/yuj/script/chloroplast/advance/calculate_pi.py all.fasta.line滑窗计算全基因组的pi
0531 /share/nas1/yuj/script/chloroplast/advance/pi/full_genome_pi_plot.py绘制全基因组pi值折线图

202406

0628 /share新增查找反向重复区的脚本，兼顾速度和准确率
/share/nas2/zhangwanruo001/project/2024/chloroplast_genomics/GP-20231122-7371-1_xizangzangyiyaodaxue_mimapanduo_1sample_ximalayadahuang_yelvti/ref_adv/02_IR.py未完成

202407

0718 /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
0718 /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
0718 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_gene_pi_plot.py显示大于阈值的基因
0723 /share/nas1/yuj/script/ddradANDreseqANDgenome/ensembl_data/downfasta.py&/share/nas1/yuj/script/ddradANDreseqANDgenome/ensembl_data/downgff.pyensembl数据库批量获取链接
0725 /share/nas1/yuj/script/ddradANDreseqANDgenome/split_genome_chromosomes_by_gff_centromere.py根据着丝粒分割染色体
0730 /share/nas1/yuj/script/ddradANDreseqANDgenome/gff_tools/filter_gff_from_gff_by_interval.shshell脚本，给定gff，染色体名，起止位置，从中提取对应区间的gff信息

202408

0807 /share/nas1/yuj/script/chloroplast/advance/pi/mt_full_gene_pi_plot.pypi显示动物线粒体基因
0816 /share/nas1/yuj/script/ddradANDreseq/BLAST_Read_and_Gene_Neighborhood_Reporter.py根据blast结果，从gff中寻找tdna插入位点附近的基因
0829 /share/nas1/yuj/script/chloroplast/annotation/repeats_ssr_lsr_plot/plot_ssr.py新增单样品的ssr柱状图

202409

0903 /share/nas1/yuj/script/chloroplast/advance/pi/position_mapping.py新增程序，获取序列比对前后位置对应关系，以及比对后基因所处位置
0905 /share/nas1/yuj/script/chloroplast/advance/kaks/boxplot_kaks.R新增动物线粒体kaks的箱线图
0906 /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线粒体rna编辑绘图，对比原版，去掉上右边框，数字显示在柱子上方
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

202410

1011 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/snp_density_plot_and_variation_region_out.py绘制snp密度，并输出高可变区域的位置信息
1011 /share/nas1/yuj/script/ddradANDreseqANDgenome/gff_tools/extract_genes_from_gff_by_regions.py给定高可变区域（染色体，起始，终止，包含3列的文件），提取gff中相关基因（输出gff中满足要求的染色体，起始，终止，基因名）
1030 /share/nas1/yuj/script/chloroplast/advance/kaks/scatter_plot_kaks_values.py新增kaks的散点图绘制

202411

1121 /share/nas1/yuj/script/chloroplast/phytree/simplify_newick.py新增简化进化树，去除置信度和枝长信息
1127 /share/nas1/yuj/script/chloroplast/annotation/draw_line_depth_v3.py新增V3版本，线性深度覆盖图修改为多个子图的样式
1127 /share/nas1/yuj/script/ddradANDreseq/T-DNA/filter_zero_coverage.py新增，多载体序列检测时过滤深度0的位点，以及输出不同载体的平均覆盖情况

202412

1217 /share/nas1/yuj/script/chloroplast/annotation/tbl2ann.py新增，tbl转注释ann文件
1230 /share/nas1/yuj/script/ddradANDreseqANDgenome/modify_fq-or-fa_ids_and_third_line.py根据第二端fastq修改第一端ID
1233 /share/nas2/zhangwanruo001/project/2024/chloroplast_genomics/GP-20221202-5360-4_nanchanshifanxueyuan_2samples_zhiwu_yelvti/adv_Pyrola_atropurpurea_Franch/analysis/pi/feature/script.py同源基因x
1231 /share/nas2/yuj/project/2024/mitochondrion/GP-20231114-7299-3_20241223/script.py新增，对分析目录中所有文件进行样品的重命名

二.修改

202404

0408 /share/nas1/yuj/pipline/reseq/v1.2/script/variant_gene.sh解决重测序流程中，富集分析因为前后ID不一致（缺少gene-前缀）不生成图片的问题
0419 /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
0426 /share/nas1/yuj/pipline/reseq/v1.2/re-report_html_for_lumpy_sv.pl当染色体结构变异文件夹不存在时，去除报告相关内容

202405

0508 /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
0508 /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
0508 /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
0508 /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
0528 /share/nas1/yuj/script/chloroplast/ir_fasta.py考虑比对中有gap时的序列长度获取
0531 /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
0531 /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
0531 /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

202406

0605 /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
0617 /share/nas1/yuj/pipline/reseq/v1.2/script/03vcf/VariationDraw_kb.pl修改显示单位，以Kb计算
0625 /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
0626 /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
0627 /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

202407

0718 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti.pl叶绿体报告增加全基因组pi分析的图片及说明
0722 /share/nas1/yuj/program/chloroplast/assembly/draw_line_depth.pl设置y轴最大值为max depth+200

202408

0812 /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
0814 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_gene_pi_plot.py新增一些绘图参数
0822 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
0828 /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
0828 /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
0828 /share/nas1/yuj/program/chloroplast/kaks/boxplot_kaks.R对比原版，修改长宽，加上最大值横线
0830 /share/nas1/yuj/script/chloroplast/phytree/cp_from_gbk_get_cds_V4.0.py增加寄生植物的处理
0830 /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
0830 /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
0830 /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

202409

0903 /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
0905 /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
0909 /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
0909 /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
0909 /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
0909 /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
1122 /share/nas1/yuj/script/mitochondrion/phytree/mt_from_gbk_get_cds_V2.0.py新增dloop区提取
1122 /share/nas1/yuj/script/mitochondrion/annotation/mt_from_gbk_get_cds_V2-0.py同上，新增dloop区
1127 /share/nas1/yuj/script/chloroplast/annotation/draw_line_depth_v2.py样品过多时，循环使用颜色列表
1128 /share/nas1/yuj/program/nuclear/tree/draw_time_tree.pl对比原版分歧时间树绘制：1.修改字体为arial；2.去除 95％ CI；3.分别绘制物种名和登录号；4.加粗测序物种

202412

1202 /share/nas1/yuj/script/ddradANDreseq/BLAST_Read_and_Gene_Neighborhood_Reporter.py增加单独查询位置功能“--query Chr5:21147931-21148148”
1205 /share/nas1/yuj/pipline/genetic_diversity_pip/v1.0/script/02variant/titv_plot.r修改titv图中字号大小
1205 /share/nas1/yuj/pipline/genetic_diversity_pip/v1.0/script/05vcf_stat/plot_var_density/popSNPNumStat.rsnp数量统计图中字号
1205 /share/nas1/yuj/pipline/genetic_diversity_pip/v1.0/script/03vcf/cmplot/cmplot.rsnp密度图中字号
1205 /share/nas1/yuj/pipline/genetic_diversity_pip/v1.0/script/10pts/structure/Population_structure.2.0.pl admixture图中样品名大小与角度
1206 /share/nas1/yuj/script/chloroplast/phytree/or_convert_to_nex.py完善str_revmat拼接的转换率矩阵的获取，用于贝叶斯建树
1216 /share/nas1/yuj/script/chloroplast/phytree/cp_extract_and_mafft_V2.0.py扩充cds列表
1218 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti.pl增加组装判断，当仅注释的时候也可以生成报告
1226 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_genome_pi_plot.py增加输出pdf