2025程序记录

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客户部<caretaker@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>

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>

18061729152
jshy-001

######2025年######

一.新增

202501

0109 /share/nas1/yuj/pipline/reseq/v1.3/script/05vcf_stat/count_deg_indel.py用python重写统计样品间indel对比的统计
0114 /share/nas1/yuj/script/ddradANDreseqANDgenome/variants_diff从list文件挑出两两样品差异情况
0115 /share/nas1/yuj/script/chloroplast/annotation/repeats_ssr_lsr_plot/plot_repeats_len_and_tye.py将散在重复序列绘制成不同样式
0117 /share/nas1/yuj/script/chloroplast/assembly增加“fa转fq”以及“将长读fq切分成短读fq”
0123 /share/nas1/yuj/script/chloroplast/personality_analysis/dnabarcode/2select_region_with_pi_s.py从dnasp输出中筛选指定结果
0123 /share/nas1/yuj/script/chloroplast/personality_analysis/dnabarcode/extract_sequence.py从fa文件的所有序列中提取指定区间

202502

0212 /share/nas1/yuj/script/ddradANDreseqANDgenome/gff_tools/gbk2gff.py新增叶绿体gbk转gff3脚本
0213 /share/nas1/yuj/script/chloroplast/phytree/IGR_PhyloPipe.py新增从gbk中提取间区序列并同源聚类比对
0220 /share/nas1/yuj/script/mitochondrion/annotation/mt_trna_structure_generator.py新增trna2级结构部分脚本，按指定规则生成，没有算法预测
0226 /share/nas1/yuj/script/chloroplast/phytree/phytree_nexus_to_newick.py新增将贝叶斯进化树nexus格式转换为mega能打开的nwk格式

202503

0311 /share/nas1/yuj/script/chloroplast/annotation/cp_cmp_update_tags.py新增对cmp.coords.csv文件中正反向tag的校正
0312 /share/nas1/yuj/script/chloroplast/phytree/fasta_sanitizer.py新增替换fasta文件序列id中不被raxml软件接受的非法字符
0317 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/count_snps.py新增从vcf文件直接统计不同染色体上snp数量
03 染色体绘图

202504

0402 /share/nas1/yuj/script/mitochondrion/annotation/mt_check_gene_annotation_info.py新增单独检查线粒体注释overlap的程序
0410 /share/nas1/yuj/script/ddradANDreseqANDgenome/phytree/vcf2fullseq.py新增vcf根据参考序列转换为完整序列（简并碱基表示）以便后续建树
0410 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment新增一系列程序：1）可视化渐渗片段；2）查找不同样品共有渐渗片段区间；3）从vcf中提取渐渗片段；4）合并同一样品不同来源渐渗片段；5）提取指定区间的基因型数据
0415 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/split_vcf_by_beds.py新增根据bed文件区域拆分vcf文件
0422 /share/nas1/yuj/script/chloroplast/personality_analysis/ssr新增一系列程序，用于特异性ssr标记引物开发
0425 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/merge_vcf-like-files.py合并多个第一二列遵循vcf规范的文件，并集

202505

0516 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/mthod2新增分析策略2：以30个snp为单位，从vcf中提取渐渗片段
0520 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/calculate_snp_density_per_sample.py新增：计算每个样本在滑动窗口中的SNP密度
0520 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/circos_plot_snp_density_per_sample.R新增：绘制每个样本的SNP密度圈图
0521 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/vcf_heterozygosity_diff_analyzer.py新增：1）杂合位点统计；2）双样品差异位点统计
0521 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/vcf_heterozygosity_barplot.py新增：绘制杂合位点及双样品差异柱状图
0521 /share/nas1/yuj/script/ddradANDreseqANDgenome/contamination_visualizer.py新增：污染比对组成成分可视化
0523 /share/nas1/yuj/script/chloroplast/personality_analysis/indel新增：indel标记区分叶绿体基因组，设计引物

202506

0604 折线图程序
0606 /share/nas1/yuj/script/chloroplast/extract_excel_columns.py新增从xlsx直接提取高级分析和进化树物种
0610 /share/nas1/yuj/script/chloroplast/personality_analysis/indel/extract_samples.py从制表符分隔的文件提取指定列，用样品名
0610 /share/nas1/yuj/script/chloroplast/personality_analysis/indel/rename_files.py根据文件名映射来修改实验提供的扩增产物fasta文件名
0610 /share/nas1/yuj/script/chloroplast/personality_analysis/indel/rename_fasta_ids.py将fasta文件内序列id改为和文件名相同
0612 /share/nas1/yuj/script/chloroplast/annotation/coor_dotplot.py重新绘制共线性图，提高dpi
0617 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/method2/split_vcf_by_samples_pair_with_simian_filter_homozygous_only.py将vcf拆分为样品对并去除杂合、未分型位点
0620 /share/nas1/yuj/script/chloroplast/annotation/draw_line_depth_perl.py将线性覆盖度图样式1改写为python版本，提高清晰度
0623 codonw计算方式
0624 /share/nas1/yuj/script/ddradANDreseqANDgenome/ssr_marker/ssr_genome2p3in.py利用基因组文件和ssr文件生成p3in
0625 /share/nas1/yuj/script/ddradANDreseqANDgenome/ssr_marker新增在基因组上开发ssr标记及引物整套程序
0626 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/vcf_like_extractor.py增加类vcf文件的提取程序

二.修改

202501

0102 /share/nas1/yuj/script/mitochondrion/annotation/mt_parse_info_table.py新增第九套密码子解析
0102 /share/nas1/yuj/script/mitochondrion/annotation/mt_add_gene_seq.py新增第九套密码子解析
0104 /share/nas1/yuj/script/mitochondrion/annotation/mt_parse_info_table.py优化缺失的trna输出结果，统一成标准形式
0108 /share/nas1/yuj/script/ddradANDreseqANDgenome/modify_fq-or-fa_ids_and_third_line.py增加修改fasta序列id功能
0109 /share/nas1/yuj/program/chloroplast/reputer/draw_reputer_len_and_tye.pl当C类型不存在时，图例不显示C类型
0109 /share/nas1/yuj/pipline/reseq/v1.3/script/05vcf_stat/count_deg_indel.pl改正样品名获取次数
0111 /share/nas1/yuj/script/chloroplast/advance/cp_irscope.py完善程序逻辑，使查找基因的输出结果更直观
0111 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_hifi.pl修改仅hifi数据叶绿体项目报告，修正文字描述
0111 /share/nas1/yuj/pipline/reseq/v1.*/script/01bam/coverage_depth.R自适应深度绘图，原来的程序归档为v1版本，重测序V1.2+V1.3流程
0113 /share/nas1/yuj/script/chloroplast/ir_fasta.py增加对序列小写或存在gap时的处理
0114 /share/nas1/yuj/pipline/reseq/v1.3/script/01bam/depth_Track_point.r修改为保留所有数据，深度高的项目也能正常绘图
0114 /share/nas1/yuj/pipline/reseq/v1.3/re-report_html_for_lumpy_sv.pl重测序报告增加样品在不同染色体上覆盖度的情况
0115 /share/nas1/yuj/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/annotation/src/plot.rscu.bar.plrscu柱状图增加配色
0115 /share/nas1/yuj/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/annotation/src/plot_rscu_table.pl增加rscu圈图配色
0115 /share/nas1/yuj/script/mitochondrion/phytree/mt_extract2mafft_V1.5.py增加真菌基因，适配所有线粒体项目的比对
0117 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_hifi.pl解决hifi数据叶绿体报告的高级分析kaks部分没有结果
0123 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_genome_pi_plot.py解决未标注区域却依旧画出区域的bug

202502

0211 /share/nas1/yuj/script/chloroplast/ir_fasta.py新增序列大写后输出到新文件
0212 /share/nas1/yuj/pipline/reseq/v1.3/re-report_html_for_lumpy_sv.pl检测是否存在sv结果，不存在也正常生成报告
0212 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.3dai.pl解决文件夹路径不可获得的bug
0224 /share/nas1/yuj/script/chloroplast/phytree/or_convert_to_nex.py1）当gamma值不存在时避免产生shapepr对应文本；2）增加手动输入rates时的文本说明
0226 /share/nas1/yuj/program/chloroplast/irscope/CPJSdraw/bin/CPJSdraw.pl增加边界分析中ycf1假基因标识
0227 /share/nas1/yuj/script/chloroplast/assembly修改两个三代转二代的脚本，加快速度
0228 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_hifi.pl增加组装结果校正的描述

202503

0305 /share/nas1/yuj/program/mt/tRNA/draw_tRNA.pl在原版基础上增加提示信息
0306 /share/nas1/yuj/pipline/reseq/v1.3/re_seq.pl样本少于2时跳过diff
0307 /share/nas1/yuj/script/chloroplast/advance/pi/cp_full_genome_pi_plot.py增加S的显示阈值
0310 /share/nas1/yuj/pipline/kasp/kasp-develop/v1.2/html_report/kasp_Web_Report.pl跳过kasp流程pca部分未生成时的报告描述
0313 /share/nas1/yuj/script/chloroplast/download_genome_from_ncbi_V2.0.py为ncbi下载登录号GI号对应基因组增加下载校验、自动重试等功能
0313 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti.pl二代叶绿体报告修改流程图描述，修改引用文献
0313 /share/nas1/yuj/script/chloroplast/advance/cp_irscope.py新增当物种不存在目标基因时跳过该物种，避免程序出错
0313 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/cp_pip_dir.pl叶绿体2+3代整理结果增加对3代数据的统计
0313 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/html_report/report2xml.yelvti_sandai.pl叶绿体2+3代报告修改1）组装描述2）高级分析的描述3）kaks表格展示
0324 /share/nas1/yuj/script/chloroplast/ir_fasta.py解决序列大小写不一致的问题
0326 /share/nas1/yuj/script/mitochondrion/annotation/mt_add_gene_seq.py解决序列小写被忽略的问题
0327 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/mt_pip_dir.pl增加对3代测序数据的统计结果
0327 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/html_report/report2xml.xianliti.3dai.pl修改报告中3代数据辅助组装的描述

202504

0401 /share/nas1/yuj/program/ddrad/html_for_ddrad_noref/ddrad_noref_report.pl将文件判断从-f改为glob，防止通配符展不开造成误判
0402 /share/nas1/yuj/script/chloroplast/phytree/phytree_trans_nwk_name_V3.0.py修改说明：1）使用 re.escape() 处理特殊字符，避免正则表达式解析错误；2）添加 \b 单词边界限制，确保完全匹配；3）使用 re.sub() 代替字符串的 replace() 方法
0408 /share/nas1/yuj/script/chloroplast/annotation/cp_add_gene_seq.py解决序列小写被忽略的问题
0408 /share/nas1/yuj/script/chloroplast/get_ass_cfg.py增加3代数据的配置生成
0414 /share/nas2/pub/pipline/dna-seq/kasp/v1.0/kasp-develop.v1.1.pl修改primer3引物设计的程序路径，原程序没有结果
0414 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/asmqc/src/dotplot.pl加入矫正程序
0423 /share/nas1/yuj/pipline2/indel-primer-pip/v1.3/indel-primer-pip.pl对比原版，修改primer3的版本以及输入文件标签

202505

0506 /share/nas1/yuj/pipline/find_genome/bwa2pip.pl对比原版，增加对fa或fasta做后缀基因组的支持，寻找比对效率最高的基因组
0513 /share/nas1/yuj/script/chloroplast/advance/cp_irscope.py1）增加了一系列ycf1筛选的阈值；2）支持从参考ycf1来比对物种，检测该物种是否存在ycf1基因
0514 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/cp_pip_dir.pl修改对01Rawdata下xls文件的存在判断，从glob改为-e
0514 /share/nas6/pub/pipline/genome-assembly-seq/mitochondrial-genome-seq/v2.0/修改线粒体报告中spades版本，更新组装流程中的spades版本为v3.15.5
0515 （1）/share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/annotation/bin/chloroplast_annotaion.pl.v2.1.pl+/share/nas1/yuj/program/chloroplast/ssr/ssr_primer_designer.pl修改primer3版本为v2.6.1；（2）p3_in.pl+p3_out.pl适配新版本的输入与输出
0520 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/snp_density_plot_and_variation_region_out.py修改SNP密度分析与可视化工具： 1. 支持不同单位的窗口参数 2. 导出SNP密度数据到TXT文件
0523 /share/nas1/yuj/pipline/find_genome/bwa2pip-v3.py+/share/nas1/yuj/pipline/find_genome/mapped_stat-v3.pl修改为python版本，可以同时处理所有样本与所有参考基因组比对

202506

0603 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/annotation/bin/chloroplast_annotaion.pl.v2.1.pl将ssr设计引物的步骤放在一开始运行，其他步骤保持不变
065 叶绿体整理结果，进化树
0605 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/method2渐渗片段策略2：修正泗棉3号同源snp的统计方式
0610 /share/nas1/yuj/script/chloroplast/personality_analysis/indel/04findmini.py+04findn-minimarker.py修改为使用全部标记的区分能力，并输出那些组的样品是一样的
0612 /share/nas1/yuj/script/chloroplast/annotation/draw_line_depth_v2.py修改为选项参数，并且输出更多格式，dpi可调
0612 /share/nas1/yuj/program/chloroplast/assembly/draw_line_depth.pl修改为选项参数，并输出更多格式，dpi可调
0613 /share/nas1/yuj/script/ddradANDreseqANDgenome/vcf_tools/auto-snp_density_plot_and_variation_region_out.py修改为自动计算窗口大小
0617
0618 /share/nas1/yuj/script/mitochondrion/annotation/mt_from_gbk_get_cds_V2-0.py修改各物种获取的seq_id，仅保留前两部分
0619 /share/nas6/pub/pipline/genome-assembly-seq/chloroplast-genome-seq/v1.2/annotation/bin/chloroplast_annotaion.pl.v2.1.pl修改其中所有涉及到的绘图脚本，统一dpi为600，字体为新罗马