产品部<marketing@genepioneer.com>
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>
######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/dnabarcode/2select_region_with_pi_s.py
从dnasp输出中筛选指定结果
- 0123
/share/nas1/yuj/script/chloroplast/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/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
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/count_snps.py
新增从vcf文件直接统计不同染色体上snp数量
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
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.pl
rscu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.py
1)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