10月15ri

1.ԭʼ

    <dependency>
        <groupId>com.github.pagehelper</groupId>
        <artifactId>pagehelper</artifactId>
        <version>5.1.2</version>
    </dependency>

原始分页
1。pageInfo 5
currentpage size list totalpage totalpage

2.dao
1.查询所要展现的数据 2.查询总条数

3.service
给pageinfo 赋值

4.controller
把pageinfo 传递给页面

5.在页面展现

pagehelper
1.导jar包
2.applicationcontext里面告诉数据库我们用了pagehelper这个插件
3.service 在执行具体sql前
PageHelper.startPage(pageNum,size);

4.controller
PageInfo pageInfo=new PageInfo<>();
pageInfo.setList(userService.findAll(pageNum,size));

逻辑图

我已经使用rmats进行可变剪接事件分析,分析结果在/home/cbw/my_result/GSE52415_project/11_rmats_result文件夹中,其中包含四个文件夹: /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C /home/cbw/my_result/GSE52415_project/11_rmats_result/4C_vs_8C /home/cbw/my_result/GSE52415_project/11_rmats_result/8C_vs_16C /home/cbw/my_result/GSE52415_project/11_rmats_result/16C_vs_Blastocyst 文件夹内容如下ls -lh /home/cbw/my_result/GSE52415_project/11_rmats_result/4C_vs_8C 总用量 11M -rw-rw-r-- 1 cbw cbw 312K 10月 27 12:53 A3SS.MATS.JCEC.txt -rw-rw-r-- 1 cbw cbw 303K 10月 27 12:53 A3SS.MATS.JC.txt -rw-rw-r-- 1 cbw cbw 227K 10月 27 12:53 A5SS.MATS.JCEC.txt -rw-rw-r-- 1 cbw cbw 198K 10月 27 12:53 A5SS.MATS.JC.txt -rw-rw-r-- 1 cbw cbw 488K 10月 27 12:53 fromGTF.A3SS.txt -rw-rw-r-- 1 cbw cbw 407K 10月 27 12:53 fromGTF.A5SS.txt -rw-rw-r-- 1 cbw cbw 188K 10月 27 12:53 fromGTF.MXE.txt -rw-rw-r-- 1 cbw cbw 8.8K 10月 27 12:53 fromGTF.novelJunction.A3SS.txt -rw-rw-r-- 1 cbw cbw 9.1K 10月 27 12:53 fromGTF.novelJunction.A5SS.txt -rw-rw-r-- 1 cbw cbw 73K 10月 27 12:53 fromGTF.novelJunction.MXE.txt -rw-rw-r-- 1 cbw cbw 1.2K 10月 27 12:53 fromGTF.novelJunction.RI.txt -rw-rw-r-- 1 cbw cbw 580K 10月 27 12:53 fromGTF.novelJunction.SE.txt -rw-rw-r-- 1 cbw cbw 102 10月 27 12:53 fromGTF.novelSpliceSite.A3SS.txt -rw-rw-r-- 1 cbw cbw 102 10月 27 12:53 fromGTF.novelSpliceSite.A5SS.txt -rw-rw-r-- 1 cbw cbw 140 10月 27 12:53 fromGTF.novelSpliceSite.MXE.txt -rw-rw-r-- 1 cbw cbw 108 10月 27 12:53 fromGTF.novelSpliceSite.RI.txt -rw-rw-r-- 1 cbw cbw 104 10月 27 12:53 fromGTF.novelSpliceSite.SE.txt -rw-rw-r-- 1 cbw cbw 213K 10月 27 12:53 fromGTF.RI.txt -rw-rw-r-- 1 cbw cbw 1.9M 10月 27 12:53 fromGTF.SE.txt -rw-rw-r-- 1 cbw cbw 69K 10月 27 12:53 JCEC.raw.input.A3SS.txt -rw-rw-r-- 1 cbw cbw 51K 10月 27 12:53 JCEC.raw.input.A5SS.txt -rw-rw-r-- 1 cbw cbw 51K 10月 27 12:53 JCEC.raw.input.MXE.txt -rw-rw-r-- 1 cbw cbw 20K 10月 27 12:53 JCEC.raw.input.RI.txt -rw-rw-r-- 1 cbw cbw 450K 10月 27 12:53 JCEC.raw.input.SE.txt -rw-rw-r-- 1 cbw cbw 67K 10月 27 12:53 JC.raw.input.A3SS.txt -rw-rw-r-- 1 cbw cbw 44K 10月 27 12:53 JC.raw.input.A5SS.txt -rw-rw-r-- 1 cbw cbw 46K 10月 27 12:53 JC.raw.input.MXE.txt -rw-rw-r-- 1 cbw cbw 16K 10月 27 12:53 JC.raw.input.RI.txt -rw-rw-r-- 1 cbw cbw 424K 10月 27 12:53 JC.raw.input.SE.txt -rw-rw-r-- 1 cbw cbw 233K 10月 27 12:53 MXE.MATS.JCEC.txt -rw-rw-r-- 1 cbw cbw 213K 10月 27 12:53 MXE.MATS.JC.txt -rw-rw-r-- 1 cbw cbw 84K 10月 27 12:53 RI.MATS.JCEC.txt -rw-rw-r-- 1 cbw cbw 71K 10月 27 12:53 RI.MATS.JC.txt -rw-rw-r-- 1 cbw cbw 1.9M 10月 27 12:53 SE.MATS.JCEC.txt -rw-rw-r-- 1 cbw cbw 1.8M 10月 27 12:53 SE.MATS.JC.txt -rw-rw-r-- 1 cbw cbw 529 10月 27 12:53 summary.txt drwxrwxr-x 12 cbw cbw 4.0K 10月 27 12:53 tmp 我想从剪接事件中提取FDR小于0.05的显著性剪接事件,已知: rmats.py \ > --b1 /home/cbw/my_result/GSE52415_project/10_rmats_input/GV.txt \ > --b2 /home/cbw/my_result/GSE52415_project/10_rmats_input/4C.txt \ > --gtf /home/cbw/my_result/GSE52415_project/6_bosTau9/genomic.gtf \ > --od /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C \ > -t single \ > --variable-read-length \ > --readLength 65 \ > --nthread 16 \ > --tmp /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/tmp gtf: 12.455834150314331 There are 32626 distinct gene ID in the gtf file There are 81403 distinct transcript ID in the gtf file There are 18451 one-transcript genes in the gtf file There are 918752 exons in the gtf file There are 8698 one-exon transcripts in the gtf file There are 6414 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.495035 Average number of exons per transcript is 11.286464 Average number of exons per transcript excluding one-exon tx is 12.517076 Average number of gene per geneGroup is 9.102162 statistic: 0.012009143829345703 read outcome totals across all BAMs USED: 70831585 NOT_PAIRED: 0 NOT_NH_1: 32943870 NOT_EXPECTED_CIGAR: 613870 NOT_EXPECTED_READ_LENGTH: 0 NOT_EXPECTED_STRAND: 0 EXON_NOT_MATCHED_TO_ANNOTATION: 6142530 JUNCTION_NOT_MATCHED_TO_ANNOTATION: 917879 CLIPPED: 7378349 total: 118828083 outcomes by BAM written to: /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/tmp/2025-10-27-12_49_29_020516_read_outcomes_by_bam.txt novel: 80.31163239479065 The splicing graph and candidate read have been saved into /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/tmp/2025-10-27-12_49_29_020516_*.rmats save: 1.478308916091919 loadsg: 0.023231983184814453 ========== Done processing each gene from dictionary to compile AS events Found 19185 exon skipping events Found 1493 exon MX events Found 10399 alt SS events There are 5664 alt 3 SS events and 4735 alt 5 SS events. Found 2458 RI events ========== ase: 0.6016833782196045 count: 2.4356465339660645 Processing count files. Done processing count files. (rmats_env) cbw@dell-PowerEdge-R7525:~$ rmats.py \ > --b1 /home/cbw/my_result/GSE52415_project/10_rmats_input/4C.txt \ > --b2 /home/cbw/my_result/GSE52415_project/10_rmats_input/8C.txt \ > --gtf /home/cbw/my_result/GSE52415_project/6_bosTau9/genomic.gtf \ > --od /home/cbw/my_result/GSE52415_project/11_rmats_result/4C_vs_8C \ > -t single \ > --variable-read-length \ > --readLength 65 \ > --nthread 16 \ > --tmp /home/cbw/my_result/GSE52415_project/11_rmats_result/4C_vs_8C/tmp gtf: 12.070105791091919 There are 32626 distinct gene ID in the gtf file There are 81403 distinct transcript ID in the gtf file There are 18451 one-transcript genes in the gtf file There are 918752 exons in the gtf file There are 8698 one-exon transcripts in the gtf file There are 6414 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.495035 Average number of exons per transcript is 11.286464 Average number of exons per transcript excluding one-exon tx is 12.517076 Average number of gene per geneGroup is 9.102162 statistic: 0.013990640640258789 read outcome totals across all BAMs USED: 85315623 NOT_PAIRED: 0 NOT_NH_1: 41656382 NOT_EXPECTED_CIGAR: 880619 NOT_EXPECTED_READ_LENGTH: 0 NOT_EXPECTED_STRAND: 0 EXON_NOT_MATCHED_TO_ANNOTATION: 8834235 JUNCTION_NOT_MATCHED_TO_ANNOTATION: 927612 CLIPPED: 8705058 total: 146319529 outcomes by BAM written to: /home/cbw/my_result/GSE52415_project/11_rmats_result/4C_vs_8C/tmp/2025-10-27-12_51_21_112895_read_outcomes_by_bam.txt novel: 86.16326379776001 The splicing graph and candidate read have been saved into /home/cbw/my_result/GSE52415_project/11_rmats_result/4C_vs_8C/tmp/2025-10-27-12_51_21_112895_*.rmats save: 1.6635279655456543 loadsg: 0.033537864685058594 ========== Done processing each gene from dictionary to compile AS events Found 21953 exon skipping events Found 1826 exon MX events Found 10423 alt SS events There are 5676 alt 3 SS events and 4747 alt 5 SS events. Found 2456 RI events ========== ase: 0.6707651615142822 count: 2.50030517578125 Processing count files. Done processing count files. (rmats_env) cbw@dell-PowerEdge-R7525:~$ rmats.py \ > --b1 /home/cbw/my_result/GSE52415_project/10_rmats_input/8C.txt \ > --b2 /home/cbw/my_result/GSE52415_project/10_rmats_input/16C.txt \ > --gtf /home/cbw/my_result/GSE52415_project/6_bosTau9/genomic.gtf \ > --od /home/cbw/my_result/GSE52415_project/11_rmats_result/8C_vs_16C \ > -t single \ > --variable-read-length \ > --readLength 65 \ > --nthread 16 \ > --tmp /home/cbw/my_result/GSE52415_project/11_rmats_result/8C_vs_16C/tmp gtf: 11.945042848587036 There are 32626 distinct gene ID in the gtf file There are 81403 distinct transcript ID in the gtf file There are 18451 one-transcript genes in the gtf file There are 918752 exons in the gtf file There are 8698 one-exon transcripts in the gtf file There are 6414 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.495035 Average number of exons per transcript is 11.286464 Average number of exons per transcript excluding one-exon tx is 12.517076 Average number of gene per geneGroup is 9.102162 statistic: 0.012091636657714844 read outcome totals across all BAMs USED: 77286714 NOT_PAIRED: 0 NOT_NH_1: 38484820 NOT_EXPECTED_CIGAR: 922886 NOT_EXPECTED_READ_LENGTH: 0 NOT_EXPECTED_STRAND: 0 EXON_NOT_MATCHED_TO_ANNOTATION: 8523239 JUNCTION_NOT_MATCHED_TO_ANNOTATION: 706280 CLIPPED: 7447971 total: 133371910 outcomes by BAM written to: /home/cbw/my_result/GSE52415_project/11_rmats_result/8C_vs_16C/tmp/2025-10-27-12_53_24_111018_read_outcomes_by_bam.txt novel: 84.98817467689514 The splicing graph and candidate read have been saved into /home/cbw/my_result/GSE52415_project/11_rmats_result/8C_vs_16C/tmp/2025-10-27-12_53_24_111018_*.rmats save: 1.671297550201416 loadsg: 0.03409314155578613 ========== Done processing each gene from dictionary to compile AS events Found 23041 exon skipping events Found 2057 exon MX events Found 10414 alt SS events There are 5673 alt 3 SS events and 4741 alt 5 SS events. Found 2452 RI events ========== ase: 0.673703670501709 count: 2.3988852500915527 Processing count files. Done processing count files. (rmats_env) cbw@dell-PowerEdge-R7525:~$ rmats.py \ > --b1 /home/cbw/my_result/GSE52415_project/10_rmats_input/16C.txt \ > --b2 /home/cbw/my_result/GSE52415_project/10_rmats_input/Blastocyst.txt \ > --gtf /home/cbw/my_result/GSE52415_project/6_bosTau9/genomic.gtf \ > --od /home/cbw/my_result/GSE52415_project/11_rmats_result/16C_vs_Blastocyst \ > -t single \ > --variable-read-length \ > --readLength 65 \ > --nthread 16 \ > --tmp /home/cbw/my_result/GSE52415_project/11_rmats_result/16C_vs_Blastocyst/tmp gtf: 11.914160251617432 There are 32626 distinct gene ID in the gtf file There are 81403 distinct transcript ID in the gtf file There are 18451 one-transcript genes in the gtf file There are 918752 exons in the gtf file There are 8698 one-exon transcripts in the gtf file There are 6414 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.495035 Average number of exons per transcript is 11.286464 Average number of exons per transcript excluding one-exon tx is 12.517076 Average number of gene per geneGroup is 9.102162 statistic: 0.014154911041259766 read outcome totals across all BAMs USED: 116519162 NOT_PAIRED: 0 NOT_NH_1: 65459731 NOT_EXPECTED_CIGAR: 1476376 NOT_EXPECTED_READ_LENGTH: 0 NOT_EXPECTED_STRAND: 0 EXON_NOT_MATCHED_TO_ANNOTATION: 7360222 JUNCTION_NOT_MATCHED_TO_ANNOTATION: 1076921 CLIPPED: 10870273 total: 202762685 outcomes by BAM written to: /home/cbw/my_result/GSE52415_project/11_rmats_result/16C_vs_Blastocyst/tmp/2025-10-27-12_56_46_019653_read_outcomes_by_bam.txt novel: 196.07467126846313 The splicing graph and candidate read have been saved into /home/cbw/my_result/GSE52415_project/11_rmats_result/16C_vs_Blastocyst/tmp/2025-10-27-12_56_46_019653_*.rmats save: 2.1658835411071777 loadsg: 0.0307466983795166 ========== Done processing each gene from dictionary to compile AS events Found 22384 exon skipping events Found 1907 exon MX events Found 10396 alt SS events There are 5668 alt 3 SS events and 4728 alt 5 SS events. Found 2451 RI events ========== ase: 0.7255954742431641 count: 2.9417178630828857 Processing count files. Done processing count files. 提取GV4C,4C8C,8C16C,16C囊胚的SE,MXE,IR,A5SS,A3SS的显著差异事件 (FDR < 0.05) 代码要求一个组一个组的提取 输出文件夹绝对路径:/home/cbw/my_result/GSE52415_project/12_rmats_result_significant 已知: head -1 /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/SE.MATS.JCEC.txt | tr '\t' '\n' | cat -n 1 ID 2 GeneID 3 geneSymbol 4 chr 5 strand 6 exonStart_0base 7 exonEnd 8 upstreamES 9 upstreamEE 10 downstreamES 11 downstreamEE 12 ID 13 IJC_SAMPLE_1 14 SJC_SAMPLE_1 15 IJC_SAMPLE_2 16 SJC_SAMPLE_2 17 IncFormLen 18 SkipFormLen 19 PValue 20 FDR 21 IncLevel1 22 IncLevel2 23 IncLevelDifference (rmats_env) cbw@dell-PowerEdge-R7525:~$ echo "=== MXE文件列结构 ===" === MXE文件列结构 === t/GSE52415_project/11_rmats_result/GV_vs_4C/MXE.MA(rmats_env) cbw@dell-PowerEdge-R7525:~$ head -1 /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/MXE.MATS.JCEC.txt | tr '\t' '\n' | cat -n 1 ID 2 GeneID 3 geneSymbol 4 chr 5 strand 6 1stExonStart_0base 7 1stExonEnd 8 2ndExonStart_0base 9 2ndExonEnd 10 upstreamES 11 upstreamEE 12 downstreamES 13 downstreamEE 14 ID 15 IJC_SAMPLE_1 16 SJC_SAMPLE_1 17 IJC_SAMPLE_2 18 SJC_SAMPLE_2 19 IncFormLen 20 SkipFormLen 21 PValue 22 FDR 23 IncLevel1 24 IncLevel2 25 IncLevelDifference (rmats_env) cbw@dell-PowerEdge-R7525:~$ echo "=== RI文件列结构 ===" === RI文件列结构 === /GSE52415_project/11_rmats_result/GV_vs_4C/RI.MATS(rmats_env) cbw@dell-PowerEdge-R7525:~$ head -1 /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/RI.MATS.JCEC.txt | tr '\t' '\n' | cat -n 1 ID 2 GeneID 3 geneSymbol 4 chr 5 strand 6 riExonStart_0base 7 riExonEnd 8 upstreamES 9 upstreamEE 10 downstreamES 11 downstreamEE 12 ID 13 IJC_SAMPLE_1 14 SJC_SAMPLE_1 15 IJC_SAMPLE_2 16 SJC_SAMPLE_2 17 IncFormLen 18 SkipFormLen 19 PValue 20 FDR 21 IncLevel1 22 IncLevel2 23 IncLevelDifference (rmats_env) cbw@dell-PowerEdge-R7525:~$ echo "=== A5SS文件列结构 ===" lt/GSE52415_project/11_rmat=== A5SS文件列结构 === s_result/GV_vs_4C/A5SS.(rmats_env) cbw@dell-PowerEdge-R7525:~$ head -1 /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/A5SS.MATS.JCEC.txt | tr '\t' '\n' | cat -n 1 ID 2 GeneID 3 geneSymbol 4 chr 5 strand 6 longExonStart_0base 7 longExonEnd 8 shortES 9 shortEE 10 flankingES 11 flankingEE 12 ID 13 IJC_SAMPLE_1 14 SJC_SAMPLE_1 15 IJC_SAMPLE_2 16 SJC_SAMPLE_2 17 IncFormLen 18 SkipFormLen 19 PValue 20 FDR 21 IncLevel1 22 IncLevel2 23 IncLevelDifference (rmats_env) cbw@dell-PowerEdge-R7525:~$ (rmats_env) cbw@dell-PowerEdge-R7525:~$ echo "=== A3SS文件列结构 ===" lt/GSE52415_project/11_rmats_result/GV_vs_4C/A3SS.=== A3SS文件列结构 === (rmats_env) cbw@dell-PowerEdge-R7525:~$ head -1 /home/cbw/my_result/GSE52415_project/11_rmats_result/GV_vs_4C/A3SS.MATS.JCEC.txt | tr '\t' '\n' | cat -n 1 ID 2 GeneID 3 geneSymbol 4 chr 5 strand 6 longExonStart_0base 7 longExonEnd 8 shortES 9 shortEE 10 flankingES 11 flankingEE 12 ID 13 IJC_SAMPLE_1 14 SJC_SAMPLE_1 15 IJC_SAMPLE_2 16 SJC_SAMPLE_2 17 IncFormLen 18 SkipFormLen 19 PValue 20 FDR 21 IncLevel1 22 IncLevel2 23 IncLevelDifference
10-28
评论
添加红包

请填写红包祝福语或标题

红包个数最小为10个

红包金额最低5元

当前余额3.43前往充值 >
需支付:10.00
成就一亿技术人!
领取后你会自动成为博主和红包主的粉丝 规则
hope_wisdom
发出的红包
实付
使用余额支付
点击重新获取
扫码支付
钱包余额 0

抵扣说明:

1.余额是钱包充值的虚拟货币,按照1:1的比例进行支付金额的抵扣。
2.余额无法直接购买下载,可以购买VIP、付费专栏及课程。

余额充值