关联突变与用药部分逻辑代码实现

项目地址
https://github.com/user-tq/anvcivi

直接用civic下载的文件进行简单的数据清洗，使用MANE下载的文件构造基因与转录本的字典(解决annovar的转录本问题)，暂只考虑氨基酸改变完全匹配情况。最结果暂生成markdown，但由于markdown无法合并单元格，且未区分癌种，结果很长，实际分析后一两个位点突变就很多了。

	AA_match	af
0	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017
1	PIK3CA:NM_006218:exon2:c.G333C:p.K111N	0.027
2	PIK3CA:NM_006218:exon21:c.A3140G:p.H1047R	0.03
3	KIT:NM_000222:exon17:c.A2447T:p.D816V	0.021
4	EGFR:NM_005228:exon18:c.G2155A:p.G719S	0.061
5	EGFR:NM_005228:exon19:c.2235_2249del:p.E746_A750del	0.011
6	EGFR:NM_005228:exon20:c.2296_2297insTGGCCAGCG:p.V769_D770insASV	0.02
7	EGFR:NM_005228:exon20:c.C2369T:p.T790M	0.019
8	EGFR:NM_005228:exon21:c.T2573G:p.L858R	0.012
9	BRAF:NM_004333:exon15:c.T1799A:p.V600E	0.026
10	KRAS:NM_004985:exon4:c.G436A:p.A146T	0.015
11	KRAS:NM_004985:exon2:c.G38A:p.G13D	0.017
12	KRAS:NM_004985:exon2:c.G35A:p.G12D	0.019
13	MAP2K1:NM_002755:exon2:c.A167C:p.Q56P	0.068

	AA_match	af	disease	drugs
0	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Neuroblastoma	Binimetinib,Everolimus
1	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Skin Melanoma	Vemurafenib
2	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Skin Melanoma	Selumetinib
3	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Colorectal Cancer	Chemotherapy,Cetuximab
4	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Colorectal Cancer	Dactolisib,Selumetinib
5	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Lung Non-small Cell Carcinoma	Trametinib,Selumetinib
6	NRAS:NM_002524:exon3:c.C181A:p.Q61K	0.017	Ovary Serous Adenocarcinoma	Trametinib
7	PIK3CA:NM_006218:exon2:c.G333C:p.K111N	0.027	Her2-receptor Positive Breast Cancer	Pictilisib
8	PIK3CA:NM_006218:exon2:c.G333C:p.K111N	0.027	Her2-receptor Positive Breast Cancer	Trastuzumab Emtansine

结果太长略

	AA_match	disease	drugs	evidence_statement
0	NRAS:NM_002524:exon3:c.C181A:p.Q61K	Neuroblastoma	Binimetinib,Everolimus	In-vitro study in 5 neuroblastoma cell lines (2 with NRAS Q61K mutation). The combination of mTOR and MEK Inhibitors synergistically blocked cell growth in NRAS mutant but not wild type cell lines. Single agent MEK inhibition (AZD6244/selumetinib, MEK162 or PD0325901) and single agent mTOR inhibition (Everolimus or AZD8055) also blocked cell growth in NRAS mutant cell lines, whereas single agent PI3K inhibitors or MEK Inhibitors in combination with PIK3CA/AKT inhibitors did not show synergistic effects.

结果太长略