Question

我有两个看起来像这样的文件：

参考面板（ ReferencePanel.csv ）

"id","position","allele0","allele1","allele1_frequency"
"seq-rs1010355",55102179,"T","C",0.098
"seq-rs272408",55103603,"C","T",0.787
"seq-rs11669899",55104559,"A","T",0.029
"imm_19_59798585",55106773,"A","G",0.499

BIM文件（ myfile.bim ）

19    19:55102179    0    55102179    C    T
19    19:55103603    0    55103603    C    T
19    19:55104559    0    55104559    G    C
19    19:55106773    0    55106773    A    T

我想在BIM文件中删除所有两个等位基因与参考面板不同的行。换句话说，我只想保留与参考面板具有完全相同等位基因的行 - 顺序无关紧要。

示例：

参考等位基因：

"seq-rs1010355",55102179,"T","C",0.098
"seq-rs272408",55103603,"C","T",0.787
"seq-rs11669899",55104559,"A","T",0.029
"imm_19_59798585",55106773,"A","G",0.499

BIM文件（myfile.bim）

19    19:55102179 0   55102179    C   T
19    19:55103603 0   55103603    C   T
19    19:55104559 0   55104559    G   C
19    19:55106773 0   55106773    A   T

仅保留以下行：

19    19:55102179 0   55102179    C   T
19    19:55103603 0   55103603    C   T

我设法使用这些行从参考面板中提取所有位置：

#Create an empty list 
positions=[]

#Populate list with positions 
for line in open("ReferencePanel.csv"):
    columns = line.split(",")
    positions.append(columns[1])
#Remove first element which corresponds to the header
positions.pop(0)

但我被困在这里。我希望有一个人可以帮助我。提前谢谢！

Answer 1

如果您不反对使用awk，则可以使用以下命令：

awk -F'[",]*' 'NR==FNR && $4 && $5 {ref[$4][$5]=1} NR>FNR {FS=" *"} NR>FNR && ref[$6][$7]' reference.csv myfile.bim

导致：

19    19:55102179    0    55102179    C    T
19    19:55103603    0    55103603    C    T
19    19:55106773    0    55106773    A    T

注意最后一行与参考文件的第4行（A，T）匹配

说明：

-F'[",]*'与CSV分隔符匹配，用于解析参考文件

NR==FNR && $4 && $5 {ref[$4][$5]=1}从参考文件中获取所有C，T，G，A

NR>FNR {FS=" *"}正在将awk字段分隔符更改为空格以解析第二个文件

NR>FNR && ref[$6][$7]是第二个文件的打印行，如果第6和第7列与数组中存储的匹配

删除具有错误等位基因的SNP

1 个答案: