grep如果word值大于值

Question

我是这样归档的：

1       51710   .       C       A       .       clustered_events;contamination;germline_risk;read_position;t_lod        DP=1;ECNT=6;POP_AF=1.000e-03;P_GERMLINE=-1.372e-02;TLOD=4.20    GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB  0/1:0,1:1.000:1:0,0:0,1:26:0,136:43:2:0|1:51637_C_T:0.990,0.00,1.00:0.025,0.028,0.947
19  27733067    .   A   G,C .   clustered_events;contamination;germline_risk;multiallelic   DP=60;ECNT=15;POP_AF=1.000e-03,1.000e-03;P_GERMLINE=-2.169e-04,-2.325e-04;TLOD=11.46,7.14   GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB  0/1/2:5,35,20:0.500,0.333:6:0,2,1:1,1,1:34,35:112,143,117:42,45:29,47:0.444,0.485,0.500:0.037,0.019,0.944
20  42199704    .   GGT G,GGTGGGTGGGTGTGTGT .   germline_risk   DP=100;ECNT=2;POP_AF=0.112,0.024;P_GERMLINE=-2.964e-04,-8.826e-06;TLOD=3.76,9.83    GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB  0/1/2:1,2,7:0.168,0.301:20:1,1,4:9,1,1:34,35:147,203,146:60,60:51,62:0.192,0.253,0.263:0.038,0.014,0.948

我想分两步对grep行进行分析：

有DP > 45的线路。然后，在最后一列中的第一个:之后具有值的行>2

因此，在第一行中，我们可以看到DP =1和后面的第一个值:在最后一列=0

在第二行中，DP = 60，后面的第一个值是:在最后一列=5

从上面的示例输入文件中，我们首先应该得到：

19  27733067    .   A   G,C .   clustered_events;contamination;germline_risk;multiallelic   DP=60;ECNT=15;POP_AF=1.000e-03,1.000e-03;P_GERMLINE=-2.169e-04,-2.325e-04;TLOD=11.46,7.14   GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB  0/1/2:5,35,20:0.500,0.333:6:0,2,1:1,1,1:34,35:112,143,117:42,45:29,47:0.444,0.485,0.500:0.037,0.019,0.944
20  42199704    .   GGT G,GGTGGGTGGGTGTGTGT .   germline_risk   DP=100;ECNT=2;POP_AF=0.112,0.024;P_GERMLINE=-2.964e-04,-8.826e-06;TLOD=3.76,9.83    GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB  0/1/2:1,2,7:0.168,0.301:20:1,1,4:9,1,1:34,35:147,203,146:60,60:51,62:0.192,0.253,0.263:0.038,0.014,0.948

第二次之后我们应该得到：

19  27733067    .   A   G,C .   clustered_events;contamination;germline_risk;multiallelic   DP=60;ECNT=15;POP_AF=1.000e-03,1.000e-03;P_GERMLINE=-2.169e-04,-2.325e-04;TLOD=11.46,7.14   GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB  0/1/2:5,35,20:0.500,0.333:6:0,2,1:1,1,1:34,35:112,143,117:42,45:29,47:0.444,0.485,0.500:0.037,0.019,0.944
92,0.253,0.263:0.038,0.014,0.948

能帮个忙吗？

Answer 1

你能试一下吗。

awk '
{
  split($8,array,"[;=]")
  if(array[1]=="DP" && array[2]>45){
    split($10,array1,"[:,]")
    if(array1[2]>2){
       print
    }
  }
}'  Input_file

解释：现在添加对上述代码的解释。

awk '                                    ##Starting awk program here.
{                                        ##Starting block for statements here.
  split($8,array,"[;=]")                 ##Using awk out of box function split for splitting 8th field and saving it to array with delimiter ;=
  if(array[1]=="DP" && array[2]>45){     ##Checking condition if 1st element of array is DP and 2nd element value is greater than 45 then:
    split($10,array1,"[:,]")             ##Splitting 10th  field to array1 with delkimter : and , here.
    if(array1[2]>2){                     ##Checking condition if array1 2nd element if its value is greater than 2 then do following.
       print                             ##Printing the current line value here.
    }                                    ##Closing block for above if condition here.
  }                                      ##Closing block for previous if condition here.
}' Input_file                            ##Mentioning Input_file name here.

Answer 2

grep是一个错误的工具，用来比较数字，看看它们是否大于或小于。

他是一个perl一行程序，它打印符合这两种条件的行：

perl -ane 'print if $F[7] =~ /DP=(\d+)/ && $1 > 45 && $F[9] =~ /:(\d+)/ && $1 > 2' input.txt

Answer 3

如果您坚持grep，您可以得到DP > 45

grep 'DP=\(4[6-9]\|[5-9][0-9]\|[1-9][0-9]\{2,\}\)[^0-9]'
#            |         |            |
#          46-49       |          100..∞
#                    50-99