awk 根据坐标范围和精确匹配在字段中打印文本

Question

在下面的 awk 中，我试图匹配 $4 中的值的 file1来自 $4 的值在 file2前第一_ .我存储了 $4 的值在 file1在 A .然后我存储 $2 中的值如 min , $3 中的值如 max ，以及 $1 中的值如 chr .
如 $1 in A等于 array[1] ，然后我使用存储在 min 中的值, max , 和 chr检查 $2 之间是否有重叠, $3 , 和 $ file2 中的 1 个值.如果有那么 overlap已打印但如果没有 missing被打印。我试图确保线条匹配并且坐标被覆盖 file1至 file2 .我的实际数据是以下格式的数千行，file2 中的每一行都应该匹配。 .我评论了 awk也希望它有所帮助，因为我遇到了语法错误，也许有更好的方法，但我想尝试看看。

如果我删除 {split($4,array,"_")}并删除 array[1] ，我得到了当前的输出，但并不是所有的行都只打印 overlap行是，我不确定只会打印完全匹配的内容。

文件 1 tab-delimited

chr19   42373737    42373856    RPS19
chr6    32790021    32790140    TAP2

文件 2 tab-delimited

chr19   42364844    42364915    RPS19_cds_1_0_chr19_42364845_f  0   +
chr19   42365180    42365281    RPS19_cds_2_0_chr19_42365181_f  0   +
chr19   42373100    42373284    RPS19_cds_3_0_chr19_42373101_f  0   +
chr19   42373768    42373823    RPS19_cds_4_0_chr19_42373769_f  0   +
chr19   42375418    42375445    RPS19_cds_5_0_chr19_42375419_f  0   +

所需的输出 tab-delimited

chr19   42364844    42364915    RPS19_cds_1_0_chr19_42364845_f  0   +     missing
chr19   42365180    42365281    RPS19_cds_2_0_chr19_42365181_f  0   +     missing 
chr19   42373100    42373284    RPS19_cds_3_0_chr19_42373101_f  0   +     missing
chr19   42373768    42373823    RPS19_cds_4_0_chr19_42373769_f  0   +     overlap
chr19   42375418    42375445    RPS19_cds_5_0_chr19_42375419_f  0   +     missing

awk

awk ' # call awk script
 BEGIN { FS=OFS="\t" }  # define FS and OFS as tab
  FNR==NR{  # start processing same line in files
   a[$4];  # store gene in 
   min[$4]=$2;  # store staring coordinate
   max[$4]=$3;  # store ending coordinate
    next         # process next line
}  # close block
 {  # start block
   split($4,array,"_");   # split $4 on _ and store in array[1]
   print $0,(array[1] in a) && ($2>=min[array[1]] && 
$2<=max[array[1]])?"overlap":"missing" # print all lines followed by 
overlap or missing depending on condition (if array[1] = a and $2 in 
file2 is greater than or equal to min and $3 in file2 greater than or 
equal to max print overlap, else missing)
}  # close block
' file1 file2  # define input

当前输出

1   42373768    42373823    RPS19_cds_4_0_chr19_42373769_f  0   +   overlap 

Answer 1

super 巨星来了awk在这里营救:
也看不到您的 Input_file(s) 是实际的 TAB 分隔，所以使用 FS="\t"之前 Input_file1在这段代码中也是如此。

awk 'FNR==NR{a[$4];min[$4]=$2;max[$4]=$3;next} {split($4,array,"_");print $0,(array[1] in a) && ($2>=min[array[1]] && $2<=max[array[1]])?"overlap":"missing"}'  Input_file1  OFS="\t"   Input_file2

现在也添加一种非单线形式的解决方案:

awk '
FNR==NR{
  a[$4];
  min[$4]=$2;
  max[$4]=$3;
  next
}
{
  split($4,array,"_");
  print $0,(array[1] in a) && ($2>=min[array[1]] && $2<=max[array[1]])?"overlap":"missing"
}
'  Input_file1  OFS="\t"  Input_file2

输出如下:

chr19   42364844    42364915    RPS19_cds_1_0_chr19_42364845_f  0   +   missing
chr19   42365180    42365281    RPS19_cds_2_0_chr19_42365181_f  0   +   missing
chr19   42373100    42373284    RPS19_cds_3_0_chr19_42373101_f  0   +   missing
chr19   42373768    42373823    RPS19_cds_4_0_chr19_42373769_f  0   +   overlap
chr19   42375418    42375445    RPS19_cds_5_0_chr19_42375419_f  0   +   missing