时间戳

首页 > 解决方案 > 如何使用 bash 按字符串拆分列？

bash - 如何使用 bash 按字符串拆分列？

问题描述

给定具有八列的制表符分隔文件：

22  51244237    rs575160859 C   T   100 PASS AC=19;AF=0.00379393;AN=5008;NS=2504;DP=13345;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0;EUR_AF=0.0099;SAS_AF=0.0061;AA=.|||;VT=SNP

如何使用 bash 从第八列中的信息创建一个新的制表符分隔文件，其中包含以下列：AF；EAS_AF；AMR_AF；AFR_AF；EUR_AF；SAS_AF 和对应的数值？

IE：

#AF         EAS_AF   AMR_AF     AFR_AF   EUR_AF     SAS_AF 
0.00379393  0        0.0043     0        0.0099     0.0061

我知道我可以用“;”分割第八列 （https://unix.stackexchange.com/questions/156919/splitting-a-column-using-awk）然后删除不需要的文本列和文本字符串（即“AF =”），但是有没有更有效的方法去做这个？

谢谢

标签： bashawkgrep

解决方案

请您尝试以下操作。

awk '
{
  match($0,/AF[^;]*/)
  af=substr($0,RSTART,RLENGTH)
  match($0,/EAS_AF[^;]*/)
  eas=substr($0,RSTART,RLENGTH)
  match($0,/AMR_AF[^;]*/)
  amr=substr($0,RSTART,RLENGTH)
  match($0,/AFR_AF[^;]*/)
  afr=substr($0,RSTART,RLENGTH)
  match($0,/EUR_AF[^;]*/)
  eur=substr($0,RSTART,RLENGTH)
  match($0,/SAS_AF[^;]*/)
  sas=substr($0,RSTART,RLENGTH)
  VAL=af OFS ac OFS eas OFS amr OFS afr OFS eur OFS sas
  split(VAL,array,"[= ]")
  print array[1],array[4],array[6],array[8],array[10],array[12] ORS array[2],array[5],array[7],array[9],array[11],array[13]
}' Input_file | column -t

说明：这里也为上述代码添加说明。

awk '
{
  match($0,/AF[^;]*/)             ##Using match out of the box awk function for matching AF string till semi colon.
  af=substr($0,RSTART,RLENGTH)    ##creating variable named af whose value is substring of indexes of RSTART to till value of RLENGTH.
  match($0,/EAS_AF[^;]*/)         ##Using match out of the box awk function for matching EAS_AF string till semi colon.
  eas=substr($0,RSTART,RLENGTH)   ##creating variable named eas whose value is substring of indexes of RSTART to till value of RLENGTH.
  match($0,/AMR_AF[^;]*/)         ##Using match out of the box awk function for matching AMR_AF string till semi colon.
  amr=substr($0,RSTART,RLENGTH)   ##creating variable named amr whose value is substring of indexes of RSTART to till value of RLENGTH.
  match($0,/AFR_AF[^;]*/)         ##Using match out of the box awk function for matching AFR_AF string till semi colon.
  afr=substr($0,RSTART,RLENGTH)   ##creating variable named afr whose value is substring of indexes of RSTART to till value of RLENGTH.
  match($0,/EUR_AF[^;]*/)         ##Using match out of the box awk function for matching EUR_AF string till semi colon.
  eur=substr($0,RSTART,RLENGTH)   ##creating variable named eur whose value is substring of indexes of RSTART to till value of RLENGTH.
  match($0,/SAS_AF[^;]*/)         ##Using match out of the box awk function for matching SAS_AF string till semi colon.
  sas=substr($0,RSTART,RLENGTH)   ##creating variable named sas whose value is substring of indexes of RSTART to till value of RLENGTH.
  VAL=af OFS ac OFS eas OFS amr OFS afr OFS eur OFS sas    ##Creating variable VAL whose value is values of all above mentioned variables.
  split(VAL,array,"[= ]")         ##Using split function of awk to split it into array named array with delimiter space OR =.
  print array[1],array[4],array[6],array[8],array[10],array[12] ORS array[2],array[5],array[7],array[9],array[11],array[13]   ##Printing all array values as per OP.
  af=ac=eas=amr=afr=eur=sas=""    ##Nullifying all variables mentioned above.
}' Input_file     | column -t     ##Mentioning Input_file name here and passing awk output to column command to take output in TAB format.

推荐阅读