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awk를 사용하여 마지막 행과 다음 행을 기준으로 12를 빼거나 합하려면 어떻게 해야 합니까?

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awk를 사용하여 마지막 행과 다음 행을 기준으로 12를 빼거나 합하려면 어떻게 해야 합니까?

나는 다음과 같은 데이터를 가지고 있습니다:

##sequence-region Q75T13 1 641
Q75T13,UniProtKB,Chain,1,641,.,.,.,ID
Q75T13,UniProtKB,Topological domain,1,60,.,.,.,Note=Cytoplasmic
Q75T13,UniProtKB,Transmembrane,61,85,.,.,.,Note=Helical
Q75T13,UniProtKB,Topological domain,86,641,.,.,.,Note=Lumenal


##sequence-region Q9BRR3 1 403
Q9BRR3,UniProtKB,Chain,1,403,.,.,.,ID
Q9BRR3,UniProtKB,Topological domain,1,22,.,.,.,Note=Lumenal
Q9BRR3,UniProtKB,Transmembrane,23,43,.,.,.,Note=Helical
Q9BRR3,UniProtKB,Topological domain,44,259,.,.,.,Note=Cytoplasmic

##sequence-region Q96FM1 1 250
Q96FM1,UniProtKB,Topological domain,120,135,.,.,.,Note=Cytoplasmic
Q96FM1,UniProtKB,Transmembrane,136,156,.,.,.,Note=Helical
Q96FM1,UniProtKB,Topological domain,157,169,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Transmembrane,170,190,.,.,.,Note=Helical
Q96FM1,UniProtKB,Topological domain,191,250,.,.,.,Note=Lumenal

awk 코드가 어떻게 생겼는지 궁금합니다.

lumenal이라는 단어가 있는 행, 이전 행에 transmembrane이라는 단어가 있는 경우 열 4에서 -12를 빼고 lumenal이라는 단어가 있는 행을 인쇄합니다. "lumenal"이라는 단어가 있는 행의 다음 행에 "transmembrane"이라는 단어가 포함되어 있으면 열 5에 +12를 추가하고 "lumenal"이라는 단어가 있는 행을 인쇄합니다. 최종 파일은 다음과 같습니다:

Q75T13,UniProtKB,Topological domain,74,641,.,.,.,Note=Lumenal
Q9BRR3,UniProtKB,Topological domain,1,34,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,145,169,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,157,181,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,179,250,.,.,.,Note=Lumenal

누구든지 나를 도와줄 수 있나요? 나는 조금 붙어 있습니다. awk와 grep을 사용하려고 합니다.

답변1

다음 명령을 시도해 보십시오:

root@u2004:~# cat test
##sequence-region Q75T13 1 641
Q75T13,UniProtKB,Chain,1,641,.,.,.,ID
Q75T13,UniProtKB,Topological domain,1,60,.,.,.,Note=Cytoplasmic
Q75T13,UniProtKB,Transmembrane,61,85,.,.,.,Note=Helical
Q75T13,UniProtKB,Topological domain,86,641,.,.,.,Note=Lumenal


##sequence-region Q9BRR3 1 403
Q9BRR3,UniProtKB,Chain,1,403,.,.,.,ID
Q9BRR3,UniProtKB,Topological domain,1,22,.,.,.,Note=Lumenal
Q9BRR3,UniProtKB,Transmembrane,23,43,.,.,.,Note=Helical
Q9BRR3,UniProtKB,Topological domain,44,259,.,.,.,Note=Cytoplasmic

##sequence-region Q96FM1 1 250
Q96FM1,UniProtKB,Topological domain,120,135,.,.,.,Note=Cytoplasmic
Q96FM1,UniProtKB,Transmembrane,136,156,.,.,.,Note=Helical
Q96FM1,UniProtKB,Topological domain,157,169,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Transmembrane,170,190,.,.,.,Note=Helical
Q96FM1,UniProtKB,Topological domain,191,250,.,.,.,Note=Lumenal
root@u2004:~# 
root@u2004:~# awk -F, -v OFS=, '{while(1){if($0~/Lumenal/){a=$0; $4-=12;p=$0; $0=a;$5+=12;n=$0; if(index(pre,"Transmembrane")>0)print p; if(getline>0){if(index($0,"Transmembrane"))print n; if($0~/Lumenal/){pre=$0; continue}}} break}} {pre=$0}' test
Q75T13,UniProtKB,Topological domain,74,641,.,.,.,Note=Lumenal
Q9BRR3,UniProtKB,Topological domain,1,34,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,145,169,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,157,181,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,179,250,.,.,.,Note=Lumenal
root@u2004:~#

답변2

3줄의 스크롤 버퍼를 유지하고 다음을 확인하세요.

$ cat tst.awk
BEGIN { FS=OFS="," }
{
    nxt = $0
    prt()
}
END {
    prt()
}

function prt() {
    if ( cur ~ /Lumenal/ ) {
        if ( pre ~ /Transmembrane/ ) {
            $0 = cur
            $4 -= 12
            print
        }

        if ( nxt ~ /Transmembrane/ ) {
            $0 = cur
            $5 += 12
            print
        }
    }

    pre = cur
    cur = nxt
    nxt = ""
}


$ awk -f tst.awk file
Q75T13,UniProtKB,Topological domain,74,641,.,.,.,Note=Lumenal
Q9BRR3,UniProtKB,Topological domain,1,34,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,145,169,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,157,181,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,179,250,.,.,.,Note=Lumenal

답변3

열 구분 기호를 쉼표로 변경하기 전에 이 문제를 해결했습니다. 첫 번째 작업은 테스트 파일의 여러 공백을 탭으로 변경하는 것입니다.

$ cat indata 
##sequence-region Q75T13 1 641
Q75T13  UniProtKB   Chain   1   641 .   .   .   ID
Q75T13  UniProtKB   Topological domain  1   60  .   .   .   Note=Cytoplasmic    
Q75T13  UniProtKB   Transmembrane   61  85  .   .   .   Note=Helical
Q75T13  UniProtKB   Topological domain  86  641 .   .   .   Note=Lumenal


##sequence-region Q9BRR3 1 403
Q9BRR3  UniProtKB   Chain   1   403 .   .   .   ID
Q9BRR3  UniProtKB   Topological domain  1   22  .   .   .   Note=Lumenal
Q9BRR3  UniProtKB   Transmembrane   23  43  .   .   .   Note=Helical
Q9BRR3  UniProtKB   Topological domain  44  259 .   .   .   Note=Cytoplasmic

##sequence-region Q96FM1 1 250
Q96FM1  UniProtKB   Topological domain  120 135 .   .   .   Note=Cytoplasmic
Q96FM1  UniProtKB   Transmembrane   136 156 .   .   .   Note=Helical
Q96FM1  UniProtKB   Topological domain  157 169 .   .   .   Note=Lumenal
Q96FM1  UniProtKB   Transmembrane   170 190 .   .   .   Note=Helical
Q96FM1  UniProtKB   Topological domain  191 250 .   .   .   Note=Lumenal

다음은 스크립트입니다. 함수의 세 번째 매개변수는 split탭 문자입니다.

#!/bin/bash
awk '
        function add12(out_line) {
                iarr = split( out_line, arr, "  " )
                arr[5] = 12 + arr[5]
                printf( "%s", arr[1])
                for (i=2 ; i<=iarr ; i++) printf( "\t%s", arr[i] )
                printf( "\n" )
        }

        function sub12(out_line) {
                iarr = split( out_line, arr, "  " )
                arr[4] = arr[4] - 12
                printf( "%s", arr[1])
                for (i=2 ; i<=iarr ; i++) printf( "\t%s", arr[i] )
                printf( "\n" )
        }

        NR == 1 { last_line = $0 ; next }
        NR == 2 { test_line = $0 ; next }

        test_line ~ /Lumenal/ {
                if (last_line ~ /Transmembrane/) sub12( test_line )
                if ($0  ~ /Transmembrane/) add12( test_line )
        }

        {
                last_line = test_line
                test_line = $0
        }

        END {
                if (test_line ~ /Lumenal/) {
                        if (last_line ~ /Transmembrane/) sub12( test_line )
                }
        }
' $1

그리고 "증거는 푸딩에 있다":

$ ./doit indata
Q75T13  UniProtKB   Topological domain  74  641 .   .   .   Note=Lumenal
Q9BRR3  UniProtKB   Topological domain  1   34  .   .   .   Note=Lumenal
Q96FM1  UniProtKB   Topological domain  145 169 .   .   .   Note=Lumenal
Q96FM1  UniProtKB   Topological domain  157 181 .   .   .   Note=Lumenal
Q96FM1  UniProtKB   Topological domain  179 250 .   .   .   Note=Lumenal

내가 만들었다 doit2:

$ diff doit*
4c4
<       iarr = split( out_line, arr, "  " )
---
>       iarr = split( out_line, arr, "," )
7c7
<       for (i=2 ; i<=iarr ; i++) printf( "\t%s", arr[i] )
---
>       for (i=2 ; i<=iarr ; i++) printf( ",%s", arr[i] )
12c12
<       iarr = split( out_line, arr, "  " )
---
>       iarr = split( out_line, arr, "," )
15c15
<       for (i=2 ; i<=iarr ; i++) printf( "\t%s", arr[i] )
---
>       for (i=2 ; i<=iarr ; i++) printf( ",%s", arr[i] )

csv 파일을 사용하십시오.

$ ./doit2 comma
Q75T13,UniProtKB,Topological domain,74,641,.,.,.,Note=Lumenal
Q9BRR3,UniProtKB,Topological domain,1,34,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,145,169,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,157,181,.,.,.,Note=Lumenal
Q96FM1,UniProtKB,Topological domain,179,250,.,.,.,Note=Lumenal

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