1

I have this data:

##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

And I was wondering what the awk code would look like for:

The rows that have the word lumenal, if in the previous row it has the word transmembrane, subtract -12 in column 4 and print the row with the word lumenal. If the row with the word lumenal has the word "transmembrane" in the next row, add +12 in column 5 and print the row with the word lumenal. The final file would be:

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

Can someone help me? I am a little bit stuck. I am trying with awk and grep

3
  • Not easy to do. Because the column separator is not clear. You use space to separate columns, but the third column also has space, like "Topological domain". May 2 at 16:30
  • I don't know why, but all the column separators should be tabs. I have tried to change it. Check it now if it's okay May 2 at 16:35
  • I have change it to a csv, now I suppose that would be easier :) May 2 at 16:41

3 Answers 3

3

Try the following command:

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:~#
12
  • Thank you so much! It seems to work perfectly May 2 at 16:58
  • @RafaelSolerOrtuño No problem. Why not give me an upvote? I need more upvotes! May 2 at 17:04
  • 2
    @EdMorton Thank you for the correction! I'm new to awk and I'll read the doc. May 2 at 23:07
  • 2
    @EdMorton Is it possible to modify my command (still in one liner) so that it produces correct result? I'm not able to delete this accepted answer. May 2 at 23:09
  • 2
    Lol, that's correct😅. I'm trying to fix my answer. Thanks for the link. You are a real awk guru, I noticed your name in the article, and it's from 2006! May 2 at 23:40
2

Just keep a rolling buffer of 3 lines and examine that:

$ 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
3
  • That's an amazing answer Mr Morton. Can I ask you other thing? I am trying to do a similar thing: - Find the rows with the word "lumenal", and if there is a row with the word transmembrane before, do the subtraction of the columns $5 and $4 of the previous row, and subtract it from the column $4 of the row with the word lumenal - Find the rows with the word "lumenal", and if there is a row after that, do the subtraction of the columns $5 and $4 of the previous row with the word transmembrane, and add it to column $5 of the row with the word lumenal. May 3 at 8:31
  • I am trying to do $5 += $5-$4, but it gives me the rest of the lumenal row, how can I store the transmembrane susbtract and calculate the operation after? Thank you so much! May 3 at 8:35
  • I'm sorry, I'm not sure I fully understand what you're asking. Please just ask a new question, don't ask additional questions in comments where you can't provide formatted sample input/output that demonstrate your requirements.
    – Ed Morton
    May 3 at 13:10
2

I worked this one out before you changed the column separators to commas. First job was to change the multiple spaces to tabs in my test file:

$ 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

Next the script. Note that the third argument in the split functions is a tab.

#!/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

and the "proof of the pudding":

$ ./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

I've created 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] )

and used the csv file:

$ ./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
1
  • Thank you for your answer Martin, I have asked another question to Ed which I am struggling, in case you have and idea. May 3 at 8:59

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