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  • regular expression in perl?

    Hi,
    I have a list contains:
    ID : 741158
    PARENT ID : 9605
    RANK : species
    GC ID : 1
    MGC ID : 2
    SCIENTIFIC NAME : Homo sp. Altai
    GENBANK COMMON NAME : Denisova hominin
    //
    In some part of this file the rank is subspecies. I just need those ID line (first line) which belong to species not subspecies:
    I used this : my @new_list = grep {$_ =~ /\bspecies$/ && /\nID +\: *([\d]+)/} @list;
    but is not working. Any suggestion? Thanks

  • #2
    cat file | awk '$1=="ID"{id=$0} $1=="RANK" && $3=="species"{print id}'

    Assuming an ID line is provided for each entry.
    If you just need the ID number, use "id=$3" instead of "id=$0".

    Comment


    • #3
      Thanks Steven. But I am not sure that it works in perl .

      Comment


      • #4
        So, you asked about perl. Here's a one-liner that roughly matches steven's awk script:
        Code:
        $ perl -ne 'if(/ID *: *(\d+)/){$id=$1};if(/RANK *: *species/){print "$id\n"}' file.txt
        9605
        If you're using it inside some other perl code, you'd probably do something like this:
        Code:
        my @new_list = ();
        my $id = "";
        # this assumes you want to store IDs from files or standard in
        while(<>){
          if(/^ID *: *(\d+)/){$id=$1};
          if($id && /^RANK *: *species/){
            push(@new_list, $id);
          }
        }
        Or if you're reading from the array @list, which contains one element per line:
        Code:
        my @new_list = ();
        my $id = "";
        foreach(@list){
          if(/^ID *: *(\d+)/){$id=$1};
          if($id && /^RANK *: *species/){
            push(@new_list, $id);
          }
        Or, assuming your example is exactly as your code looks (i.e. each element in @list contains a number of lines, but only one record per list element):
        Code:
        my @new_list = ();
        foreach (@list){
          if(/^RANK *: *species/){
            if(/^ID *: *(\d+)/){
              push(@new_list, $1);
            }
          }
        }
        [but if that were the case, your code would probably work, but would spit out the entire record, rather than just the ID]


        I would advise you to stay away from using grep in situations like this where you're modifying things inside a loop. It would do weird things like not adding to your result array if $id were 0, and changing $_ would alter your original list. See here for more information:

        Comment


        • #5
          Yes, that is not perl indeed but awk. If you really need to include this in a bigger perl code, the equivalent can be obtained by splitting the lines and adding a couple of "if" and "else". And I bet the same can be obtained by just using linux command lines, directly from the shell.

          Comment


          • #6
            Nice job gringer, that is a complete answer

            Comment


            • #7
              I bet the same can be obtained by just using linux command lines, directly from the shell
              I think an awk one-liner is close enough to 'linux commands, directly from the shell'. A command-line equivalent using multiple grep pipes would go something like this:
              $ grep '^\(ID\|RANK\)' file.txt | grep -B 1 '^RANK : species' | grep -v '^RANK'
              ID : 741158
              Although you'd run into problems with that if any IDs didn't have associated ranks following them.

              Comment


              • #8
                Thanks so much Gringer and Steven.

                Comment

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