awk for text processing Post: 303017767

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Top Forums Shell Programming and Scripting awk for text processing Post 303017767 by biofreek on Tuesday 22nd of May 2018 03:12:47 AM

05-22-2018

Registered User

awk for text processing

Hi,my file is in this format

Code:

"[ {
  \"_id\": \"56190\",
  \"_score\": 1.0,
  \"generif\": [
    {
      \"pubmed\": 21764855,
      \"text\": \"loss of RNPC1 in mouse embryonic fibroblasts increased the level of p53 protein, leading to enhanced premature senescence in a p53-dependent manner\"
    },
    {
      \"pubmed\": 22371495,
      \"text\": \"a novel mechanism by which HuR is regulated by RNPC1 via mRNA stability and HuR is a mediator of RNPC1-induced growth suppression.\"
    },
    {
      \"pubmed\": 22508983,
      \"text\": \"knockdown of p73 or p21, another target of RNPC1, attenuates the inhibitory effect of RNPC1 on cell proliferation and premature senescence, whereas combined knockdown of p73 and p21 completely abolishes it\"
    },
    {
      \"pubmed\": 23836903,
      \"text\": \"knockdown of MIC-1 can decrease RNPC1-induced cell growth suppression.\"
    },
    {
      \"pubmed\": 25512531,
      \"text\": \"Rbm38 deficiency markedly decreases the tumor penetrance in mice heterozygous for p53 via enhanced p53 expression.\"
    },
    {
      \"pubmed\": 28850611,
      \"text\": \"The hearts of Rbm38 -/- mice were mildly hypertrophic, but cardiac function was not affected. Furthermore, Rbm38 deficiency did not affect cardiac remodeling (i.e. hypertrophy, LV dilation and fibrosis) or performance (i.e. fractional shortening) after pressure-overload induced by transverse aorta constriction.\"
    }
  ],
  \"symbol\": \"Rbm38\"
} ]"

I want to convert it to a more user readable format

Code:

_id pubmed  text  symbol    
67196 18667844  Overexpression of UBE2T in NIH3T3 cells significantly promoted colony formation in mouse cell cultures  Ube2t
56190 21764855  loss of RNPC1 in mouse embryonic fibroblasts increased the level of p53 protein, leading to enhanced premature senescence in a p53-dependent manner Rbm38
56190 22371495  a novel mechanism by which HuR is regulated by RNPC1 via mRNA stability and HuR is a mediator of RNPC1-induced growth suppression Rbm38
56190 22508983  knockdown of p73 or p21, another target of RNPC1, attenuates the inhibitory effect of RNPC1 on cell proliferation and premature senescence, whereas combined knockdown of p73 and p21 completely abolishes it  Rbm38
56190 23836903  knockdown of MIC-1 can decrease RNPC1-induced cell growth suppression.  Rbm38
56190 25512531  Rbm38 deficiency markedly decreases the tumor penetrance in mice heterozygous for p53 via enhanced p53 expression Rbm38
56190 28850611  The hearts of Rbm38 -/- mice were mildly hypertrophic, but cardiac function was not affected. Furthermore, Rbm38 deficiency did not affect cardiac remodeling (i.e. hypertrophy, LV dilation and fibrosis) or performance (i.e. fractional shortening) after pressure-overload induced by transverse aorta constriction. Rbm38

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LEARN ABOUT REDHAT

igawk

IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME

       igawk - gawk with include files

SYNOPSIS

       igawk [ all gawk options ] -f program-file [ -- ] file ...
       igawk [ all gawk options ] [ -- ] program-text file ...

DESCRIPTION

       Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).

       AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like

	      @include getopt.awk

       in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.

OPTIONS

       See gawk(1) for a full description of the AWK language and the options that gawk supports.

EXAMPLES

       cat << EOF > test.awk
       @include getopt.awk

       BEGIN {
	    while (getopt(ARGC, ARGV, "am:q") != -1)
		 ...
       }
       EOF

       igawk -f test.awk

SEE ALSO

       gawk(1)

       Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.

AUTHOR

       Arnold Robbins (arnold@skeeve.com).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)