Numbering by field Post: 302925629

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Top Forums Shell Programming and Scripting Numbering by field Post 302925629 by cmccabe on Tuesday 18th of November 2014 10:09:58 AM

11-18-2014

Registered User

I seem to be getting the below error with the code. Thank you Smilie

Code:

awk -f exon.awk
awk: exon.awk:2: awk 'BEGIN { prev="";cur="";cursign="";prevsign="";}
awk: exon.awk:2: ^ invalid char ''' in expression
awk: exon.awk:2: awk 'BEGIN { prev="";cur="";cursign="";prevsign="";}
awk: exon.awk:2: ^ syntax error

exon.awk

Code:

 #!/bin/awk -f
awk 'BEGIN { prev="";cur="";cursign="";prevsign="";}
{
if($5!="")
cursign=$5;
cur=$4;
#print "prev =" prev " cur= " cur " cursign= " cursign " prevsign=" prevsign
if($5=="-")
        {
        if(cur!=prev)
                {
  if(prevsign=="+" || prevsign=="")
   {
   i=1; 
   a[i]=$0
   }
  else
   {  
   k=i;
   for(j=1;j<=k;j++)
    {
    print a[j] " " i
    i=i-1;
    }
                 i=1;
   a[i]=$0
                 }
  }
        else
                {
  i=i+1
  a[i]=$0
                }
  prev=cur;
        }
if($5=="+")
        {
        if(cur!=prev)
                {
  if(prevsign=="-" || prevsign=="")
     {
   k=i;
   for(j=1;j<=k;j++)
    {
    print a[j] " " i
    i=i-1;
    }
   i=1;
                 print $0 " " i
   } 
  else
   {
                 i=1;
                 print $0 " " i
                 }
  }
        else
                {
                i=i+1
                print $0 " " i
                }
prev=cur;
 }
prevsign=$5;
}
END { 
if(cursign=="-")
 {
   k=i;
   for(j=1;j<=k;j++)
    {
    print a[j] " " i
    i=i-1;
    }
 }
}
' output.txt > exon_number.txt

Last edited by Don Cragun; 11-18-2014 at 02:17 PM.. Reason: Get rid of extraneous SIZE tags.

cmccabe

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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)

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