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[Solved] Insert tabs as delimiter

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Top Forums Shell Programming and Scripting [Solved] Insert tabs as delimiter
# 8  
Old 01-27-2014
Quote:
Originally Posted by ritakadm
The code is working perfectly for a few lines the exits with the error

Code:
awk: rita.awk:9:  (FILENAME=GOdesc_switchgrass_forAgriGO_sortedongenes.txt FNR=471) fatal:  attempt to access field -2147483648

how do I identify FNR=471 ?
Code:
$ awk 'FNR==471' filename

This User Gave Thanks to Akshay Hegde For This Post:
ritakadm
# 9  
Old 01-27-2014
what does the line 471 look like?
Empty line?
# 10  
Old 01-27-2014
It just has the first two columns. sorry, I was not aware of this. can this be dealt with? just make the fields tab separated that is.
# 11  
Old 01-27-2014
Quote:
Originally Posted by ritakadm
It just has the first two columns. sorry, I was not aware of this. can this be dealt with? just make the fields tab separated that is.
Code:
BEGIN {
   OFS="\t"
   nk=split("biological_process cellular_component molecular_function", t, FS)
   for(i in t)
     keys[t[i]]
}
NF < 3 {gsub(FS, OFS); print;next}
{
   f3=frest=""
   for(i=3; !($i in keys); i++)
      f3=(f3)?f3 FS $i:$i

   key=$i

   for(i=i+2; i<=NF; i++)
      frest=(frest)?frest FS $i:$i

   print $1, $2, f3, key, frest
}

This User Gave Thanks to vgersh99 For This Post:
ritakadm
# 12  
Old 01-27-2014
thank you so very much
# 13  
Old 01-27-2014
Try also
Code:
sed -r 's/ /\t/;s/ /\t/;s/ (biological_process|cellular_component|molecular_function) /\t\1\t/' file|
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