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[Solved] Insert tabs as delimiter

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# 1  
Old 01-27-2014
[Solved] Insert tabs as delimiter
Hello all,

I have an unstructured file with space as delimiter , which I want to structure.

The output file should actually have only 5 columns with tab as delimiter.
The 4th column can have only 3 values ( biological_process , cellular_component , molecular_function )

Here is how the input structure is (with only space as delimiter).
Col 1,2 and 4 are just one word, col 3 and 5 can have multiple words delimited by space. The keywords in col 4 viz. biological_process , cellular_component , molecular_function separate col 3 from col 5.

Sample input
Code:
goterm1_oneword gene1_oneword some description multiple words biological_process some description multiple words
goterm2_oneword gene1_oneword some description biological_process some description multiple words
goterm2_oneword gene1_oneword some description multiple words cellular_component  some description multiple words

Output format with tab delimiter, I have placed a [tab] where there should be an actual
Code:
\t

instead of space.
Code:
goterm1_oneword[tab]gene1_oneword[tab]some description multiple words[tab]biological_process[tab]some description multiple words
goterm2_oneword[tab]gene1_oneword[tab]some description multiple words[tab]biological_process[tab]some description multiple words
goterm2_oneword[tab]gene1_oneword[tab]some description multiple words[tab]cellular_component[tab]some description multiple words

# 2  
Old 01-27-2014
Code:
tr ' ' '\t' < inputfile

# 3  
Old 01-27-2014
Quote:
Originally Posted by anbu23
Code:
tr ' ' '\t' < inputfile

This is not as simple as replacing space with tab, col 3 and col 5 have spaces within.

Anything between col2 and col4 is col3... and anything after col4 is col5..if this makes is easier to understand.
# 4  
Old 01-27-2014
Hello,

Following may help you in same.

Code:
awk '{$2=" "$2} {$3=" "$3" "$4" "$5" "$6} {$4==""} {$5==""} {$6==""} gsub(/ /,"\t",$0);{print}' file_name

Output wil be as follows.


Code:
goterm1_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   biological_process      some  description      multiple        words
goterm1_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   biological_process      some  description      multiple        words
goterm2_oneword         gene1_oneword           some    description     biological_process      some    description     biological_process      some    description   multiple words
goterm2_oneword         gene1_oneword           some    description     biological_process      some    description     biological_process      some    description   multiple words
goterm2_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   cellular_component      some  description      multiple        words
goterm2_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   cellular_component      some  description      multiple        words



EDIT:

please let us know the expected Output with proper info it will help us more to understand the same please.



Thanks,
R. Singh
Last edited by RavinderSingh13; 01-27-2014 at 01:27 PM..
# 5  
Old 01-27-2014
Hi Ravinder,

Col 4 should be determined by the keywords biological_process , cellular_component , molecular_function , without that it is not possible to isolate col3 because it can have variable number of words.

---------- Post updated at 01:46 PM ---------- Previous update was at 01:28 PM ----------

Code:
goterm1_oneword gene1_oneword description of gene biological_process this should be col 5 

goterm2_oneword gene1_oneword gene description biological_process col 5 

goterm2_oneword gene1_oneword describing the gene product multiple words cellular_component  col 5 this is

Output

Code:
goterm1_oneword[tab]gene1_oneword[tab]description of gene[tab]biological_process[tab]this should be col 5 

goterm2_oneword[tab]gene1_oneword[tab]gene description[tab]biological_process[tab]col 5 

goterm2_oneword[tab]gene1_oneword[tab]describing the gene product multiple words[tab]cellular_component[tab]col 5 this is

---------- Post updated at 01:48 PM ---------- Previous update was at 01:46 PM ----------

Quote:
Originally Posted by RavinderSingh13
Hello,

Following may help you in same.

Code:
awk '{$2=" "$2} {$3=" "$3" "$4" "$5" "$6} {$4==""} {$5==""} {$6==""} gsub(/ /,"\t",$0);{print}' file_name

Output wil be as follows.


Code:
goterm1_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   biological_process      some  description      multiple        words
goterm1_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   biological_process      some  description      multiple        words
goterm2_oneword         gene1_oneword           some    description     biological_process      some    description     biological_process      some    description   multiple words
goterm2_oneword         gene1_oneword           some    description     biological_process      some    description     biological_process      some    description   multiple words
goterm2_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   cellular_component      some  description      multiple        words
goterm2_oneword         gene1_oneword           some    description     multiple        words   description     multiple        words   cellular_component      some  description      multiple        words

EDIT:

please let us know the expected Output with proper info it will help us more to understand the same please.



Thanks,
R. Singh
I have modified the input and output if that helps understand better, thanks
# 6  
Old 01-27-2014
something along these lines...
awk -f rita.awk myFile
rita.awk:
Code:
BEGIN {
   OFS="\t"
   nk=split("biological_process cellular_component molecular_function", t, FS)
   for(i in t)
     keys[t[i]]
}
{
   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
# 7  
Old 01-27-2014
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 ?
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