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Modify text file using awk

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# 8  
Old 05-23-2013
Please use code tags in lieu of quote tags!

Try this:
Code:
awk     '       {n  = split ($8,TMP,";")
                 $8 = ""
                 for (i=1; i<=n; i++)
                    if (match (TMP[i], /^DP=|^MQ=|^resource.EFF/))
                        {sub  (/^.*=/, "", TMP[i])
                         gsub (/[()\|]+/, " ", TMP[i])
                         $8=$8 ($8?"\t":"") TMP[i]
                        }
                }
         1
        '  FS="\t" file
chr1 412573 . A C 2758.77 . 71    58.36    INTERGENIC MODIFIER  GT:ADP:GQ:PL 1/1:0,71:71:99:2787,214,0 GATKSAM
       
chr1 602567 rs21953190 A G 5481.77 . 152    59.09    SYNONYMOUS_CODING LOW SILENT gaT/gaC D1034 ADNP2 protein_coding CODING ENSCAFT00000000008 5  GT:ADP:GQ:PL 1/1:0,151:151:99:5510,430,0 GATKSAM

# 9  
Old 05-23-2013
Ubuntu
Thanks, i have the similar fix which is doing what i need. Here is the code.

Code:
awk 'BEGIN{OFS="\t"}{n=split ($8,TMP,";"); $8=""; for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^resource.EFF=/)) {sub (/^.*=/, "" ,TMP[i]); $12=$12 ($12?"\t":"") TMP[i]} {gsub("[\\|()]", "\t")}}1' file

But i have a new problem,

Code:
chr1	    901534	rs21932296	   T	G	34.77	0/1:3,2:5:63:63,0,64	GATKSAM	5	55.21	INTRON	MODIFIER				CTDP1	protein_coding	CODING	ENSCAFT00000000012	11

If we observe after MODIFIER i have a series of empty tabs. When i am piping this input to another awk command to perform s0me other action with the command,
Code:
awk 'BEGIN{OFS="\t"}{split ($7,TMP,":"); $7= TMP[1]}1'

it is replacing multiple empty tabs into a single tab and gives the output like below:

Code:
chr1	    901534	rs21932296	  T	G	34.77	 0/1	GATKSAM	5	55.21	INTRON	MODIFIER	CTDP1	protein_coding	CODING	ENSCAFT00000000012	11


I don't want the multiple tabs to be replaced by single tab. Could you help where im going wrong?
Last edited by mehar; 05-23-2013 at 03:48 PM..
# 10  
Old 05-23-2013
Assigning to/modifying any field will make awk reevaluate $0, eliminating empty fields. I don't know how to circumvent that, except by running through all the fields and assign a space to all empty ones - not sure that will work, btw.
# 11  
Old 05-23-2013
Quote:
Originally Posted by mehar
Thanks, i have the similar fix which is doing what i need. Here is the code.

Code:
awk 'BEGIN{OFS="\t"}{n=split ($8,TMP,";"); $8=""; for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^resource.EFF=/)) {sub (/^.*=/, "" ,TMP[i]); $12=$12 ($12?"\t":"") TMP[i]} {gsub("[\\|()]", "\t")}}1' file

But i have a new problem,

Code:
chr1	    901534	rs21932296	   T	G	34.77	0/1:3,2:5:63:63,0,64	GATKSAM	5	55.21	INTRON	MODIFIER				CTDP1	protein_coding	CODING	ENSCAFT00000000012	11

If we observe after MODIFIER i have a series of empty tabs. When i am piping this input to another awk command to perform s0me other action with the command,
Code:
awk 'BEGIN{OFS="\t"}{split ($7,TMP,":"); $7= TMP[1]}1'

it is replacing multiple empty tabs into a single tab and gives the output like below:

Code:
chr1	    901534	rs21932296	  T	G	34.77	 0/1	GATKSAM	5	55.21	INTRON	MODIFIER	CTDP1	protein_coding	CODING	ENSCAFT00000000012	11


I don't want the multiple tabs to be replaced by single tab. Could you help where im going wrong?
You're just setting the output field separator to tab, you also need to set the input field separator. Change: BEGIN{OFS="\t"} to: BEGIN{FS=OFS="\t"}.
# 12  
Old 05-23-2013
Well!! I have tried that too, it still gives the same output.

---------- Post updated at 02:05 PM ---------- Previous update was at 01:59 PM ----------

Okay. Then could you help to do in the following way.

Code:
chr1	758630	.	T	TC	2221.73	.	AC=2;AF=1.00;AN=2;DP=61;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.14;MQ0=0;QD=36.42;RPA=1,2;RU=C;STR;resource.EFF=INTRON(MODIFIER||||PQLC1|protein_coding|CODING|ENSCAFT00000000011|2)	GT:AD:DP:GQ:PL	1/1:0,55:61:99:2259,165,0	GATKSAM

Could you modify the code given, such that it transforms in the following way:

Code:
chr1	758630	.	T	TC	2221.73	.	61 51.14 INTRON MODIFIER NA  NA   NA PQLC1 protein_coding CODING ENSCAFT00000000011 2	GT:AD:DP:GQ:PL	1/1:0,55:61:99:2259,165,0	GATKSAM

i.e replacing the empty fields in between |||| with NA?
# 13  
Old 05-23-2013
Why don't you extend your similar fix in post#9 to what you require above? Should be easily doable.
# 14  
Old 05-23-2013
Sorry if i have put some stupid questions. I have tried doing that but couldn't find the logic as im novice in using awk.
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