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Split column using awk in a text file

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# 8  
Old 05-23-2013
Code:
awk '{n=split ($8,TMP,";"); $8=""; for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^SNPEFF/)) {sub (/^.*=/,"",TMP[i]); $8=$8 ($8?"\t":"") TMP[i]}}1' FS="\t"

# 9  
Old 05-23-2013
Quote:
Originally Posted by mehar
. . .
Hi,

The original question is slightly modified with slightly different input in the 8th column. Could you help? Thanks in advance.
Can't see what has been modified. What's going wrong?

BTW - why do you need a one liner?
# 10  
Old 05-23-2013
Ubuntu
In the initial question, 8th column is of type

Code:
chr1	   602567	rs21953190	A	G	5481.77	.
AC=2;AF=1.00;AN=2;DB;DP=152;Dels=0.00;FS=0.000;HaplotypeScore=6.8385;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0=0;QD=36.06;SNPEFF_AMINO_ACID_CHANGE=D1034;SNPEFF_CODON_CHANGE=gaT/gaC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=5;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=ADNP2;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENSCAFT00000000008 1/1:0,151:151:99:5510,430,0

In the modified question, the data is like,
Quote:
chr1 602567 rs21953190 A G 5481.77 . AC=2;AF=1.00;AN=2;DB;DP=152;Dels=0.00;FS=0.000;HaplotypeScore=6.8385;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0 =0;QD=36.06;resource.EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1034|ADNP2|protein_coding|CODING|ENSCAFT00000000008|5) GT:ADSmilieP:GQ:PL 1/1:0,151:151:99:5510,430,0
---------- Post updated at 01:01 PM ---------- Previous update was at 12:27 PM ----------

Anyways i have modified the code and it works now. 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 awk 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?
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