Modify text file using awk Post: 302811163

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Top Forums Shell Programming and Scripting Modify text file using awk Post 302811163 by mehar on Thursday 23rd of May 2013 07:10:25 AM

05-23-2013

Registered User

Modify text file using awk

Quote:

chr1 412573 . A C 2758.77 . AC=2;AF=1.00;AN=2;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=2.8822;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;Q D=38.86;resource.EFF=INTERGENIC(MODIFIER||||||||) GT:AD Smilie

P:GQ:PL 1/1:0,151:151:99:5510,430,0 GATKSAM

I have text file with lines as shown here. Each row has 11 columns separated by tab. In each row, i want to split the 8th column such that the output should look like shown below. Here value in the 9th column is DP value and in the 10th column is MQ value followed by the values after resource.EFF=.

Quote:

chr1 412573 . A C 2758.77 . 71 58.36 INTERGENIC MODIFIER GT:AD Smilie

P: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:AD Smilie

P:GQ:PL 1/1:0,151:151:99:5510,430,0 GATKSAM

Which means the 8th column has to be cleaned up such that, it has only DP value, MQ value and the information after resource.EFF= separated by tabs.

Could anyone help?

mehar

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db2_field_scale

DB2_FIELD_SCALE(3)							 1							DB2_FIELD_SCALE(3)

db2_field_scale - Returns the scale of the indicated column in a result set

SYNOPSIS

       int db2_field_scale (resource  $stmt, mixed  $column)

DESCRIPTION

	Returns the scale of the indicated column in a result set.

PARAMETERS

	      o $stmt
		- Specifies a statement resource containing a result set.

	      o $column
		-  Specifies  the  column in the result set. This can either be an integer representing the 0-indexed position of the column, or a
		string containing the name of the column.

RETURN VALUES

	Returns an integer containing the  scale  of  the  specified  column.  If  the	specified  column  does  not  exist  in  the  result  set,
       db2_field_scale(3) returns FALSE.

SEE ALSO

       db2_field_display_size(3), db2_field_name(3), db2_field_num(3), db2_field_precision(3), db2_field_type(3), db2_field_width(3).

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