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Top Forums Shell Programming and Scripting selecting specific fields in a file (maybe with sed?) Post 302491295 by menenuh on Thursday 27th of January 2011 05:57:02 AM
Old 01-27-2011
selecting specific fields in a file (maybe with sed?)

Hi,

I have a file with following lines:
Code:
chr1    10   AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.00;MQ0=0;QD=14.33;SB=-10.01
chrX    18   AB=0.52;AC=1;AF=0.50;AN=2;DP=203;DS;Dels=0.00;HRun=0;HaplotypeScore=20.01;MQ=15.63;MQ0=85;QD=12.80;SB=-1289.58

I need to extract 4 fields from these lines, the 1st and 2nd column, and AF and DP values. I could have used cut command if AF and DP were printed in the same order, but this is not the case.

I think forming columns (by separating the 3rd line) and removing any column not containing AF or DP would be a nice solution, but I am not an expert on sed. I tried a couple of commands, but to no avail.

Last edited by Yogesh Sawant; 01-27-2011 at 07:45 AM.. Reason: added code tags
 

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COMM(1) 						    BSD General Commands Manual 						   COMM(1)

NAME
comm -- select or reject lines common to two files SYNOPSIS
comm [-123i] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which should be sorted lexically, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. The filename ``-'' means the standard input. The following options are available: -1 Suppress printing of column 1. -2 Suppress printing of column 2. -3 Suppress printing of column 3. -i Case insensitive comparison of lines. Each column will have a number of tab characters prepended to it equal to the number of lower numbered columns that are being printed. For example, if column number two is being suppressed, lines printed in column number one will not have any tabs preceding them, and lines printed in column number three will have one. The comm utility assumes that the files are lexically sorted; all characters participate in line comparisons. ENVIRONMENT
The LANG, LC_ALL, LC_COLLATE, and LC_CTYPE environment variables affect the execution of comm as described in environ(7). EXIT STATUS
The comm utility exits 0 on success, and >0 if an error occurs. SEE ALSO
cmp(1), diff(1), sort(1), uniq(1) STANDARDS
The comm utility conforms to IEEE Std 1003.2-1992 (``POSIX.2''). The -i option is an extension to the POSIX standard. HISTORY
A comm command appeared in Version 4 AT&T UNIX. BUGS
Input lines are limited to LINE_MAX (2048) characters in length. BSD
January 26, 2005 BSD
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