Collapsing and counting by key column in a sorted file Post: 302537146

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Top Forums Shell Programming and Scripting Collapsing and counting by key column in a sorted file Post 302537146 by mirni on Thursday 7th of July 2011 08:11:44 AM

07-07-2011

Registered User

The deal with associative arrays in awk is that they come out in pretty much unpredictable order, not in the order they were being added to the structure. So, if you care to have the order of entries kept the same, you have to use something like you see there -- an auxilliary array (i) that stores the keys ($1):

Code:

i[cnt++]=$1;

Then, you can retrieve the original order, by sorting this aux array, and thus you'll get the original order of keys.
Hope this makes sense, if you want more, just look up associative arrays in awk.

Perhaps there would be a different way to approach the problem, without the use of as. arrays, and use the fact that they are sorted already....

Like this:

Code:

awk '
  $1==last{
    third=third","$3; 
    fourth=fourth","$4; 
    cnt++
  }
  $1!=last{
    if(last)
       print last" "second" "third" "fourth" "cnt; 
    last=$1; 
    second=$2; 
    third=$3; 
    fourth=$4;
    cnt=1;
}' mappings.txt
HWI-EA332_0036:5:100:10131:16361#ATGC/1 GACTTGAGGTCTCCCCCGCA 1,1,1,1 TZRTMR_40497:317:+,YSXAZZ_40497:317:+,AZZOL148119:523:+,VCXT148119:523:+ 4
HWI-EA332_0036:5:100:10554:9799#ATGC/1 GACTCCTAAATTAACAACAA 1,1 YSXAZZ_35135:573:+,TZRTMR_35135:573:+ 2
HWI-EA332_0036:5:100:10791:13901#ATGC/1 GACTAGTGAGTGACCCGCTC 1,1 TZRTMR_7034:497:+,YSXAZZ_7034:497:+ 2
HWI-EA332_0036:5:100:11825:11517#ATGC/1 GACTAATATAAATAAGTCTC 1,1,1,1 YSXAZZ_3676:148:+,TZRTMR_3676:148:+,TZRTMR_2085:139:+,YSXAZZ_2085:139:+ 4
HWI-EA332_0036:5:100:13509:3643#ATGC/1 GACTACCCGCCAAACCCCAG 2,2 YTTSTZ_566255:526:-,YYTWQ_566255:526:- 2

Last edited by mirni; 07-07-2011 at 09:24 AM..

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LEARN ABOUT FREEBSD

comm

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, lines only in file1.

     -2      Suppress printing of column 2, lines only in file2.

     -3      Suppress printing of column 3, lines common to both.

     -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.

BSD
								 December 12, 2009							       BSD