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 BSD

sortbib

SORTBIB(1)						      General Commands Manual							SORTBIB(1)

NAME

       sortbib - sort bibliographic database

SYNOPSIS

       sortbib [ -sKEYS ] database  ...

DESCRIPTION

       Sortbib	sorts files of records containing refer key-letters by user-specified keys.  Records may be separated by blank lines, or by .[ and
       .] delimiters, but the two styles may not be mixed together.  This program reads through each database and pulls out key fields, which  are
       sorted  separately.   The  sorted key fields contain the file pointer, byte offset, and length of corresponding records.  These records are
       delivered using disk seeks and reads, so sortbib may not be used in a pipeline to read standard input.

       By default, sortbib alphabetizes by the first %A and the %D fields, which contain the senior author and date.  The -s  option  is  used	to
       specify	new  KEYS.   For  instance, -sATD will sort by author, title, and date, while -sA+D will sort by all authors, and date.  Sort keys
       past the fourth are not meaningful.  No more than 16 databases may be sorted together at one time.  Records  longer  than  4096	characters
       will be truncated.

       Sortbib	sorts  on  the	last  word  on	the %A line, which is assumed to be the author's last name.  A word in the final position, such as
       ``jr.'' or ``ed.'', will be ignored if the name beforehand ends with a comma.  Authors with two-word last names	or  unusual  constructions
       can  be	sorted	correctly by using the nroff convention ``'' in place of a blank.  A %Q field is considered to be the same as %A, except
       sorting begins with the first, not the last, word.  Sortbib sorts on the last word of the %D line, usually the year.  It also ignores lead-
       ing  articles  (like  ``A''  or ``The'') when sorting by titles in the %T or %J fields; it will ignore articles of any modern European lan-
       guage.  If a sort-significant field is absent from a record, sortbib places that record before other records containing that field.

SEE ALSO

       refer(1), addbib(1), roffbib(1), indxbib(1), lookbib(1)

AUTHORS

       Greg Shenaut, Bill Tuthill

BUGS

       Records with missing author fields should probably be sorted by title.

4.2 Berkeley Distribution					  April 29, 1985							SORTBIB(1)