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Full Discussion: Inconsistent results using sort function
Top Forums UNIX for Beginners Questions & Answers Inconsistent results using sort function Post 303027265 by aberg on Wednesday 12th of December 2018 04:17:55 PM
Old 12-12-2018
Inconsistent results using sort function
Could you please advise on the following: I have two space-delimited files with 9 and 10 columns, respectively, with exactly the same values in column 1. However, the order of column 1 differs between the two files, so I want to sort both files by column 1, so that I can align them and concatenate them into a 19 column file.


If I want to sort by column 1, I usually use "sort -k 1,1 -g". I have done this hundreds of times and I have never had a problem with it.
This is the first time ever that the sort function has given a different output for the two files, despite using identical commands:

Code:
sort -k 1,1 -g file1.txt | head

rs1000000 12 126890980 G A 0.772687 0.999152 -6.53289e-05 0.000341777  
rs10000003 4 57561647 A G 0.298872 0.997534 -0.000308206 0.000313536 
rs10000005 4 85161558 G A 0.468352 0.994261 0.000392384 0.000287513 
rs10000010 4 21618674 T C 0.517001 0.986406 -0.000387116 0.000288364  
rs10000011 4 138223055 C T 0.957162 0.987603 -0.000466108 0.000710431  
rs10000012 4 1357325 C G 0.85952 0.999131 -0.000544182 0.000412222  
rs10000017 4 84778125 C T 0.777348 0.989758 0.00024644 0.000345697  
rs10000018 4 100458448 A G 0.707724 0.999129 -5.96813e-05 0.000315027  
rs10000021 4 159441457 G T 0.185355 0.99682 0.000127756 0.000369005  
rs1000002 3 183635768 C T 0.513401 1 -0.000269255 0.000286993 3.5E-01

and

Code:
sort -k 1,1 -g file2.txt | head 

rs10000003 G A 0.707825 1.010846 0.015580 0.980310 1.042333 0.490663
rs10000005 A G 0.550104 0.988740 0.014283 0.960744 1.017551 0.439681
rs1000000 G A 0.780117 0.987172 0.017380 0.953108 1.022454 0.471168 
rs10000010 C T 0.503288 1.009101 0.014611 0.980464 1.038574 0.537391 
rs10000011 C T 0.950554 0.997444 0.026380 0.945740 1.051976 0.924913 
rs10000012 C G 0.866931 0.966905 0.021645 0.924482 1.011276 0.141498 
rs10000017 C T 0.791953 1.003966 0.019870 0.965021 1.044483 0.844517 
rs10000018 A G 0.699162 1.006137 0.014434 0.977846 1.035245 0.674194 
rs10000021 T G 0.827782 0.991092 0.021206 0.949529 1.034474 0.682292 
rs10000023 T G 0.579281 1.024738 0.014014 0.997270 1.052962 0.077937

Why is this happening despite identical commands? I'm especially puzzled because I have never encountered this before.

Thank you for any advice.

aberg
 

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LEARN ABOUT NETBSD

comm

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

NAME

     comm -- select or reject lines common to two files

SYNOPSIS

     comm [-123f] 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.

     -f      Fold case in line comparisons.

     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.

     comm assumes that the files are lexically sorted; all characters participate in line comparisons.

EXIT STATUS

     comm exits 0 on success, >0 if an error occurred.

SEE ALSO

     cmp(1), diff(1), sort(1), uniq(1)

STANDARDS

     The comm utility conforms to IEEE Std 1003.2-1992 (``POSIX.2'').

BSD
								   June 6, 1993 							       BSD
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