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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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comm(1) 							   User Commands							   comm(1)

NAME
comm - select or reject lines common to two files SYNOPSIS
comm [-123] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating sequence of the original lines. If not, the results are unspecified. OPTIONS
The following options are supported: -1 Suppresses the output column of lines unique to file1. -2 Suppresses the output column of lines unique to file2. -3 Suppresses the output column of lines duplicated in file1 and file2. OPERANDS
The following operands are supported: file1 A path name of the first file to be compared. If file1 is -, the standard input is used. file2 A path name of the second file to be compared. If file2 is -, the standard input is used. USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). EXAMPLES
Example 1: Printing a list of utilities specified by files If file1, file2, and file3 each contain a sorted list of utilities, the command example% comm -23 file1 file2 | comm -23 - file3 prints a list of utilities in file1 not specified by either of the other files. The entry: example% comm -12 file1 file2 | comm -12 - file3 prints a list of utilities specified by all three files. And the entry: example% comm -12 file2 file3 | comm -23 -file1 prints a list of utilities specified by both file2 and file3, but not specified in file1. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were successfully output as specified. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.10 3 Mar 2004 comm(1)
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