-g option break conservative linux sort











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hi I just ran into either a bug or more certainly an error from me.
I am trying to sort a file that has 5 column by three specific column.



I am using -k option.



sort  -k1,1 -k3,3  -k4,4 < abundance_key_60.tsv



SO90    TARA_031_SRF    M00370  0.0004796352593680699   5380.716788521779

SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538

WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574

WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709

WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


Everything work fine then I realised one of my column is numeric and I add the -g option for this column. At this point sort seems to only filter by this column :



sort -k1,1 -k3,3  -gk4,4 <  test_.sort.txt 



SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779

WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593

WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709

WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574

SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538


I try to use -s option but I did not change the results.
any help appreciated!



ps: this is sample from my file that reproduce the bug.



I am on ubuntu 16.04 with default bash and sort for this distribution.






sorting ubuntu gnu-sort







share|improve this question




























    up vote
    0
    down vote

    favorite












    hi I just ran into either a bug or more certainly an error from me.
    I am trying to sort a file that has 5 column by three specific column.



    I am using -k option.



    sort  -k1,1 -k3,3  -k4,4 < abundance_key_60.tsv
    

    
SO90    TARA_031_SRF    M00370  0.0004796352593680699   5380.716788521779
    
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
    
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
    
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
    
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


    Everything work fine then I realised one of my column is numeric and I add the -g option for this column. At this point sort seems to only filter by this column :



    sort -k1,1 -k3,3  -gk4,4 <  test_.sort.txt 
    

    
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
    
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593
    
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
    
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
    
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538


    I try to use -s option but I did not change the results.
    any help appreciated!



    ps: this is sample from my file that reproduce the bug.



    I am on ubuntu 16.04 with default bash and sort for this distribution.






    sorting ubuntu gnu-sort







    share|improve this question


























      up vote
      0
      down vote

      favorite









      up vote
      0
      down vote

      favorite











      hi I just ran into either a bug or more certainly an error from me.
      I am trying to sort a file that has 5 column by three specific column.



      I am using -k option.



      sort  -k1,1 -k3,3  -k4,4 < abundance_key_60.tsv
      

      
SO90    TARA_031_SRF    M00370  0.0004796352593680699   5380.716788521779
      
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
      
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
      
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
      
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


      Everything work fine then I realised one of my column is numeric and I add the -g option for this column. At this point sort seems to only filter by this column :



      sort -k1,1 -k3,3  -gk4,4 <  test_.sort.txt 
      

      
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
      
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593
      
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
      
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
      
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538


      I try to use -s option but I did not change the results.
      any help appreciated!



      ps: this is sample from my file that reproduce the bug.



      I am on ubuntu 16.04 with default bash and sort for this distribution.






      sorting ubuntu gnu-sort







      share|improve this question















      hi I just ran into either a bug or more certainly an error from me.
      I am trying to sort a file that has 5 column by three specific column.



      I am using -k option.



      sort  -k1,1 -k3,3  -k4,4 < abundance_key_60.tsv
      

      
SO90    TARA_031_SRF    M00370  0.0004796352593680699   5380.716788521779
      
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
      
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
      
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
      
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


      Everything work fine then I realised one of my column is numeric and I add the -g option for this column. At this point sort seems to only filter by this column :



      sort -k1,1 -k3,3  -gk4,4 <  test_.sort.txt 
      

      
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
      
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593
      
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
      
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
      
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538


      I try to use -s option but I did not change the results.
      any help appreciated!



      ps: this is sample from my file that reproduce the bug.



      I am on ubuntu 16.04 with default bash and sort for this distribution.






      sorting ubuntu gnu-sort




      sorting ubuntu gnu-sort






      share|improve this question















      share|improve this question













      share|improve this question




      share|improve this question








      edited 2 days ago

























      asked 2 days ago









      RomainL.

      190212




      190212
























          1 Answer
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          You want to specify the g only for -k4,4, like this:



          bash$ sort -k1,1 -k3,3 -k4,4g test_.sort.txt
          
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
          
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
          
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
          
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
          
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


          (Experimentally verified by changing the number to 6.704622779795495E-10 and observing how that changes the sort order. A better test case would contain samples which trivially reveal when you get the correct result.)






          share|improve this answer





















          • perfect thanks just had to add LC_ALL=C for exponential and works like a charm
            – RomainL.
            yesterday











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          You want to specify the g only for -k4,4, like this:



          bash$ sort -k1,1 -k3,3 -k4,4g test_.sort.txt
          
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
          
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
          
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
          
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
          
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


          (Experimentally verified by changing the number to 6.704622779795495E-10 and observing how that changes the sort order. A better test case would contain samples which trivially reveal when you get the correct result.)






          share|improve this answer





















          • perfect thanks just had to add LC_ALL=C for exponential and works like a charm
            – RomainL.
            yesterday















          up vote
          1
          down vote



          accepted










          You want to specify the g only for -k4,4, like this:



          bash$ sort -k1,1 -k3,3 -k4,4g test_.sort.txt
          
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
          
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
          
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
          
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
          
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


          (Experimentally verified by changing the number to 6.704622779795495E-10 and observing how that changes the sort order. A better test case would contain samples which trivially reveal when you get the correct result.)






          share|improve this answer





















          • perfect thanks just had to add LC_ALL=C for exponential and works like a charm
            – RomainL.
            yesterday













          up vote
          1
          down vote



          accepted







          up vote
          1
          down vote



          accepted






          You want to specify the g only for -k4,4, like this:



          bash$ sort -k1,1 -k3,3 -k4,4g test_.sort.txt
          
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
          
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
          
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
          
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
          
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


          (Experimentally verified by changing the number to 6.704622779795495E-10 and observing how that changes the sort order. A better test case would contain samples which trivially reveal when you get the correct result.)






          share|improve this answer












          You want to specify the g only for -k4,4, like this:



          bash$ sort -k1,1 -k3,3 -k4,4g test_.sort.txt
          
SO90    TARA_031_SRF    M00370 0.0004796352593680699    5380.716788521779
          
SO90    TARA_072_MES    M00370  6.704622779795495   889.5003464019538
          
WDU TARA_072_MES    M00165  0.00010342611234558623  1372.1512123790574
          
WDU TARA_046_SRF    M00165  0.00011353279569781544  582.9204804414709
          
WDU TARA_025_DCM    M00165  0.00028966684296873025  2486.7113286682593


          (Experimentally verified by changing the number to 6.704622779795495E-10 and observing how that changes the sort order. A better test case would contain samples which trivially reveal when you get the correct result.)







          share|improve this answer












          share|improve this answer



          share|improve this answer










          answered 2 days ago









          tripleee

          86.8k12121175




          86.8k12121175












          • perfect thanks just had to add LC_ALL=C for exponential and works like a charm
            – RomainL.
            yesterday


















          • perfect thanks just had to add LC_ALL=C for exponential and works like a charm
            – RomainL.
            yesterday
















          perfect thanks just had to add LC_ALL=C for exponential and works like a charm
          – RomainL.
          yesterday




          perfect thanks just had to add LC_ALL=C for exponential and works like a charm
          – RomainL.
          yesterday


















           

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