[Emacs-bug-tracker] bug#8067: closed (sort fails to sort completely, due to "similar" keys.)

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Your message dated Thu, 17 Feb 2011 22:51:47 +0100
with message-id <address@hidden>
and subject line Re: bug#8067: sort fails to sort completely, due to "similar" 
keys.
has caused the GNU bug report #8067,
regarding sort fails to sort completely, due to "similar" keys.
to be marked as done.

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8067: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=8067
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> --- Begin Message ---
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> Subject: 
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> sort fails to sort completely, due to "similar" keys.
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> Date: 
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> Thu, 17 Feb 2011 15:46:16 -0500
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> Howdy,
>
> (note: I know I should give you version information with this, but (1)  
> I am not sure that this message will be read by anyone, and (2) I  
> think the problem probably transcends versions.  If I get a response  
> and the actual version is important, I will take the time to find it.)
>
> I have a file of genomic short sequence info in which it so happens  
> that two of my sort key values are similar.  The two keys are
>         HWI-ST407_110127_0082_A80L25ABXX:5:2:11746:46371#0/1
>         HWI-ST407_110127_0082_A80L25ABXX:5:21:17464:6371#0/1
> As you can see, these are identical if one removes the colons.
>
> Unfortunately, I have a file with something on the order of 4 million  
> lines, and there are roughly a dozen lines with each of these keys.  I  
> am using sort with the intent of collecting the lines for each key  
> together.  (I don't really care about ordering, I just need to group  
> lines with the same key together to facilitate downstream  
> processing).  The unfortunate part is that sort considers the two keys  
> as equal.  And so it fails to create the grouping I need.
>
> I have tried several different options but none seem to work.  -d  
> seems to be the default, and it has the behavior indicated above.  -n  
> fails completely.  -g also fails.  Reading the man page, I don't see  
> any other options to control the comparison function.  I have also  
> tried massaging my file prior to piping into sort, replacing colons  
> with other characters (e.g. underscore or tilde) but with no success.
>
> I understand *why* -d considers these two keys equal.  What I don't  
> understand is why there is no option that says "order them  
> lexicographically".
>
> Is there a hidden sort option that will do what I need?
>
> About the only way I can think to force sort to actually sort on such  
> a key is to pre-process the file and replace the keys with a hash code  
> (rendered with nothing but A-Z).  But this introduces additional  
> issues, such as maintaining a table so I can convert the keys back  
> after sorting, and making sure my hash is unique, etc. etc.
>
> I'm pretty sure I'm not the first person to run into this problem.
>
> Thanks for any help or advice.
> Bob H
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> --- Begin Message ---
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> Subject: 
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> Re: bug#8067: sort fails to sort completely, due to "similar" keys.
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> Date: 
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> Thu, 17 Feb 2011 22:51:47 +0100
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> Eric Blake wrote:
> ...
> >> I'm pretty sure I'm not the first person to run into this problem.
> >
> > You're not.  It's a FAQ:
> >
> > http://www.gnu.org/software/coreutils/faq/#Sort-does-not-sort-in-normal-order_0021
>
> Thanks for replying, Eric.
> I'm marking this ticket as closed.
>
>
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