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Bug#629641: ITP: filo -- FILe and stream Operations

June 08th, 2011 - 07:10 am ET by Charles Plessy | Report spam
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Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

Package name : filo
Version : 1.1.0
Upstream Author : Aaron Quinlan, University of Virginia; Assaf Gordon, Cold Spring Harbor Laboratories
URL : https://github.com/arq5x/filo
License : GPL-2.0
Programming Lang: C++
Description : FILe and stream Operations

The following tools are available as part of the filo package:
.
groupBy is a useful tool that mimics the "groupBy" clause in database
systems.
.
shuffle will randomize the order of lines in a file. In other words,
if you have a sorted file, shuffle will undo the sort.
.
stats is a small utility for computing descriptive statistic on a
given column of a tab-delimited file or stream.

groupBy is a command that was formerly part of the BEDtools package
for bioinformatics, very recently accepted in Debian, and that its
users will probably miss if it is not available.



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#1 Andrey Rahmatullin
June 08th, 2011 - 08:00 am ET | Report spam

On Wed, Jun 08, 2011 at 08:02:34PM +0900, Charles Plessy wrote:
shuffle will randomize the order of lines in a file. In other words,
if you have a sorted file, shuffle will undo the sort.


sort -R
Also, biosquid package contains /usr/bin/shuffle.

stats is a small utility for computing descriptive statistic on a
given column of a tab-delimited file or stream.


I think this binary name is too generic.

WBR, wRAR






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#2 The Fungi
June 08th, 2011 - 07:00 pm ET | Report spam
On Wed, Jun 08, 2011 at 05:53:06PM +0600, Andrey Rahmatullin wrote:
On Wed, Jun 08, 2011 at 08:02:34PM +0900, Charles Plessy wrote:
> shuffle will randomize the order of lines in a file. In other
> words, if you have a sorted file, shuffle will undo the sort.
sort -R


[...]

Also worth noting is that /usr/bin/shuf in coreutils is
traditionally used to this end as well.
{ IRL(Jeremy_Stanley); WWW(http://fungi.yuggoth.org/); PGP(43495829);
WHOIS(STANL3-ARIN); SMTP(); FINGER();
MUD(:6669); IRC(#ccl);
ICQ(114362511); YAHOO(crawlingchaoslabs); AIM(dreadazathoth); }



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#3 Charles Plessy
June 08th, 2011 - 08:10 pm ET | Report spam
Le Wed, Jun 08, 2011 at 10:54:53PM +0000, The Fungi a écrit :
On Wed, Jun 08, 2011 at 05:53:06PM +0600, Andrey Rahmatullin wrote:
> On Wed, Jun 08, 2011 at 08:02:34PM +0900, Charles Plessy wrote:
> > shuffle will randomize the order of lines in a file. In other
> > words, if you have a sorted file, shuffle will undo the sort.
> sort -R
[...]

Also worth noting is that /usr/bin/shuf in coreutils is
traditionally used to this end as well.



Thanks for your comments. I have presented Upstream the classical approaches
of Debian with too generic command names (wrapper, renaming,
/usr/lib/<package>), and asked him what shuffle does, that alternatives do not.

Have a nice day,

Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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