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Re: [PATCH] Add Ribotaper.

From: Ricardo Wurmus
Subject: Re: [PATCH] Add Ribotaper.
Date: Sat, 9 Jul 2016 21:43:44 +0200
User-agent: mu4e 0.9.16; emacs 24.5.1

Ben Woodcroft <address@hidden> writes:

>> I think in the ribotaper/bedtools case we should just name the variable
>> “bedtools-2.18”  and make it public.
> I agree with should call it 'bedtools-2.18' and make it public (but with 
> a comment explaining why the old version is kept), just as in e.g. 
> 'python-flake8-2.2.4'.
> Are you suggesting we keep bedtools-2.18 even if ribotaper updates to a 
> newer version? I thought accepted practice was to delete old packages 
> when they are no longer needed.

No, I agree.  We keep bedtools-2.18 as long as it’s needed for

> The patch LGTM otherwise, except that I would unpack 'ORF' and use the 
> term 'ribo-seq' in the description. I've never looking at ribo-seq data 
> before and I'm not familiar, so I wasn't sure what 'ribosome profiling' 
> meant exactly e.g. is it measuring the amount of ribosome in a cell? I 
> realise that isn't true, just illustrating the point. Perhaps I am too 
> naive.

I don’t know how to naturally include the term “ribo-seq”, so how about
simply this:

   Ribotaper is a method for defining translated @dfn{open reading
   frames} (ORFs) using ribosome profiling (ribo-seq) data.  This
   package provides the Ribotaper pipeline.

Is this better?

~~ Ricardo

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