On Wed, Oct 19, 2011 at 2:31 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi Florent,
> Sorry for the delay.  I did try the patch out shortly after you contributed
> it, but it caused the functional to fail.  I was able to fix the issue and
> allow the existing tests to start passing, but I've been bogged down lately
> and haven't been able to perform a more thorough review of the code. If you
> could provide tests with files (e.g. for the tools affected) that test the
> new functionality, that would be a great help.
> The use of partition removes python compatibility for <2.5, although this is
> a lesser/non-concern.

I guess you could use split, but special case on there being no space.

> Also, I'm not entirely sold on having the "Identifier line" being parsed as
>  "identifier" + <space> + "description" instead a single identifier line.

That is the normal convention, just like with FASTA.

> This would mean that identifiers could not themselves contain spaces,
> but "There is no standardization for identifiers" (so they could technically
> have spaces?). Could two different reads be identified as "Read A" and "Read
> B", but then would no longer be uniquely identifiable as each would then be
> identified as "Read".  If this added functionalilty were introduced as
> optional behavior (e.g. a user needs to click a checkbox on the tools to
> apply the id line splitting), these concerns can be mitigated.

That is expected, "@Read A" and "@Read B" have the same identifier, "Read".

> Peter, Florent, anyone else: I'd be very interested to hear your thoughts on
> the above, particularly in respect to know real-world data. For now, lets
> discount SRA data from this discussion.

See also the new Illumina 1.8 naming convention where they dropped
the /1 and /2 and hit it in the description. It should be tested, but I think
Florent's patch will work here (while the current Galaxy behaviour won't).


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