On Thu, Feb 21, 2013 at 2:03 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Thu, Feb 21, 2013 at 6:12 PM, Carlos Borroto
> <carlos.borr...@gmail.com> wrote:
>> On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock <p.j.a.c...@googlemail.com> 
>> wrote:
>>> [*] This is one reason why I've just switched the default BLAST+
>>> output from the standard 12 column output to the extended 24
>>> column output in v0.0.17 of the wrappers:
>>> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
>> Hi Peter,
>> Would you consider adding the option to set a custom tabular output? I
>> would like to be able to select exactly which fields to include. For
>> example the alignment data I rarely need it and if I choose 24 column
>> output I'll be wasting a lot of space by including it.
> Hi Carlos,
> I had deliberately avoid letting users pick the columns - it is
> doable, but has two major downsides. First a more complex
> GUI (if we don't allow the order to change then it is still ~24
> options), and then the worse problem of it being hard to know
> what the output columns are in later work. If the columns are
> consistent, it is much easier to write general instructions (e.g.
> for filtering on percentage identity). If Galaxy let us label the
> columns on the current 'tabular' format, then I'd be more
> positive about this, but until that happens I would prefer not
> to offer arbitrary columns in the BLAST tabular output.

I was thinking more like a text box where an advance user could type
in the strings that would be attached to '-outfmt  "6 ...."'. We could
add as a default value the current strings in tabular 24 to help guide
the user to what is possible. I see your point about this would make
harder to later know what each columns is, but this is an advanced use
and could be labelled as such.

> In the mean time, would you prefer I revert the default to 12
> column tabular output? Just how big are your BLAST files if
> the extra disk space is a serious concern (compared to raw
> sequencing data)?

I'm fine with 24 being the default. In fact I'm currently rerunning a
big blast exactly cause I now realized I needed more information than
what is provided by 12. I'm expecting 25 million hits with HSPs of
300bp. I'm expecting to double or triple the previous output. The
current output is around 2.1gb and the raw sequencing data is 1gb. As
you can see it would be nice to get rid of the alignments if I'm not
using them.

> (Separately I was asking about how to offer automatic datatype
> conversion - that would allow easy conversion of BLAST XML
> or even BLAST archive ASN.1 format into tabular on demand,
> making them viable default output formats from a usability point
> of view - but both of those are larger than the default 12 column
> or even 24 column tabular formats.)

This would be great and I will probably use it for smaller blast jobs.

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