Pick-you-own columns in BLAST+ tabular output

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Pick-you-own columns in BLAST+ tabular output

Peter Cock
Hello all,

I've mentioned before that a forthcoming update to the BLAST+
Galaxy wrappers would be adding a most customisable output
option with pick-your-own columns. This is available to test now
from the Test Tool Shed, along with other enhancements like
more masking tools and an update to BLAST+ 2.2.29:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

(This will be released as the ncbi_blast_plus wrappers v0.1.0,
and includes recent contributions from Jim Johnson and
Björn Grüning - thank you both):

Previously (for tabular output) we've only offered the standard
12 column output (-outfmt 6), and an extended set which has
grown to currently include 25 columns.

The new custom column mode offers the 12 standard columns,
and the extended set (making 25 columns), plus other (to me
less interesting) identifiers, some other miscellaneous
columns, and the taxonomy columns (44 columns in all):

Inline image 1
Inline image 2

As previously discussed, the list of columns has been grouped
- the first two groups reflect the standard 12 columns and the
columns used in Galaxy's (default) 25 column extended tabular
output.

The remaining columns I have split into three groups (assorted
identifiers, miscellaneous, and taxonomy) which I hope is self
explanatory.

Note that this does not allow you pick the column order - they
will be produced in the order shown. The underlying BLAST+
tools would support this, but the Galaxy GUI would I feel be
too complicated.

Some community testing/comments would be appreciated.

Thanks,

Peter



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Pick-you-own columns in BLAST+ tabular output

Björn Grüning-3
Hi Peter,

> Hello all,
>
> I've mentioned before that a forthcoming update to the BLAST+
> Galaxy wrappers would be adding a most customisable output
> option with pick-your-own columns. This is available to test now
> from the Test Tool Shed, along with other enhancements like
> more masking tools and an update to BLAST+ 2.2.29:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
>
> (This will be released as the ncbi_blast_plus wrappers v0.1.0,
> and includes recent contributions from Jim Johnson and
> Björn Grüning - thank you both):
>
> Previously (for tabular output) we've only offered the standard
> 12 column output (-outfmt 6), and an extended set which has
> grown to currently include 25 columns.
>
> The new custom column mode offers the 12 standard columns,
> and the extended set (making 25 columns), plus other (to me
> less interesting) identifiers, some other miscellaneous
> columns, and the taxonomy columns (44 columns in all):
>
> [image: Inline image 1]
> [image: Inline image 2]
>
> As previously discussed, the list of columns has been grouped
> - the first two groups reflect the standard 12 columns and the
> columns used in Galaxy's (default) 25 column extended tabular
> output.
>
> The remaining columns I have split into three groups (assorted
> identifiers, miscellaneous, and taxonomy) which I hope is self
> explanatory.
>
> Note that this does *not* allow you pick the column order - they
> will be produced in the order shown. The underlying BLAST+
> tools would support this, but the Galaxy GUI would I feel be
> too complicated.

I think that is fine, I can't imagine of any real use case where that is
needed.

> Some community testing/comments would be appreciated.

I tested it briefly on my test instance and it looks all fine and seems
to work :)

Thanks, looking forward to see it in MainTS.
Bjoern


> Thanks,
>
> Peter
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Pick-you-own columns in BLAST+ tabular output

Peter Cock
On Tue, Mar 4, 2014 at 10:35 AM, Björn Grüning
<[hidden email]> wrote:

> Hi Peter,
>
>> Hello all,
>>
>> I've mentioned before that a forthcoming update to the BLAST+
>> Galaxy wrappers would be adding a most customisable output
>> option with pick-your-own columns. This is available to test now
>> from the Test Tool Shed, along with other enhancements like
>> more masking tools and an update to BLAST+ 2.2.29:
>>
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
>>
>> ...
>>
>> Note that this does *not* allow you pick the column order - they
>>
>> will be produced in the order shown. The underlying BLAST+
>> tools would support this, but the Galaxy GUI would I feel be
>> too complicated.
>
>
> I think that is fine, I can't imagine of any real use case where
> that is needed.
>
>>
>> Some community testing/comments would be appreciated.
>
> I tested it briefly on my test instance and it looks all fine and
> seems to work :)
>
> Thanks, looking forward to see it in MainTS.
> Bjoern

Great - thanks. I'm about to update our local production
server, and barring any problems will push this BLAST+
update to the main Tool Shed later this week.

Thanks,

Peter

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Pick-you-own columns in BLAST+ tabular output

Peter Cock
On Tue, Mar 4, 2014 at 12:19 PM, Peter Cock <[hidden email]> wrote:

> On Tue, Mar 4, 2014 at 10:35 AM, Björn Grüning <[hidden email]> wrote:
>> Hi Peter,
>>
>>> Hello all,
>>>
>>> I've mentioned before that a forthcoming update to the BLAST+
>>> Galaxy wrappers would be adding a most customisable output
>>> option with pick-your-own columns. This is available to test now
>>> from the Test Tool Shed, along with other enhancements like
>>> more masking tools and an update to BLAST+ 2.2.29:
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
>>>
>>> ...
>>>
>>>
>>> Some community testing/comments would be appreciated.
>>
>> I tested it briefly on my test instance and it looks all fine and
>> seems to work :)
>>
>> Thanks, looking forward to see it in MainTS.
>> Bjoern
>
> Great - thanks. I'm about to update our local production
> server, and barring any problems will push this BLAST+
> update to the main Tool Shed later this week.

This is now live, with a regression about output formats
caught and fixed:

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

Peter

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/