Blast+: new feature filter/mask... by taxid before job in one task

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Blast+: new feature filter/mask... by taxid before job in one task

Thomas

Hi guys,

We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask … by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the  job will be performed in one task.

However searching in the documentation and the mailing list, I did not find anything about this.
So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration.

We believe this could be of common interest. It would be great if anybody could comment on this. 


Thanks a lot, Thomas

 


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Re: Blast+: new feature filter/mask... by taxid before job in one task

Björn Grüning
Hi Thomas,

are you interested in implementing it on your own?

I'm not an blast expert, so sorry for the question, but is there an
public repository where all unit-counts can be download as
wmasker.obinary format, preferable in the correct folder structure as
described in http://www.ncbi.nlm.nih.gov/books/NBK1763/. Or do you need
to create such files on your own?

What we/you probably can do is to create a new windowmasker.loc file
pointing to each taxid and add a that new parameter to the wrapper.
 
Cheers,
Björn

> Hi guys,
>
> We recently installed NCBI BLAST + to our local Galaxy instance and
> now we need to provide the possibility to filter/mask … by taxon id
> (taxid) using the command line option (-window_masker_taxid) of BLAST
> (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the  job will
> be performed in one task.
>
>
>
> However searching in the documentation and the mailing list, I did not
> find anything about this.
> So it would be great to provide the possibility to subselect by taxid
> (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by
> changing the BLAST integration.
>
> We believe this could be of common interest. It would be great if
> anybody could comment on this.  
>
>
> Thanks a lot, Thomas
>
>  
>
>
> ___________________________________________________________
> 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/



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Re: Blast+: new feature filter/mask... by taxid before job in one task

Peter Cock
In reply to this post by Thomas
On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas
<[hidden email]> wrote:

> Hi guys,
>
> We recently installed NCBI BLAST + to our local Galaxy instance and now we
> need to provide the possibility to filter/mask … by taxon id (taxid) using
> the command line option (-window_masker_taxid) of BLAST (cf.
> http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the  job will be
> performed in one task.
>
> However searching in the documentation and the mailing list, I did not find
> anything about this.
> So it would be great to provide the possibility to subselect by taxid (e.g.
> NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the
> BLAST integration.
>
> We believe this could be of common interest. It would be great if anybody
> could comment on this.
>
>
> Thanks a lot, Thomas


Hi Thomas,

Full support allowing making your own database with taxid
support will be more complicated - but using databases setup
via the *.loc file (e.g. a downloaded copy of the NR database)
ought not to be too complicated. I think we just need to add
another integer parameter under the advanced options to
set the -window_masker_taxid value. Would that be enough
for your needs?

I wrote the NCBI BLAST+ wrappers but this is starting to
turn into a team effort. There is a lot of other work in progress
on extending the Galaxy BLAST+ wrappers further - I'm
setting up a meeting with the other people already working
on this during the GCC2013 - perhaps this should be a listed
BoF session?
http://wiki.galaxyproject.org/Events/GCC2013/BoF

Regards,

Peter

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Re: Blast+: new feature filter/mask... by taxid before job in one task

Thomas
Hi Peter,

We edited the ncbi_blastn_wrapper.xml (attachment) a little bit as you can see and created a taxid_name.loc file for testing by our own. This is what we were thinking of in a very simple way. But if the list spreads out we would like to have textbox for pre-selection above the drop-down-menu like it is in the "edit Attributes" menu if it is possible...

Regards,

Thomas

-----Ursprüngliche Nachricht-----
Von: Peter Cock [mailto:[hidden email]]
Gesendet: Donnerstag, 13. Juni 2013 11:59
An: Berner, Thomas
Cc: [hidden email]
Betreff: Re: [galaxy-dev] Blast+: new feature filter/mask... by taxid before job in one task

On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas <[hidden email]> wrote:

> Hi guys,
>
> We recently installed NCBI BLAST + to our local Galaxy instance and
> now we need to provide the possibility to filter/mask . by taxon id
> (taxid) using the command line option (-window_masker_taxid) of BLAST (cf.
> http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the  job will be
> performed in one task.
>
> However searching in the documentation and the mailing list, I did not
> find anything about this.
> So it would be great to provide the possibility to subselect by taxid (e.g.
> NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing
> the BLAST integration.
>
> We believe this could be of common interest. It would be great if
> anybody could comment on this.
>
>
> Thanks a lot, Thomas

Hi Thomas,

Full support allowing making your own database with taxid support will be more complicated - but using databases setup via the *.loc file (e.g. a downloaded copy of the NR database) ought not to be too complicated. I think we just need to add another integer parameter under the advanced options to set the -window_masker_taxid value. Would that be enough for your needs?

I wrote the NCBI BLAST+ wrappers but this is starting to turn into a team effort. There is a lot of other work in progress on extending the Galaxy BLAST+ wrappers further - I'm setting up a meeting with the other people already working on this during the GCC2013 - perhaps this should be a listed BoF session?
http://wiki.galaxyproject.org/Events/GCC2013/BoF

Regards,

Peter

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ncbi_blastn_wrapper.xml (17K) Download Attachment
taxid_name.loc (194 bytes) Download Attachment
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Re: Blast+: new feature filter/mask... by taxid before job in one task

Peter Cock
Hello again Thomas,

Unfortunately I forgot about your email from last summer - which
was shortly before the GCC2013 conference where we had some
productive discussions about the BLAST+ wrappers, e.g.
http://wiki.galaxyproject.org/Events/GCC2013/BoF

Further replies in-line below...

Peter wrote:

> On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas <[hidden email]> wrote:
>>> Hi guys,
>>>
>>> We recently installed NCBI BLAST + to our local Galaxy instance and
>>> now we need to provide the possibility to filter/mask . by taxon id
>>> (taxid) using the command line option (-window_masker_taxid) of BLAST (cf.
>>> http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the  job will be
>>> performed in one task.
>>>
>>> However searching in the documentation and the mailing list, I did not
>>> find anything about this.
>>> So it would be great to provide the possibility to subselect by taxid (e.g.
>>> NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing
>>> the BLAST integration.
>>>
>>> We believe this could be of common interest. It would be great if
>>> anybody could comment on this.
>>>
>>>
>>> Thanks a lot, Thomas
>>
>>
>> Hi Thomas,
>>
>> Full support allowing making your own database with taxid support will
>> be more complicated - but using databases setup via the *.loc file (e.g.
>> a downloaded copy of the NR database) ought not to be too complicated.

That's done now, and will be in the forthcoming v0.1.0 release of the
Galaxy BLAST wrappers - available for early testing here:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

>> I think we just need to add another integer parameter under the advanced
>> options to set the -window_masker_taxid value. Would that be enough
>> for your needs?
>>
>> I wrote the NCBI BLAST+ wrappers but this is starting to turn into a team
>> effort. There is a lot of other work in progress on extending the Galaxy
>> BLAST+ wrappers further - I'm setting up a meeting with the other people
>> already working on this during the GCC2013 - perhaps this should be a
>> listed BoF session?
>> http://wiki.galaxyproject.org/Events/GCC2013/BoF
>>
>> Regards,
>>
>> Peter

The BLAST+ wrappers have turned into a team effort, managed from
this GitHub repository: https://github.com/peterjc/galaxy_blast/

On Fri, Jun 14, 2013 at 1:59 PM, Berner, Thomas
<[hidden email]> wrote:

> Hi Peter,
>
> We edited the ncbi_blastn_wrapper.xml (attachment) a little bit as you
> can see and created a taxid_name.loc file for testing by our own. This
> is what we were thinking of in a very simple way. But if the list spreads
> out we would like to have textbox for pre-selection above the
> drop-down-menu like it is in the "edit Attributes" menu if it is possible...
>
> Regards,
>
> Thomas

Now we have an issue tracker for the BLAST+ wrappers, I've filed an
enhancement issue on this with notes from your email - I don't think
the negative filtering by taxid would work though:

https://github.com/peterjc/galaxy_blast/issues/36

If you have a GitHub account you are welcome to subscribe to the
issue and comment there - or reply by email.

Regards,

Peter
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