Blast+: new feature filter/mask... by taxid before job in one task
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, 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
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On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas <thomas.berner@jki.bund.de> 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
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:p.j.a.cock@googlemail.com] Gesendet: Donnerstag, 13. Juni 2013 11:59 An: Berner, Thomas Cc: galaxy-dev@lists.bx.psu.edu 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 <thomas.berner@jki.bund.de> 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
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 <thomas.berner@jki.bund.de> 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 <thomas.berner@jki.bund.de> 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
participants (3)
-
Berner, Thomas -
Björn Grüning -
Peter Cock