[Gmod-tripal-devel] Programmatically importing BLAST XML into Tripal

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[Gmod-tripal-devel] Programmatically importing BLAST XML into Tripal

Mara Kim-2
Hi guys,

Is it possible to have BLAST results be imported programmatically?  I have a system that does a lot of BLAST and it would be very time consuming to manually import each result.  Is there a PHP function that can pass in a file for import?

--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: [Gmod-tripal-devel] Programmatically importing BLAST XML into Tripal

Stephen Ficklin-2
Hi Mara,

There is not an official 'API' function in the Tripal Analysis Blast
module to do it.  But, you can use the function
tripal_analysis_blast_parseXML() (line #149 of
tripal_analysis_blast.xml_parser.inc file).  So long as you provide the
proper arguments it should work.   It would not be hard to create a
proper API function with arguments that follow the API style.   We could
even add a drush command to do it so they can be imported from the
command-line if desired.

If you want to talk a bit more about a design that would facilitate your
needs let us know.  Perhaps it's something we could also address in our
Tripal Developer's meeting next Tuesday.

Stephen

On 10/1/2014 2:32 PM, Mara Kim wrote:

> Hi guys,
>
> Is it possible to have BLAST results be imported programmatically?  I
> have a system that does a lot of BLAST and it would be very time
> consuming to manually import each result.  Is there a PHP function
> that can pass in a file for import?
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN


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Re: [Gmod-tripal-devel] Programmatically importing BLAST XML into Tripal

Mara Kim-2
That sounds great, especially the drush command.

While we are on the subject, would it be possible to add a drush command to create organism and feature pages?  Or at the very least, are there functions for those as well?

On Wed, Oct 1, 2014 at 2:30 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

There is not an official 'API' function in the Tripal Analysis Blast module to do it.  But, you can use the function tripal_analysis_blast_parseXML() (line #149 of tripal_analysis_blast.xml_parser.inc file).  So long as you provide the proper arguments it should work.   It would not be hard to create a proper API function with arguments that follow the API style.   We could even add a drush command to do it so they can be imported from the command-line if desired.

If you want to talk a bit more about a design that would facilitate your needs let us know.  Perhaps it's something we could also address in our Tripal Developer's meeting next Tuesday.

Stephen


On 10/1/2014 2:32 PM, Mara Kim wrote:
Hi guys,

Is it possible to have BLAST results be imported programmatically?  I have a system that does a lot of BLAST and it would be very time consuming to manually import each result.  Is there a PHP function that can pass in a file for import?

--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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