question about pipeline output

[Roxanne]

The pipeline splits the incoming fasta, and then ends up producing one bsml file for each sequence. Is there a component I can use to join them to create one bsml  or gff file?
Thanks,

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
[hidden email]
[phone]





------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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[Joshua Orvis]

Roxanne -

It's a bit hard to answer that question without knowing what component is in your pipeline that's creating the BSML.  There is a bsml2gff3 component in Ergatis you could try, but it probably supports a specific subset of features that could be encoded in the BSML.

Joshua

On Wed, Sep 21, 2011 at 4:30 PM, Roxanne Tapia <[hidden email]> wrote:

The pipeline splits the incoming fasta, and then ends up producing one bsml file for each sequence. Is there a component I can use to join them to create one bsml  or gff file?
Thanks,

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
[hidden email]
<a href="tel:%28505%29665-0206" value="[phone]">[phone]





------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

[Roxanne]

Well, I am using that but, it creates many gff files - I'd like it to take all the bsml files (from pipeline summary) and create one gff3 file.   Or insert a step to join all the bsml files into one file, then call bsml2gff3.   Does that make sense?

Roxanne Tapia

Software Developer 3

B-6, Genome Science

Bioscience Division

[hidden email]

[phone]

On Sep 22, 2011, at 8:20 AM, Joshua Orvis wrote:

Roxanne -

It's a bit hard to answer that question without knowing what component is in your pipeline that's creating the BSML.  There is a bsml2gff3 component in Ergatis you could try, but it probably supports a specific subset of features that could be encoded in the BSML.

Joshua

On Wed, Sep 21, 2011 at 4:30 PM, Roxanne Tapia <[hidden email]> wrote:

The pipeline splits the incoming fasta, and then ends up producing one bsml file for each sequence. Is there a component I can use to join them to create one bsml  or gff file?
Thanks,

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
[hidden email]
<a href="tel:%28505%29665-0206" value="[phone]">[phone]





------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

[Joshua Orvis]

The BSML file format doesn't allow you to just concatenate the files together and still form a valid XML document.  It should work just fine with the GFF though, so I'd run your pipeline, add bsml2gff3 to do the conversion, them combine all the GFF3 files together.  You could either do that manually after your pipeline is done or use a generic utility like the run_command component to do it at the end of your pipeline.

Joshua

2011/9/22 Roxanne Tapia <[hidden email]>

Well, I am using that but, it creates many gff files - I'd like it to take all the bsml files (from pipeline summary) and create one gff3 file.   Or insert a step to join all the bsml files into one file, then call bsml2gff3.   Does that make sense?

Roxanne Tapia

Software Developer 3

B-6, Genome Science

Bioscience Division

[hidden email]

<a href="tel:%28505%29665-0206" value="[phone]" target="_blank">[phone]

On Sep 22, 2011, at 8:20 AM, Joshua Orvis wrote:

Roxanne -

It's a bit hard to answer that question without knowing what component is in your pipeline that's creating the BSML.  There is a bsml2gff3 component in Ergatis you could try, but it probably supports a specific subset of features that could be encoded in the BSML.

Joshua

On Wed, Sep 21, 2011 at 4:30 PM, Roxanne Tapia <[hidden email]> wrote:

The pipeline splits the incoming fasta, and then ends up producing one bsml file for each sequence. Is there a component I can use to join them to create one bsml  or gff file?
Thanks,

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
[hidden email]
<a href="tel:%28505%29665-0206" value="[phone]" target="_blank">[phone]





------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

[gary_xie]

Hi, Joshua,

I had a similar question: The ergatis can produce various output, but as biologist, they are mainly interested in Genbank file initially. It looks like the genbank feature table is at dir " pipeline_summary", protein seq is at "translate_sequence", we have to manually put them together to make a genbank file, Is there a component built-in Ergatis for this purpose??

Thanks

Gary

On Sep 22, 2011, at 10:27 AM, Joshua Orvis wrote:

The BSML file format doesn't allow you to just concatenate the files together and still form a valid XML document.  It should work just fine with the GFF though, so I'd run your pipeline, add bsml2gff3 to do the conversion, them combine all the GFF3 files together.  You could either do that manually after your pipeline is done or use a generic utility like the run_command component to do it at the end of your pipeline.

Joshua

2011/9/22 Roxanne Tapia <[hidden email]>

Well, I am using that but, it creates many gff files - I'd like it to take all the bsml files (from pipeline summary) and create one gff3 file.   Or insert a step to join all the bsml files into one file, then call bsml2gff3.   Does that make sense?

Roxanne Tapia

Software Developer 3

B-6, Genome Science

Bioscience Division

[hidden email]

<a href="tel:%28505%29665-0206" value="[phone]" target="_blank">[phone]

On Sep 22, 2011, at 8:20 AM, Joshua Orvis wrote:

Roxanne -

It's a bit hard to answer that question without knowing what component is in your pipeline that's creating the BSML.  There is a bsml2gff3 component in Ergatis you could try, but it probably supports a specific subset of features that could be encoded in the BSML.

Joshua

On Wed, Sep 21, 2011 at 4:30 PM, Roxanne Tapia <[hidden email]> wrote:

The pipeline splits the incoming fasta, and then ends up producing one bsml file for each sequence. Is there a component I can use to join them to create one bsml  or gff file?
Thanks,

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
[hidden email]
<a href="tel:%28505%29665-0206" value="[phone]" target="_blank">[phone]





------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
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[Chris Hemmerich]

Are the modular pipeline templates (using the INCLUDE statement)
functional in r16b1? In my local installation, these statements aren't
processed when I select a template to run:

  * build_pipeline.js calls get_pipeline_layout.cgi, which returns the raw
    XML (i.e. INCLUDE statements are not expanded).

  * build_pipeline.js then processes this XML, but only looks at commandSet
    tags, ignoring the INCLUDE statements.

The end result is that my run only contains components defined in the top
pipeline.layout. I tested the Ergatis installation on DIAG and see the
same behavior.

Is this expected, or do I have a problem somewhere?

Thanks,
   Chris

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users