[Gmod-tripal-devel] Tribal sequence export

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[Gmod-tripal-devel] Tribal sequence export

Michael Dondrup-3
Hi,

I am trying to bulk export sequences from Tripal, using:

find/sequences
However that shows only “Array”. Is there a working version of the feature exporter?

Sequence Retrieval
Status messageOperating in maintenance mode. Go online.
INFO: Administrators, the organism_feature_count and analysis_organism materialized views must be populated before using this form. Those views should be re-populated when new data is added.
Array


Best
Michael



Michael Dondrup
Researcher
Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


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Re: [Gmod-tripal-devel] Tribal sequence export

Stephen Ficklin-2
Hi Michael,

Thanks for pointing out the problem with the sequence retrieval tool.  There was indeed a problem with it.   I have applied a fix to the development branch of the code.   Can you update to the most recent development branch and try again?  You'll want to clear the cache after updating.

Stephen

On 2/26/2016 4:46 AM, Michael Dondrup wrote:
Hi,

I am trying to bulk export sequences from Tripal, using:

find/sequences
However that shows only “Array”. Is there a working version of the feature exporter?

Sequence Retrieval
Status messageOperating in maintenance mode. Go online.
INFO: Administrators, the organism_feature_count and analysis_organism materialized views must be populated before using this form. Those views should be re-populated when new data is added.
Array


Best
Michael



Michael Dondrup
Researcher
Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway



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Re: [Gmod-tripal-devel] Tripal sequence export

Michael Dondrup-3
Hi Stephen,

thanks for the quick fix. I can see the export page and export some sequences, but this seems to
be limited to sequences with residues. For features based on alignments, I only get fasta headers but
no sequence.

Best
Michael

> On Feb 29, 2016, at 9:07 AM, Stephen Ficklin <[hidden email]> wrote:
>
> Hi Michael,
>
> Thanks for pointing out the problem with the sequence retrieval tool.  There was indeed a problem with it.   I have applied a fix to the development branch of the code.   Can you update to the most recent development branch and try again?  You'll want to clear the cache after updating.
>
> Stephen
>
> On 2/26/2016 4:46 AM, Michael Dondrup wrote:
>> Hi,
>>
>> I am trying to bulk export sequences from Tripal, using:
>>
>> find/sequences
>> However that shows only “Array”. Is there a working version of the feature exporter?
>>
>> Sequence Retrieval
>> Status messageOperating in maintenance mode. Go online.
>> INFO: Administrators, the organism_feature_count and analysis_organism materialized views must be populated before using this form. Those views should be re-populated when new data is added.
>> Array
>>
>>
>> Best
>> Michael
>>
>>
>>
>> Michael Dondrup
>> Researcher
>> Sea Lice Research Centre
>> Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>
>>
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>>
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
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Re: [Gmod-tripal-devel] Tripal sequence export

Stephen Ficklin-2
Hi Michael,

There are multiple ways that sequences can be derived via Chado and the
sequence retrieval form tries to handle all of them, but the side effect
is that the form seem a bit confusing.   Here are the cases:

1)  Sequences can come directly from the feature.residues field for any
given set of features
2)  Sequences can come from an alignment. In this case you would need to
check the 'Use Parent' option under 'Advanced' section.
3)  Sequences can come from an alignment but are aggregates.  This is
the case for CDS sequences or spliced mRNA sequences.  In this case but
'Use Parent' and 'Aggregate' should be checked and a list of feature
types to aggregate should be listed (e.g. five_prime_UTR, CDS,
three_prime_UTR).
4)  Sequences can come from relationships (e.g. proteins).   This is
currently not supported by the sequence download tool.  Although you can
specify the protein type and get those directly.

This sequence exporter tool was written quite a while ago and now that
I've been able to take a look at it again I think it is probably a bit
overwhelming and confusing.

I'd be happy to receive any thoughts on how we could make this tool more
friendly.

Stephen

On 3/2/2016 2:24 AM, Michael Dondrup wrote:

> Hi Stephen,
>
> thanks for the quick fix. I can see the export page and export some sequences, but this seems to
> be limited to sequences with residues. For features based on alignments, I only get fasta headers but
> no sequence.
>
> Best
> Michael
>
>> On Feb 29, 2016, at 9:07 AM, Stephen Ficklin <[hidden email]> wrote:
>>
>> Hi Michael,
>>
>> Thanks for pointing out the problem with the sequence retrieval tool.  There was indeed a problem with it.   I have applied a fix to the development branch of the code.   Can you update to the most recent development branch and try again?  You'll want to clear the cache after updating.
>>
>> Stephen
>>
>> On 2/26/2016 4:46 AM, Michael Dondrup wrote:
>>> Hi,
>>>
>>> I am trying to bulk export sequences from Tripal, using:
>>>
>>> find/sequences
>>> However that shows only “Array”. Is there a working version of the feature exporter?
>>>
>>> Sequence Retrieval
>>> Status messageOperating in maintenance mode. Go online.
>>> INFO: Administrators, the organism_feature_count and analysis_organism materialized views must be populated before using this form. Those views should be re-populated when new data is added.
>>> Array
>>>
>>>
>>> Best
>>> Michael
>>>
>>>
>>>
>>> Michael Dondrup
>>> Researcher
>>> Sea Lice Research Centre
>>> Department of Informatics
>>> University of Bergen
>>> Thormøhlensgate 55, N-5008 Bergen,
>>> Norway
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>
>>>
>>> _______________________________________________
>>> Gmod-tripal-devel mailing list
>>>
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>> ------------------------------------------------------------------------------
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>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
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