drag-and-drop behavior different than add_features_from_gff3_to_annotations.pl

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drag-and-drop behavior different than add_features_from_gff3_to_annotations.pl

Jacques Dainat-3
Hello,

I don’t get why the result to drag and drop a gene into the “User-created Annotations” is different than the use of the add_features_from_gff3_to_annotations.pl script.

When I drag-and-drop a gene, the Name stay but all other metadata disapear.

While using the  add_features_from_gff3_to_annotations.pl script I loose the Name  but all the other metadata stay.

Is there any explanation for this differences ?
Is it plan to homogenised those two tasks ?

/Jacques





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Re: drag-and-drop behavior different than add_features_from_gff3_to_annotations.pl

nathandunn
This is a very good question.  

In the case when you are doing a manual annotation (drag and drop), the assumption is that you are editing an already valid annotation with one or more annotations so copying the annotation metadata may not be appropriate or desired (though in many cases it is).   We may decide to allow adding additional metadata in the future.     We create a best-guess name the annotation based on information on the transcript, but it can definitely be changed.

In the case where you are adding it, we assume that all of the information you provide are the annotations you want to see.   My guess is that providing a feature / name or transcript / name those values would be preserved.  Would have to see the JSON you are posting versus the resulting annotation.   In your example, Is the type in both is mRNA can you show the feature details for both the annotation (above), evidence (below), and the command you used to upload (and relevant data snippets if possible)?  

Nathan


On Mar 16, 2018, at 5:04 AM, Jacques Dainat <[hidden email]> wrote:

Hello,

I don’t get why the result to drag and drop a gene into the “User-created Annotations” is different than the use of the add_features_from_gff3_to_annotations.pl script.

When I drag-and-drop a gene, the Name stay but all other metadata disapear.
<Screen Shot 2018-03-16 at 12.44.02.png><Screen Shot 2018-03-16 at 12.52.45.png>

While using the  add_features_from_gff3_to_annotations.pl script I loose the Name  but all the other metadata stay.
<Screen Shot 2018-03-16 at 12.40.55.png><Screen Shot 2018-03-16 at 12.55.20.png>

Is there any explanation for this differences ?
Is it plan to homogenised those two tasks ?

/Jacques




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: drag-and-drop behavior different than add_features_from_gff3_to_annotations.pl

nathandunn

Its because we don't attach properties to the CDS / Exon values, and so we can't delete those when they come in.       When we drag things up to the manual annotation area, there could be multiple property annotations present, so we don’t import anything and require the user to dadd. 

Quick Solutions:
1 - don’t import GFF3’s with properties other than id and parent attached them
2 - run SQL like this:   delete  from feature_property as fp where fp.feature_id in (select f.id from feature f where f.class like '%CDS' or f.class like '%Exon');

Other, longer-term solutions:
3 - ignore properties on exons / CDS’s, etc. or propagate up the the mRNA when doing a manual import
4 - deletion of non-visible properties 



Nathan



On Mar 16, 2018, at 8:51 AM, Nathan Dunn <[hidden email]> wrote:

This is a very good question.  

In the case when you are doing a manual annotation (drag and drop), the assumption is that you are editing an already valid annotation with one or more annotations so copying the annotation metadata may not be appropriate or desired (though in many cases it is).   We may decide to allow adding additional metadata in the future.     We create a best-guess name the annotation based on information on the transcript, but it can definitely be changed.

In the case where you are adding it, we assume that all of the information you provide are the annotations you want to see.   My guess is that providing a feature / name or transcript / name those values would be preserved.  Would have to see the JSON you are posting versus the resulting annotation.   In your example, Is the type in both is mRNA can you show the feature details for both the annotation (above), evidence (below), and the command you used to upload (and relevant data snippets if possible)?  

Nathan


On Mar 16, 2018, at 5:04 AM, Jacques Dainat <[hidden email]> wrote:

Hello,

I don’t get why the result to drag and drop a gene into the “User-created Annotations” is different than the use of the add_features_from_gff3_to_annotations.pl script.

When I drag-and-drop a gene, the Name stay but all other metadata disapear.
<Screen Shot 2018-03-16 at 12.44.02.png><Screen Shot 2018-03-16 at 12.52.45.png>

While using the  add_features_from_gff3_to_annotations.pl script I loose the Name  but all the other metadata stay.
<Screen Shot 2018-03-16 at 12.40.55.png><Screen Shot 2018-03-16 at 12.55.20.png>

Is there any explanation for this differences ?
Is it plan to homogenised those two tasks ?

/Jacques




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.