UGENE Forum - Sequence Loads But Not Annotations of GB File

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Sequence Loads But Not Annotations of GB File (Read 13013 times)

Dec 15^th, 2011 at 3:00pm

R Smith Offline
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Posts: 17

I have a GB file saved to my disk and in Project subwindow I select the *.gb file and hit Enter to load. Sequence file loads, but not its annotations. From WinExplorer, if I double-click the GB file, a new UGENE window opens with no project name and only the GB file in the Project subwindow, with both annotations ("features") and sequence showing. When I look at the .GB file with a text editor, the flatfile record fields are all present.

Is this a bug?

Note, my repeated attempts to click the annotations object or the gb document and re-open it produces no diagnostic (no error message).

-RS

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Reply #1 - Dec 15^th, 2011 at 6:31pm

Mikhail Fursov Offline
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Hi!
If you have annotations in the file and UGENE does not show them this is a bug.
Could you please share the file with us?

---
UGENE team

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Reply #2 - Dec 15^th, 2011 at 6:53pm

Agu Offline
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You can solve it dragging and dropping the feature on the corresponding sequence to make a new association. But then you will have to save a copy or you can loose the association (I've just reported a bug about that).

associated.png (46 KB | )

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Reply #3 - Dec 15^th, 2011 at 7:10pm

R Smith Offline
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Posts: 17

Actually, every one of the documents in the project file do not open the annotations object, only the sequence object.

I have attached a 7zip file containing all the files in a directory named "UGENE data" (the 7z archive is the name of the directory).

For the time being, until I get more familiar with UGENE, my organizational style is to put all UGENE related activity and work into a single subdirectory under my own projects. In this case, I have created a directory named "UGENE data" and have within it the base UPRJ file and I try to save all relevant files to it (GenBank, FASTA, alignments, etc). All in one pile (directory) for now.

The 7z archive actually contains GB files in the directory which should be listed on the Project subwindow when the UPRJ file is opened, but they are not. I supposed I deleted them from the Project subwindow although they were not deleted as files from the disk.

I am also creating a document now--in the Project subwindow, it is 'pHIL-S1'---and I see a sequence object under one document and an annotations object under another document but I want them to be in one document. Going over the user guide to see what I am doing wrong.

Anyway, having the UPRJ and data document files should be of use. I imagine any init files of UGENE under the %AppData% could be helpful too in debugging (but I prefer not to post these to public forum).

UGENE_data.7z (38 KB | )

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Reply #4 - Dec 15^th, 2011 at 7:18pm

R Smith Offline
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Posts: 17

In reply to Agu:

Yes, your instruction did fix that problem.

Dragging the [a] annotation object directly on to the sequence view subwindow did load the annotations.

But is that supposed to be the proper action of the interface when opening up a Document that contains an [a] annotations and [s] sequence object?

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Reply #5 - Dec 15^th, 2011 at 7:27pm

Agu Offline
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Nop, that's not normal. There is a problem with that file, so the question is: where is that gb coming from? I found a bug in workflow designer that generates those gb in Ugene 1.10. Was your file also created with workflow designer?

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Reply #6 - Dec 15^th, 2011 at 8:19pm

R Smith Offline
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Posts: 17

Agu wrote on Dec 15^th, 2011 at 7:27pm:

Nop, that's not normal. There is a problem with that file, so the question is: where is that gb coming from?

All files obtained from the NCBI Nuc DB.

Quote:

I found a bug in workflow designer that generates those gb in Ugene 1.10. Was your file also created with workflow designer?

Not by any workflow I created. If it is, all processing is done by the core modules of UGENE.

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Reply #7 - Dec 16^th, 2011 at 12:28am

Agu Offline
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Now that your sequence and features are associated, you will see them together only if you open the project. If you try to open only the file, then you will see just the plain sequence.

To merge the annotations with your sequence, export it including the annotations: right button over the sequence on the left panel "Export/Export sequences", and then choose GenBank as file type and mark "Export with annotations" (and you can have the reverse complementary by choosing "Save complement strand").

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