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Workflow: extract accession number with write annotation and filtering (Read 175 times)
Jan 30th, 2020 at 12:14am

ANTOINE   Offline
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Hello happy Ugene users,
I try, in parallel to ORF sequence extraction with a workflow Smiley, to extract annotation from multigenbank to a csv table.

I use a "write annotation" in CSV connected to the read sequence,  It's works but:

1- In my CSV file I have sequence name but not the accession number (very useful to manage data)

2- I parse csv file on R after, because I need only some data:
country, collection_date... .  If I'm not stupid the element "Filter annotations by names" is the solution but i am unable to filter successfully with  Annotation names neither Annotation names file  (it make something because I have a difference if "accept or filter" is true or false,  but what?).
Maybe is not the function of this element.
An advice?
PS: I have 4 outup in the workflow, it's possible to manage save directory as a parameter of the workflow?

Thanks
Antoine

 
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Reply #1 - Jan 31st, 2020 at 2:50pm

Olga Golosova   Offline
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Hello, Antoine. Thank you for your feedback!

Quote:
If I'm not stupid the element "Filter annotations by names" is the solution but i am unable to filter successfully with  Annotation names neither Annotation names file  (it make something because I have a difference if "accept or filter" is true or false,  but what?).
Maybe is not the function of this element.
An advice?

The trick is to check the input data of the "Write Annotations" element (see the screenshot). Input port "Set of annotations" should receive messages from the filter element only, not from both elements (the filter and the reader).

Quote:
In my CSV file I have sequence name but not the accession number (very useful to manage data)

OK, we'll add one more option to the writer element in case of saving to CSV. Hopefully, it will be added to UGENE version 35 (there is already feature freeze for upcoming version 34).

Quote:
PS: I have 4 outup in the workflow, it's possible to manage save directory as a parameter of the workflow?

So, by default UGENE puts data of a particular workflow run into a separate folder - a sub-folder of the Workflow Output Folder. For example, you have two writer elements, for one of them you set "Output file" parameter to "result1.csv", for another one you set "Output file" to "result2.csv". Both result files will be written to the same folder.

Note that the Workflow Output Folder can be specified in the UGENE Application Settings. See "Use directory for output file" on the "Workflow Designer" page of the dialog.

Could you please explain in more detail how you'd like this to be modified?


 
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Reply #2 - Feb 4th, 2020 at 9:04pm

ANTOINE   Offline
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France

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thanks Olga for your response.
I have tested
1- Filtering annotations:
With the check only on set of annotations (by filter....) it is works better... but I succed to filter only the first level of annotations: I can filter all source but not only country.
In the genbank file is look like:
FEATURES
    sources
           /country="Sweden"
I can extract all sources data but not only country
You have a trick for that?

2- directory output:
For the moment, set the workflow output folder in Ugene settings is the best way to have all output in a specified folder. Indeed I want to have a folder containing my input data and output data, to keep the each step of the analysis.
As I share my workflow to colleagues, I would to avoid a problem in the multiple output folder configuration   
Another way could be to transform workflow as sample, to have a step by step configuration of input and output file. It's easy?

thanks for all
Antoine
 
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Reply #3 - Feb 5th, 2020 at 4:48pm

Olga Golosova   Offline
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Quote:
You have a trick for that?

Yes.  Smiley The "second level of annotations" is called qualifiers. In the Workflow Designer you can add element "Filter Annotations by Qualifier" into your workflow. And in the element set, for example, "Qualifier name" parameter to "country", "Qualifier value" parameter to "Sweden".
Make sure to properly setup the input/output ports for the elements in the workflow.

Quote:
Indeed I want to have a folder containing my input data and output data, to keep the each step of the analysis.
As I share my workflow to colleagues, I would to avoid a problem in the multiple output folder configuration 

I see.

Quote:
Another way could be to transform workflow as sample, to have a step by step configuration of input and output file. It's easy?

How will this help in this scenario? Actually, we plan to support importing of sample workflows into UGENE, so that researchers have an easier way to share their workflows with colleagues.

For now, note that you can simply share a workflow's *.uwl file. See e.g. "Actions > Save workflow" item in the UGENE main menu when the WD window is active.
 
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