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WorkFlow: Write Annotation AND the GenID from multifasta (Read 2164 times)
Jan 17th, 2018 at 8:20pm

ANTOINE   Offline
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Hello,
I use a workflow to extract ORF from a multifasta file:
Read Sequence-> ORF Marker ->Write Annotation (in CSV).
It works fine but I need the GenID indicating the origin of each extracted ORF.
Myabe Dump sequence info could help me but it is not cooperative (no parameters)
thanks for the help
Antoine
 
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Reply #1 - Jan 17th, 2018 at 10:11pm

ANTOINE   Offline
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Just to precise,
in the element Write Annotation, with CSV format, I have selected TRUE for the option Write Sequence names,.
 
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Reply #2 - Jan 17th, 2018 at 11:55pm

ANTOINE   Offline
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France

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I found myself the solution...
By changing in the element ORF marker, the parameter "Annotate as" (by default ORF). I choice user script and by analogy with the sample Dump add
Code:
out_text=getName(sequence); 


I have my GenID on group and name but is useful!
Thanks
 
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Reply #3 - Jan 18th, 2018 at 2:21pm

Olga Golosova   Offline
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Hi ANTOINE! You're a guru of the Workflow Designer!!  Smiley

However, there is indeed an error in the "Wrtie Annotations" element. The "Write sequence names" parameter is not taken into account. I've created an issue, we'll fix it until 1.30.
 
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Reply #4 - Jan 18th, 2018 at 5:20pm

ANTOINE   Offline
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France

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Posts: 18
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thanks,
but it's my first use of a script with the workflow. (just a padawan)
Thanks to the Custom Element of the samples where I can see script examples. (I am a not coding people).
Is it possible to see a script of a existing element to have a base to create a new element?
Antoine
 
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Reply #5 - Jan 22nd, 2018 at 8:34am

Olga Golosova   Offline
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Quote:
Is it possible to see a script of a existing element to have a base to create a new element?

You can select the "Edit script of the element" item in the "Actions" menu to open a dialog with the script.
 
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