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Message started by ANTOINE on Jan 17th, 2018 at 8:20pm

Title: WorkFlow: Write Annotation AND the GenID from multifasta
Post by ANTOINE on Jan 17th, 2018 at 8:20pm
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

Title: Re: WorkFlow: Write Annotation AND the GenID from multifasta
Post by ANTOINE on Jan 17th, 2018 at 10:11pm
Just to precise,
in the element Write Annotation, with CSV format, I have selected TRUE for the option Write Sequence names,.

Title: Re: WorkFlow: Write Annotation AND the GenID from multifasta
Post by ANTOINE on Jan 17th, 2018 at 11:55pm
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

Title: Re: WorkFlow: Write Annotation AND the GenID from multifasta
Post by Olga Golosova on Jan 18th, 2018 at 2:21pm
Hi ANTOINE! You're a guru of the Workflow Designer!!  :)

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.

Title: Re: WorkFlow: Write Annotation AND the GenID from multifasta
Post by ANTOINE on Jan 18th, 2018 at 5:20pm
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

Title: Re: WorkFlow: Write Annotation AND the GenID from multifasta
Post by Olga Golosova on Jan 22nd, 2018 at 8:34am

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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