Need Help with Cytoscape CLI Command for STRING App

Question

[Harsh]

I'm encountering an error while trying to fetch a Protein-Protein Interaction Network using the STRING App in Cytoscape's Command Line Interface. I'd greatly appreciate assistance in understanding the correct command structure and troubleshooting this issue.

Here's the command I'm using:

string protein query query=PNPLA3,PARD3,PRKAG2,CTNND2,RBFOX1,PRKCA,TIAM1,ABCA13 species="homo sapiens" networkType=full STRING network

The error message I'm receiving:

Error handling command "Failed to find command: 'protein query PARD3 PRKAG2 CTNND2 RBFOX1 PRKCA TIAM1 ABCA13 STRING network' (from namespace: string)"

Could you please:

• Explain what's incorrect in my command syntax?
• Provide tips for using Cytoscape CLI commands effectively within Python scripts?
• Offer any additional guidance for using the STRING App with Cytoscape CLI for network analysis pipelines?

Background Information:

• I'm new to Cytoscape's Command Line Interface.
• I aim to integrate this command into a pipeline for network analysis.

Thank you in advance for your prompt assistance!

Best Regards,
Harsh

[Mensur Dlakic]

I was just writing in a separate thread how I don't respond well when people show entitlement.

Writing [URGENT] in the title and Thank you in advance for your prompt assistance! will usually get you nowhere fast. You may think that highlights the importance of your problem, but it only shows us how you think your problems are greater than the problems of others. I consider this entitlement, even if you explained this supposed urgency - which you most definitely didn't. Anyway, good luck getting a response on such a post, especially on the weekend.

[Harsh]

I am sorry if this is inappropriate. I am still a beginner (undergrad student) in computer science, let alone using a public forum for help. I see your point and won't continue this in the future.

Thank you for bringing this to my attention.

Answer 1

[Scooter]

Hi Harsh,

You need to quote the query: string protein query query="PNPLA3,PARD3,PRKAG2,CTNND2,RBFOX1,PRKCA,TIAM1,ABCA13" species="homo sapiens" networkType="full STRING network"

-- scooter

[Harsh]

Thank you, so much