removing quotation marks

[Aditi Vyas]

When I import a .csv network interaction file to Cytoscape, the interactor names (such as rad1 or clp1 etc) are added in the source / name columns with quotation marks about them (so rad1 changes to "rad1")

I checked under the advanced options of the import tool, and made sure only comma separated values are selected, and also that the names of the columns are taken as strings and not integers. However no matter what I chose, the quotation marks show up in the imported network file and also on the graph. 

Could someone please help me understand how I can get around this?

Thank you!

[Alex Pico]

Can you share your .csv file or at least a few lines it? Hard to diagnose without reproducing.

 - Alex

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[Aditi Vyas]

Sure! Attached the file here.. Thanks for looking into it!

-Aditi.

On Friday, April 12, 2019 at 5:51:29 PM UTC-7, Alex Pico wrote:

Can you share your .csv file or at least a few lines it? Hard to diagnose without reproducing.

 - Alex

On Apr 12, 2019, at 4:58 PM, Aditi Vyas <aditi...@gmail.com> wrote:

When I import a .csv network interaction file to Cytoscape, the interactor names (such as rad1 or clp1 etc) are added in the source / name columns with quotation marks about them (so rad1 changes to "rad1")

I checked under the advanced options of the import tool, and made sure only comma separated values are selected, and also that the names of the columns are taken as strings and not integers. However no matter what I chose, the quotation marks show up in the imported network file and also on the graph. 

Could someone please help me understand how I can get around this?

Thank you!

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[Alex Pico]

The file imports without any problems: without quotes and no special settings.

Are you using Cytoscape 3.7.1?

Are you using the right importer: File > Import > Network from file… ?

It should look like the attached screenshot. Then you just click OK.

 - Alex

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<Sample file.csv>

[Aditi Vyas]

Hi! 

Yes that's exactly what I've been doing but it imports with those quotations around every protein name. And I have the same version of cytoscape as well and am confused as to what is going awry.

I've attached screenshots below.

Import settings:

But Imports with quotations: 

Not sure what I'm doing wrong or how to correct it.

-Aditi.

 - Alex

[Dawn Apostolakou]

Hello

I tried importing Aditi's file, as well as another csv, and I also see the quotation marks being imported, even though they are not shown in the Import Network from Table dialog.

Not sure if it matters but I have Cytoscape 3.7.1 on Windows 10.

A "solution" would be to open the file in Excel and copy paste the contents in a plain text file, basically just make it into a tab separated file with no quotation. 

Hope this helps,

Dawn

[Aditi Vyas]

That works great! 

Thanks so much Dawn and Alex for looking into this! :)

-Aditi.

[Scooter Morris]

I think you can also save the file as a text file (not a csv) and the quotes should be gone (or maybe I got that backwards?)

-- scooter