Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ignoring line with invalid Entrez_Id NA #4

Open
forus opened this issue Jan 24, 2024 · 0 comments
Open

Ignoring line with invalid Entrez_Id NA #4

forus opened this issue Jan 24, 2024 · 0 comments

Comments

@forus
Copy link
Contributor

forus commented Jan 24, 2024

According to the documentation, one or both of Hugo_Symbol, Entrez_Gene_Id can be specified.

However, if you miss Entrez_Gene_Id the loader will produce a warning per each row in the CNA data file.

Warnings / Errors:
-------------------
0.  Ignoring line with invalid Entrez_Id NA; 20x

Despite the message, records get loaded to the database:

-> records inserted into `sample_cna_event` table: 1720

Expected behavior: The loader won't show a warning when there is no Entrez_Gene_Id column specified.

The issue in the code:
If there is no entrez id column, entrezAsString will be assigned to "NA" here
The warning gets generated few lines below here

Proposed solution: check entrezAsString for NA and return 0 without warning in this case.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant