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WGLab / PhenoSV

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
MIT License
16 stars 3 forks source link

Processing a large number of sv #9

Closed realmanlxw closed 5 months ago

realmanlxw commented 5 months ago

Hello, a great job, I tried to use your tools. There are no problems running 10 SVs, but I will report an error when I have more than 3,000 SV. What is the SV of this tool at the same time? This command is running: Bash Phenosv/Model/Phenosv.sh 'Path/to/SV/Data.csv' 'Folder/PATH/TO/Store/Results' 4. And the error is the picture below：Very much looking forward to your reply. 419f13aef563dbf6ee6c78b68d42699

Karenxzr commented 5 months ago

Hi, thank you for your interest. Have you tried scoring the sample data of 'data/sampledata.csv'?

realmanlxw commented 5 months ago

Yes, the sample data is totally fine, even if I take some of my 3000+ sv's it's fine

Karenxzr commented 5 months ago

I guess the error is cause by specific SVs in your csv file. Can you identify which one? Alternatively, I can help look into it if you can send me your csv file.

realmanlxw commented 5 months ago

output.csv This is my sv data, you can use it as a reference

Karenxzr commented 5 months ago

There are many SVs on sex chromosome that PhenoSV did not treat them as valid. I fixed the bug now. Please pull and test. Let me know if it works this time, thank you!

realmanlxw commented 5 months ago

Hello, the task has been completed, thank you for your correction.

poddarharsh15 commented 3 days ago

Hello, a great job, I tried to use your tools. There are no problems running 10 SVs, but I will report an error when I have more than 3,000 SV. What is the SV of this tool at the same time? This command is running: Bash Phenosv/Model/Phenosv.sh 'Path/to/SV/Data.csv' 'Folder/PATH/TO/Store/Results' 4. And the error is the picture below：Very much looking forward to your reply. 419f13aef563dbf6ee6c78b68d42699

Hi @realmanlxw,

Apologies for opening this thread here. I noticed you have experience manipulating VCF files to create BED or CSV formats for PhenoSV analysis. Could you please suggest some tools or methods that you use for this process? Any guidance or recommendations would be highly appreciated.

Thank you in advance for your help!