search

clivehoggart / BridgePRS

Estimation of trans-ancestry PRS
MIT License
5 stars 1 forks source link

'Sumstats' object has no attribute 'snp_handle' #4

Open pdpalupi opened 1 month ago

pdpalupi commented 1 month ago

Dear. Clive and Tade

I have 2 sumstats file (1 sumstats from plink and 1 downloaded from GWAS catalog). I tried to run bridgePRS using these two sumstats and it ended

AttributeError: 'Sumstats' object has no attribute 'snp_handle".

My question is : What is the required data in the Sumstat? my header for the downloaded GWAS catalog sumstats are: CHR, BP, SNP, EA, NEA, BETA, SE, P. Thank you so much for your reply.

tadesouaiaia commented 1 month ago

You need the following five fields: SNP ID, Ref Base, Alt Base, P-value and Effect Size

However, if you don't have Ref/Alt bases, bridgePRS can figure it out for you, so I don't think this is the problem. Can you send us the command you typed and the log file or the print out that saw on the terminal?

Thanks,

Tade

On Fri, Sep 13, 2024 at 5:20 AM pdpalupi @.***> wrote:

Dear. Clive and Tade

I have 2 sumstats file (1 sumstats from plink and 1 downloaded from GWAS catalog). I tried to run bridgePRS using these two sumstats and it ended

AttributeError: 'Sumstats' object has no attribute 'snp_handle".

My question is : What is the required data in the Sumstat? my header for the downloaded GWAS catalog sumstats are: CHR, BP, SNP, EA, NEA, BETA, SE, P. Thank you so much for your reply.

— Reply to this email directly, view it on GitHub https://github.com/clivehoggart/BridgePRS/issues/4, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABRCX7TGRZPQO76QXMG33NTZWKU7NAVCNFSM6AAAAABOE64I4KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDIMZTGI4TKMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

clivehoggart commented 1 month ago

The file handle error could be a problem with how bridge uses relative paths to and in the config files, try using absolute paths throughout and let me know. Thanks

On Fri, 13 Sept 2024 at 10:20, pdpalupi @.***> wrote:

Dear. Clive and Tade

I have 2 sumstats file (1 sumstats from plink and 1 downloaded from GWAS catalog). I tried to run bridgePRS using these two sumstats and it ended

AttributeError: 'Sumstats' object has no attribute 'snp_handle".

My question is : What is the required data in the Sumstat? my header for the downloaded GWAS catalog sumstats are: CHR, BP, SNP, EA, NEA, BETA, SE, P. Thank you so much for your reply.

— Reply to this email directly, view it on GitHub https://github.com/clivehoggart/BridgePRS/issues/4, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJUD6OC5H45MQ5NPYUJQ42LZWKU7NAVCNFSM6AAAAABOE64I4KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDIMZTGI4TKMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

pdpalupi commented 1 month ago

Dear. Clive and Tade

The problems solved. The absolute paths in my .config files was the problems, Thanks.