SyntaxError

[seyoun209]

Dear Marc Jan Bonder,

I am sharing what I have noticed to see if other people had the same error. I have noticed syntax errors in both [run_QTL_analysis.py] and the [run_interaction_QTL_analysis.py].

The error was below in my log file:
 File "Limix_QTL/run_QTL_analysis.py", line 161
    print("Feature: "+feature_id+" not tested not enough samples do QTL test (n="+str(sum(~np.isnan(phenotype_df.loc[feature_id,:])))+").")")

                     ^
SyntaxError: EOL while scanning string literal

And I have modified the code to be below: print("Feature: "+feature_id+" not tested not enough samples do QTL test (n="+str(sum(~np.isnan(phenotype_df.loc[feature_id,:])))+")")

Another error I have noticed is that while I was running the run_interaction_QTL_analysis.py The error was below UnboundLocalError: local variable 'u_snp_matrix' referenced before assignment

And I have included this before line 618 of the qtl_utilities.py

 if not isinstance(snp_matrix_DF, pd.DataFrame):
snp_matrix_DF = pd.DataFrame(snp_matrix_DF)

It seems to be running and providing results :) Let me know if this works too 👍

[Bonder-MJ]

Thanks. Im realizing some of my fixes are not online. I was doing a redesign to limit the memory use. Which I hope to finish soon and that will replace the current version.

Great to learn that you are using it!

Best, Marc

On Wed, Oct 16, 2024, 18:56 Jess Byun @.***> wrote:

Dear Marc Jan Bonder,

I am sharing what I have noticed to see if other people had the same error. I have noticed syntax errors in both [run_QTL_analysis.py] and the [run_interaction_QTL_analysis.py].

The error was below in my log file: File "Limix_QTL/run_QTL_analysis.py", line 161 print("Feature: "+feature_id+" not tested not enough samples do QTL test (n="+str(sum(~np.isnan(phenotype_df.loc[feature_id,:])))+").")")

                 ^

SyntaxError: EOL while scanning string literal

And I have modified the code to be below: print("Feature: "+feature_id+" not tested not enough samples do QTL test (n="+str(sum(~np.isnan(phenotype_df.loc[feature_id,:])))+")")

Another error I have noticed is that while I was running the run_interaction_QTL_analysis.py

The error was below UnboundLocalError: local variable 'u_snp_matrix' referenced before assignment

And I have included this before line 618 of the qtl_utilities.py

if not isinstance(snp_matrix_DF, pd.DataFrame): snp_matrix_DF = pd.DataFrame(snp_matrix_DF)

It seems to be running and providing results :) Let me know if this works too 👍

— Reply to this email directly, view it on GitHub https://github.com/single-cell-genetics/limix_qtl/issues/37, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6IAM5ON4R7OCWFCM5BP2DZ32LEBAVCNFSM6AAAAABQB5FBQ2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TENBZGM2DEMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[seyoun209]

Thank you very much for telling me about memory use. I noticed that 1000 permutations took a long time. I still couldn't figure out the option for the -blocksize, so I broke down to make my own -feature_filename and made my block(?) (ex, ten genes at a time) run simultaneously. Would it be great to know memory usage, etc updates :)

[Bonder-MJ]

Please see the running via snakemake in the wiki. That is meant for this option. Alternatively you can use the -gr option directly. the block size is meant to indicate how many variants are being loaded from disk at a time. This can limit the memory use but requires more time.

I would recommend keeping that fixed.

Best, Marc

On Wed, Oct 16, 2024, 19:06 Jess Byun @.***> wrote:

Thank you very much for telling me about memory use. I noticed that 1000 permutations took a long time. I still couldn't figure out the option for the -blocksize, so I broke down to make my own -feature_filename and made my block(?) (ex, ten genes at a time) run simultaneously. Would it be great to know memory usage, etc updates :)

— Reply to this email directly, view it on GitHub https://github.com/single-cell-genetics/limix_qtl/issues/37#issuecomment-2417423859, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6IAMZ4OVXRSA2ZGNZKJU3Z32MKJAVCNFSM6AAAAABQB5FBQ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJXGQZDGOBVHE . You are receiving this because you commented.Message ID: @.***>