deconPeaker.py does not work

[jingyu0602]

Hi Huamei,

I'm trying to predict cell proportions with your tools for ATAC-seq data and it does not work even I'm running the example data. The command with issue is "deconPeaker.py deconvolution --lib-strategy=ATAC-Seq --mixture=test\examples\ATAC-Seq\GSE74912_Corces_MR_synthetic_mixture_counts_data.xls --pure=test\examples\ATAC-Seq\GSE74912_Corces_MR_pure_readcounts_signature_matrix.xls --format=TABLE --pvalue=FALSE --outdir=results\GSE74912_Corces_MR". It does not generate a result folder and results, it finishes quickly and seems like not running but no error is shown. Is there something I did wrong or issues with the script? Look forward to your reply

Jingyu

[lihuamei]

Dear Jingyu, I will check the bugs and get back to you as soon as they are fixed. greetings, Huamei Li

At 2021-07-15 13:45:40, "jingyu0602" @.***> wrote:

Hi Huamei,

I'm trying to predict cell proportions with your tools for ATAC-seq data and it does not work even I'm running the example data. The command with issue is "deconPeaker.py deconvolution --lib-strategy=ATAC-Seq --mixture=test\examples\ATAC-Seq\GSE74912_Corces_MR_synthetic_mixture_counts_data.xls --pure=test\examples\ATAC-Seq\GSE74912_Corces_MR_pure_readcounts_signature_matrix.xls --format=TABLE --pvalue=FALSE --outdir=results\GSE74912_Corces_MR". It does not generate a result folder and results, it finishes quickly and seems like not running but no error is shown. Is there something I did wrong or issues with the script? Look forward to your reply

Jingyu

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[jingyu0602]

Great! Thanks for your reply!

[lihuamei]

Hi, jingyu! I have refactored the code and updated the python version to 3. Since DeconPeaker will call R, please make sure that all the dependency packages are installed correctly. If you have any questions, please feel free to contact me.

在 2021-07-15 14:22:55，"jingyu0602" @.***> 写道：

Great! Thanks for your reply!

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[jingyu0602]

Hi Huamei,

Thanks for fixing bugs! I'm trying the example data, should I type something after (Pdb) to run? I'm not sure what to input here. Look forward to your reply.

Jingyu

[lihuamei]

Hi Jingyu, I have deleted the pdb debug line, please clone DeconPeaker again.

[jingyu0602]

Hi Huamei, thanks for fixing this bug and it runs!

Cheers

[jingyu0602]

Hi Huamei,

Maybe true_VS_est_scatter_plot.py also has issues? or something I did wrong? The error is shown below: File "./test/true_VS_est_scatter_plot.py", line 32 if len(sys.argv[1 : ]) <> 3: ^ SyntaxError: invalid syntax

Look forward to your reply Jingyu

[lihuamei]

Hi Huamei,

Maybe true_VS_est_scatter_plot.py also has issues? or something I did wrong? The error is shown below: File "./test/true_VS_est_scatter_plot.py", line 32 if len(sys.argv[1 : ]) <> 3: ^ SyntaxError: invalid syntax

Look forward to your reply Jingyu

Hi, Jingyu, this is an error caused by the python version, I have fixed it, please re-run it.

[jingyu0602]

Hi Huamei,

Thanks for all you did. But it still failed when I tried running example data to plot. Is it issue of myself or the code?

Jingyu

[lihuamei]

Hi Huamei,

Thanks for all you did. But it still failed when I tried running example data to plot. Is it issue of myself or the code?

Jingyu

Hi Yu Jing, just warning messages, not errors. I have reset the warning level and can re-clone it.

[jingyu0602]

Hi Huamei, it works smoothly. Thanks for all you done. Cheers