Remove hardcoded paths in `maxatac prepare` and in maxatac_data so users can provide custom chromosome sets

[tacazares]

Some users have interest in making predictions for chrX and chrY. Right now, maxATAC is hardcoded for autosomal chromosomes only when preparing signal tracks. We should remove these hardcoded paths and make them arguments. A warning should also be posted that changing these arguments means the user will min-max normalize and make predictions on chromosomes that have not been tested before.

scATAC prepare: https://github.com/MiraldiLab/maxATAC/blob/4ad3cdc3f4eab06ebbe490c5da70ba42a4d4d2a4/maxatac/analyses/prepare.py#L93

bulk ATAC prepare: https://github.com/MiraldiLab/maxATAC_data/blob/86f415f59771f4f205efbb87afd7451cda4ad40b/scripts/ATAC/ATAC_bowtie2_pipeline.sh#L34

[jeffsteimle]

I downloaded and was testing out maxATAC today. When I run maxatac prepare, I set: -chroms chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19

but the outputs still show:

Chr Keep: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22

Which suggested to me that it is still hardcoded...? Am I doing something wrong?

Thank you!

[tacazares]

Hey @jeffsteimle, I am no longer supporting this project as I have moved to a new position, but the Miraldi Lab will be continuing to work on maxATAC with @FaizRizvi acting as one of the main contacts.

The changes to help with chromosomes where made to the "tests" branch. https://github.com/MiraldiLab/maxATAC/tree/tests . This branch has not been completely approved for use or submission to pypi, but has many quality of life updates, additional documentation, examples, and flags. The pull request will show changes that were made: https://github.com/MiraldiLab/maxATAC/pull/113

Good luck, Tareian

[jeffsteimle]

Totally, understand. Thank you, I will take a look at the test branch.

[emiraldi]

Hi @jeffsteimle ! Thanks for using maxATAC! We're soliciting feedback to see if the test branch is ready for merging into the main. How was your experience with the test branch? Did you run into any issues? What functions did you use? Thank you, Emily

[jeffsteimle]

Hi @emiraldi I got busy with something else and never got around to trying out the test branch, sorry! Jeff

[emiraldi]

No worries! I hope you try again soon -- and thanks again for the feedback! Emily

On Tue, Jan 17, 2023 at 12:55 PM Jeff Steimle @.***> wrote:

Hi @emiraldi https://github.com/emiraldi I got busy with something else and never got around to trying out the test branch, sorry! Jeff

— Reply to this email directly, view it on GitHub https://github.com/MiraldiLab/maxATAC/issues/112#issuecomment-1385811392, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUJXVP2JJNLCAOG7SAFN4DWS3MHPANCNFSM6AAAAAARC3KCPU . You are receiving this because you were mentioned.Message ID: @.***>

-- Emily Miraldi, Ph.D. Assistant Professor Divisions of Immunobiology and Biomedical Informatics Cincinnati Children's Hospital