Fix SNP writers related to pathlib. Refactor and document Ancestry Objects, SNPObject, and dim reduction classes #5
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- Rename average_strands to is_phased. - Add common_variants_intersection to subset_to_common_variants. - Add common_markers_intersection to subset_to_common_markers. - Rename filename to file. - Rename correct_snp_variants to correct_flipped_variants. - Refine docstrings for improved clarity and consistency.
…ean_ attributes. Remove repeated properties and setters. Solve bug in SNP_PCA.ipynb
salcc
approved these changes
Nov 15, 2024
salcc
approved these changes
Nov 15, 2024
salcc
requested changes
Nov 15, 2024
There was a problem hiding this comment.
I tried doing:
import snputils as su
input_path = "/private/groups/ioannidislab/salcc/snputils_data/bed/"
filename = "ALL.chr22.shapeit2_integrated_v1a.GRCh38.20181129.phased"
output_path = "/private/home/mcomajoa/snputils/"
snpobj = su.read_bed(input_path + filename)and then either of these options:
snpobj.save_vcf(output_path + filename)snpobj.save_bed(output_path + filename)snpobj.save_pgen(output_path + filename)
and all of them result in a different error. I think only the save_bed error is related to the changes in this PR, and I see that before the PR it also resulted in another error, but it would still be nice to have all the writers working. If you think it's too much work let me know, and I can approve this PR for the doc changes and we create another one later to fix these issues.
- Fixed issue with when handling filenames not ending in . - Resolved unintended modification of within the BEDWriter class by using a deep copy.
salcc
approved these changes
Nov 15, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.