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feat: Add prototype code for validating fragement file #1095

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@Bento007 Bento007 commented Nov 14, 2024

Reason for Change

Changes

  • add cli command
$ cellxgene-schema validate-fragment -h                                                                                                    
Usage: cellxgene-schema validate-fragment [OPTIONS] H5AD_FILE FRAGMENT_FILE

  Check that an ATAC SEQ fragment follows the cellxgene data integration schema. If
  validation fails this command will return an exit status of 1 otherwise 0. When
  the '--generate-index' tag is present, the command will generate a tabix
  compatible version of the fragment and tabix index. The generated fragment will
  have the file suffix .bgz and the index will have the file suffix .bgz.tbi.

Options:
  -i, --generate-index  Generate index for fragment
  -h, --help            Show this message and exit.
  • add requirements to run dask in local distributed mode
  • add validation steps for ATAC-SEQ fragment file
  • add tabix index generation steps.

Testing

  • TESTS NEEDED
pip install git+https://github.com/chanzuckerberg/single-cell-curation/@tsmith/10x-ATAC#subdirectory=cellxgene_schema_cli

Remaining Work

chanzuckerberg/single-cell#724

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