bed-reader 1.2.0__cp313-cp313-win_arm64.whl

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Files changed (58) hide show
  1. bed_reader/__init__.py +32 -0
  2. bed_reader/_open_bed.py +1843 -0
  3. bed_reader/_sample_data.py +159 -0
  4. bed_reader/_to_bed.py +605 -0
  5. bed_reader/bed_reader.cp313-win_arm64.pyd +0 -0
  6. bed_reader/tests/__init__.py +1 -0
  7. bed_reader/tests/benchmark/bench2.ipynb +251 -0
  8. bed_reader/tests/benchmark/benchmark.py +135 -0
  9. bed_reader/tests/data/500x400_o640_array.memmap +0 -0
  10. bed_reader/tests/data/badfile.bed +1 -0
  11. bed_reader/tests/data/empty.bed +0 -0
  12. bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bed +0 -0
  13. bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bim +100 -0
  14. bed_reader/tests/data/plink_sim_10s_100v_10pmiss.fam +10 -0
  15. bed_reader/tests/data/small.bad_bim +4 -0
  16. bed_reader/tests/data/small.bed +1 -0
  17. bed_reader/tests/data/small.bim +4 -0
  18. bed_reader/tests/data/small.bim_bad_positions.bim +4 -0
  19. bed_reader/tests/data/small.deb +1 -0
  20. bed_reader/tests/data/small.fam +3 -0
  21. bed_reader/tests/data/small.fam_bad +4 -0
  22. bed_reader/tests/data/small.maf +3 -0
  23. bed_reader/tests/data/small.mib +4 -0
  24. bed_reader/tests/data/small2_array.memmap +0 -0
  25. bed_reader/tests/data/small_array.memmap +0 -0
  26. bed_reader/tests/data/small_no_bim.bed +1 -0
  27. bed_reader/tests/data/small_no_bim.fam +3 -0
  28. bed_reader/tests/data/small_no_fam.bed +1 -0
  29. bed_reader/tests/data/small_no_fam.bim +4 -0
  30. bed_reader/tests/data/small_too_short.bed +1 -0
  31. bed_reader/tests/data/small_too_short.bim +4 -0
  32. bed_reader/tests/data/small_too_short.fam +3 -0
  33. bed_reader/tests/data/smallmode0.bed +0 -0
  34. bed_reader/tests/data/smallmode0.bim +3 -0
  35. bed_reader/tests/data/smallmode0.fam +4 -0
  36. bed_reader/tests/data/smallmodebad.bed +1 -0
  37. bed_reader/tests/data/some_missing.bed +0 -0
  38. bed_reader/tests/data/some_missing.bim +100 -0
  39. bed_reader/tests/data/some_missing.fam +100 -0
  40. bed_reader/tests/data/some_missing.properties.npz +0 -0
  41. bed_reader/tests/data/some_missing.val.npy +0 -0
  42. bed_reader/tests/data/sparse.bed +1 -0
  43. bed_reader/tests/data/sparse.bim +20 -0
  44. bed_reader/tests/data/sparse.fam +10 -0
  45. bed_reader/tests/data/toydata.5chrom.bed +0 -0
  46. bed_reader/tests/data/toydata.5chrom.bim +10000 -0
  47. bed_reader/tests/data/toydata.5chrom.fam +500 -0
  48. bed_reader/tests/registry.txt +41 -0
  49. bed_reader/tests/test_file_dot.py +359 -0
  50. bed_reader/tests/test_open_bed.py +1463 -0
  51. bed_reader/tests/test_open_bed_cloud.py +1166 -0
  52. bed_reader/tests/test_opt_dep.py +29 -0
  53. bed_reader-1.2.0.dist-info/METADATA +158 -0
  54. bed_reader-1.2.0.dist-info/RECORD +58 -0
  55. bed_reader-1.2.0.dist-info/WHEEL +4 -0
  56. bed_reader-1.2.0.dist-info/licenses/AUTHORS.txt +2 -0
  57. bed_reader-1.2.0.dist-info/licenses/LICENSE.md +203 -0
  58. bed_reader-1.2.0.dist-info/sboms/bed-reader.cyclonedx.json +9801 -0
bed_reader/__init__.py ADDED
@@ -0,0 +1,32 @@
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+ """Read and write the PLINK BED format, simply and efficiently."""
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+
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+ # flake8: noqa: F401
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+
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+ # See: https://towardsdatascience.com/nine-rules-for-writing-python-extensions-in-rust-d35ea3a4ec29?sk=f8d808d5f414154fdb811e4137011437
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+ # for an article on how this project uses Rust to create a Python extension.
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+
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+ from bed_reader._open_bed import get_num_threads, open_bed
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+ from bed_reader._sample_data import sample_file, sample_url, tmp_path
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+ from bed_reader._to_bed import create_bed, to_bed
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+
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+ from .bed_reader import (
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+ encode1_i8,
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+ file_aat_piece_f32_orderf,
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+ file_aat_piece_f64_orderf,
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+ file_ata_piece_f32_orderf,
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+ file_ata_piece_f64_orderf,
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+ file_b_less_aatbx,
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+ file_dot_piece,
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+ read_cloud_i8,
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+ read_f32,
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+ read_f64,
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+ read_i8,
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+ standardize_f32,
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+ standardize_f64,
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+ subset_f32_f32,
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+ subset_f32_f64,
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+ subset_f64_f64,
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+ write_f32,
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+ write_f64,
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+ write_i8,
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+ )