biobit 0.0.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (138) hide show
  1. biobit-0.0.1/Cargo.lock +633 -0
  2. biobit-0.0.1/Cargo.toml +24 -0
  3. biobit-0.0.1/PKG-INFO +30 -0
  4. biobit-0.0.1/modules/py/Cargo.toml +22 -0
  5. biobit-0.0.1/modules/py/README.md +0 -0
  6. biobit-0.0.1/modules/py/python/biobit/__init__.py +3 -0
  7. biobit-0.0.1/modules/py/python/biobit/algo/__init__.py +3 -0
  8. biobit-0.0.1/modules/py/python/biobit/algo/misc.py +22 -0
  9. biobit-0.0.1/modules/py/python/biobit/analysis/__init__.py +0 -0
  10. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/__init__.py +3 -0
  11. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/fetchngs/__init__.py +3 -0
  12. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/fetchngs/load_bioproj.py +202 -0
  13. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/rnaseq/__init__.py +5 -0
  14. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/rnaseq/descriptor.py +59 -0
  15. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/rnaseq/design.py +60 -0
  16. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/rnaseq/experiment.py +73 -0
  17. biobit-0.0.1/modules/py/python/biobit/analysis/nfcore/rnaseq/project.py +47 -0
  18. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/__init__.py +6 -0
  19. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/counter/__init__.py +5 -0
  20. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/counter/joblib_counter.py +131 -0
  21. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/counter/partition.py +65 -0
  22. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/counter/reads_counter.py +46 -0
  23. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/resolve.py +156 -0
  24. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/source/__init__.py +5 -0
  25. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/source/adapters.py +58 -0
  26. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/source/bam.py +69 -0
  27. biobit-0.0.1/modules/py/python/biobit/analysis/rcount/source/source.py +38 -0
  28. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/__init__.py +8 -0
  29. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/adapter/__init__.py +3 -0
  30. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/adapter/yaml.py +69 -0
  31. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/experiment.py +55 -0
  32. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/filtering_schema.py +97 -0
  33. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/library.py +73 -0
  34. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/project.py +99 -0
  35. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/sample.py +49 -0
  36. biobit-0.0.1/modules/py/python/biobit/analysis/seqproj/seqrun.py +126 -0
  37. biobit-0.0.1/modules/py/python/biobit/core/__init__.py +7 -0
  38. biobit-0.0.1/modules/py/python/biobit/core/interval.py +11 -0
  39. biobit-0.0.1/modules/py/python/biobit/core/orientation.py +45 -0
  40. biobit-0.0.1/modules/py/python/biobit/core/range.py +53 -0
  41. biobit-0.0.1/modules/py/python/biobit/core/strand.py +47 -0
  42. biobit-0.0.1/modules/py/python/biobit/core/strdeductor.py +101 -0
  43. biobit-0.0.1/modules/py/python/biobit/db/__init__.py +3 -0
  44. biobit-0.0.1/modules/py/python/biobit/db/ensembl/__init__.py +5 -0
  45. biobit-0.0.1/modules/py/python/biobit/db/ensembl/abc.py +33 -0
  46. biobit-0.0.1/modules/py/python/biobit/db/ensembl/assembly.py +42 -0
  47. biobit-0.0.1/modules/py/python/biobit/db/ensembl/biomart.py +31 -0
  48. biobit-0.0.1/modules/py/python/biobit/db/ensembl/gene/__init__.py +4 -0
  49. biobit-0.0.1/modules/py/python/biobit/db/ensembl/gene/attributes.py +102 -0
  50. biobit-0.0.1/modules/py/python/biobit/db/ensembl/gene/descriptor.py +139 -0
  51. biobit-0.0.1/modules/py/python/biobit/db/ensembl/loader.py +170 -0
  52. biobit-0.0.1/modules/py/python/biobit/db/ensembl/transcript/__init__.py +4 -0
  53. biobit-0.0.1/modules/py/python/biobit/db/ensembl/transcript/attributes.py +141 -0
  54. biobit-0.0.1/modules/py/python/biobit/db/ensembl/transcript/descriptor.py +151 -0
  55. biobit-0.0.1/modules/py/python/biobit/db/repmasker/GRCh38.tsv.gz +0 -0
  56. biobit-0.0.1/modules/py/python/biobit/db/repmasker/GRCm39.tsv.gz +0 -0
  57. biobit-0.0.1/modules/py/python/biobit/db/repmasker/__init__.py +6 -0
  58. biobit-0.0.1/modules/py/python/biobit/db/repmasker/repmasker.py +29 -0
  59. biobit-0.0.1/modules/py/python/biobit/ds/__init__.py +3 -0
  60. biobit-0.0.1/modules/py/python/biobit/ds/gindex/__init__.py +4 -0
  61. biobit-0.0.1/modules/py/python/biobit/ds/gindex/genomic_index.py +130 -0
  62. biobit-0.0.1/modules/py/python/biobit/ds/gindex/overlap.py +61 -0
  63. biobit-0.0.1/modules/py/python/biobit/io/__init__.py +3 -0
  64. biobit-0.0.1/modules/py/python/biobit/io/bam.py +217 -0
  65. biobit-0.0.1/modules/py/python/biobit/paths.py +4 -0
  66. biobit-0.0.1/modules/py/python/biobit/plot/__init__.py +0 -0
  67. biobit-0.0.1/modules/py/src/lib.rs +7 -0
  68. biobit-0.0.1/pyproject.toml +49 -0
  69. biobit-0.0.1/python/biobit/__init__.py +3 -0
  70. biobit-0.0.1/python/biobit/algo/__init__.py +3 -0
  71. biobit-0.0.1/python/biobit/algo/misc.py +22 -0
  72. biobit-0.0.1/python/biobit/analysis/__init__.py +0 -0
  73. biobit-0.0.1/python/biobit/analysis/nfcore/__init__.py +3 -0
  74. biobit-0.0.1/python/biobit/analysis/nfcore/fetchngs/__init__.py +3 -0
  75. biobit-0.0.1/python/biobit/analysis/nfcore/fetchngs/load_bioproj.py +202 -0
  76. biobit-0.0.1/python/biobit/analysis/nfcore/rnaseq/__init__.py +5 -0
  77. biobit-0.0.1/python/biobit/analysis/nfcore/rnaseq/descriptor.py +59 -0
  78. biobit-0.0.1/python/biobit/analysis/nfcore/rnaseq/design.py +60 -0
  79. biobit-0.0.1/python/biobit/analysis/nfcore/rnaseq/experiment.py +73 -0
  80. biobit-0.0.1/python/biobit/analysis/nfcore/rnaseq/project.py +47 -0
  81. biobit-0.0.1/python/biobit/analysis/rcount/__init__.py +6 -0
  82. biobit-0.0.1/python/biobit/analysis/rcount/counter/__init__.py +5 -0
  83. biobit-0.0.1/python/biobit/analysis/rcount/counter/joblib_counter.py +131 -0
  84. biobit-0.0.1/python/biobit/analysis/rcount/counter/partition.py +65 -0
  85. biobit-0.0.1/python/biobit/analysis/rcount/counter/reads_counter.py +46 -0
  86. biobit-0.0.1/python/biobit/analysis/rcount/resolve.py +156 -0
  87. biobit-0.0.1/python/biobit/analysis/rcount/source/__init__.py +5 -0
  88. biobit-0.0.1/python/biobit/analysis/rcount/source/adapters.py +58 -0
  89. biobit-0.0.1/python/biobit/analysis/rcount/source/bam.py +69 -0
  90. biobit-0.0.1/python/biobit/analysis/rcount/source/source.py +38 -0
  91. biobit-0.0.1/python/biobit/analysis/rcount/test_resolution.py +139 -0
  92. biobit-0.0.1/python/biobit/analysis/seqproj/__init__.py +8 -0
  93. biobit-0.0.1/python/biobit/analysis/seqproj/adapter/__init__.py +3 -0
  94. biobit-0.0.1/python/biobit/analysis/seqproj/adapter/test_adapters.py +38 -0
  95. biobit-0.0.1/python/biobit/analysis/seqproj/adapter/yaml.py +69 -0
  96. biobit-0.0.1/python/biobit/analysis/seqproj/experiment.py +55 -0
  97. biobit-0.0.1/python/biobit/analysis/seqproj/filtering_schema.py +97 -0
  98. biobit-0.0.1/python/biobit/analysis/seqproj/library.py +73 -0
  99. biobit-0.0.1/python/biobit/analysis/seqproj/project.py +99 -0
  100. biobit-0.0.1/python/biobit/analysis/seqproj/sample.py +49 -0
  101. biobit-0.0.1/python/biobit/analysis/seqproj/seqrun.py +126 -0
  102. biobit-0.0.1/python/biobit/analysis/seqproj/test_seqproj.py +141 -0
  103. biobit-0.0.1/python/biobit/core/__init__.py +7 -0
  104. biobit-0.0.1/python/biobit/core/interval.py +11 -0
  105. biobit-0.0.1/python/biobit/core/orientation.py +45 -0
  106. biobit-0.0.1/python/biobit/core/range.py +53 -0
  107. biobit-0.0.1/python/biobit/core/strand.py +47 -0
  108. biobit-0.0.1/python/biobit/core/strdeductor.py +101 -0
  109. biobit-0.0.1/python/biobit/core/test_orientation.py +29 -0
  110. biobit-0.0.1/python/biobit/core/test_range.py +103 -0
  111. biobit-0.0.1/python/biobit/core/test_strdeductor.py +42 -0
  112. biobit-0.0.1/python/biobit/db/__init__.py +3 -0
  113. biobit-0.0.1/python/biobit/db/ensembl/__init__.py +5 -0
  114. biobit-0.0.1/python/biobit/db/ensembl/abc.py +33 -0
  115. biobit-0.0.1/python/biobit/db/ensembl/assembly.py +42 -0
  116. biobit-0.0.1/python/biobit/db/ensembl/biomart.py +31 -0
  117. biobit-0.0.1/python/biobit/db/ensembl/gene/__init__.py +4 -0
  118. biobit-0.0.1/python/biobit/db/ensembl/gene/attributes.py +102 -0
  119. biobit-0.0.1/python/biobit/db/ensembl/gene/descriptor.py +139 -0
  120. biobit-0.0.1/python/biobit/db/ensembl/loader.py +170 -0
  121. biobit-0.0.1/python/biobit/db/ensembl/transcript/__init__.py +4 -0
  122. biobit-0.0.1/python/biobit/db/ensembl/transcript/attributes.py +141 -0
  123. biobit-0.0.1/python/biobit/db/ensembl/transcript/descriptor.py +151 -0
  124. biobit-0.0.1/python/biobit/db/repmasker/GRCh38.tsv.gz +0 -0
  125. biobit-0.0.1/python/biobit/db/repmasker/GRCm39.tsv.gz +0 -0
  126. biobit-0.0.1/python/biobit/db/repmasker/__init__.py +6 -0
  127. biobit-0.0.1/python/biobit/db/repmasker/repmasker.py +29 -0
  128. biobit-0.0.1/python/biobit/db/repmasker/test_repmasker.py +55 -0
  129. biobit-0.0.1/python/biobit/ds/__init__.py +3 -0
  130. biobit-0.0.1/python/biobit/ds/gindex/__init__.py +4 -0
  131. biobit-0.0.1/python/biobit/ds/gindex/genomic_index.py +130 -0
  132. biobit-0.0.1/python/biobit/ds/gindex/overlap.py +61 -0
  133. biobit-0.0.1/python/biobit/ds/gindex/test_index.py +123 -0
  134. biobit-0.0.1/python/biobit/ds/gindex/test_overlap.py +114 -0
  135. biobit-0.0.1/python/biobit/io/__init__.py +3 -0
  136. biobit-0.0.1/python/biobit/io/bam.py +217 -0
  137. biobit-0.0.1/python/biobit/paths.py +4 -0
  138. biobit-0.0.1/python/biobit/plot/__init__.py +0 -0
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+ Requires-Dist: pandas >=2.0.0, <3
15
+ Requires-Dist: joblib >=1.2.0, <2
16
+ Requires-Dist: sortedcontainers-stubs >=2.4.2, <2.4.3 ; extra == 'dev'
17
+ Requires-Dist: pandas-stubs >=2.1.4, <2.1.5 ; extra == 'dev'
18
+ Requires-Dist: mypy >=1.9.0, <2.0.0 ; extra == 'dev'
19
+ Requires-Dist: pytest >=8.1.1, <8.1.2 ; extra == 'dev'
20
+ Requires-Dist: ruff >=0.3.5, <0.3.6 ; extra == 'dev'
21
+ Provides-Extra: dev
22
+ Summary: Rust-powered Python library for biological data analysis
23
+ Home-Page: https://github.com/terabio
24
+ Author: Aleksandr Fedorov
25
+ License: MIT
26
+ Requires-Python: >=3.8
27
+ Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
28
+ Project-URL: Source Code, https://github.com/terabio
29
+
30
+
biobit-0.0.1/modules/py/Cargo.toml ADDED
@@ -0,0 +1,22 @@
1
+ [package]
2
+ name = "biobit-py"
3
+ readme = "README.md"
4
+ description = "Rust-powered Python library for biological data analysis"
5
+ version.workspace = true
6
+ edition.workspace = true
7
+ rust-version.workspace = true
8
+ authors.workspace = true
9
+ homepage.workspace = true
10
+ repository.workspace = true
11
+ license.workspace = true
12
+ categories.workspace = true
13
+ exclude = ["test_*.py"]
14
+
15
+ [lib]
16
+ name = "_rs"
17
+ crate-type = ["cdylib", "rlib"]
18
+
19
+ [dependencies]
20
+ pyo3 = { workspace = true }
21
+ itertools = { workspace = true }
22
+ eyre = { workspace = true }