isoforge 1.0.0__tar.gz

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  1. isoforge-1.0.0/.gitignore +46 -0
  2. isoforge-1.0.0/CITATION.cff +14 -0
  3. isoforge-1.0.0/Cargo.lock +2532 -0
  4. isoforge-1.0.0/Cargo.toml +54 -0
  5. isoforge-1.0.0/LICENSE +21 -0
  6. isoforge-1.0.0/PKG-INFO +266 -0
  7. isoforge-1.0.0/README.md +238 -0
  8. isoforge-1.0.0/environment.yml +14 -0
  9. isoforge-1.0.0/install.sh +263 -0
  10. isoforge-1.0.0/pyproject.toml +55 -0
  11. isoforge-1.0.0/rust_core/src/admission.rs +692 -0
  12. isoforge-1.0.0/rust_core/src/align.rs +508 -0
  13. isoforge-1.0.0/rust_core/src/annotation_engine.rs +4168 -0
  14. isoforge-1.0.0/rust_core/src/annotation_hypergraph.rs +363 -0
  15. isoforge-1.0.0/rust_core/src/approximate_chain.rs +516 -0
  16. isoforge-1.0.0/rust_core/src/bam_reader.rs +2577 -0
  17. isoforge-1.0.0/rust_core/src/cage_peaks.rs +188 -0
  18. isoforge-1.0.0/rust_core/src/consistent_assignment.rs +505 -0
  19. isoforge-1.0.0/rust_core/src/data_structures.rs +684 -0
  20. isoforge-1.0.0/rust_core/src/edge_matching.rs +215 -0
  21. isoforge-1.0.0/rust_core/src/errors.rs +47 -0
  22. isoforge-1.0.0/rust_core/src/fusion.rs +2429 -0
  23. isoforge-1.0.0/rust_core/src/fusion_place.rs +2270 -0
  24. isoforge-1.0.0/rust_core/src/fusion_rescue.rs +305 -0
  25. isoforge-1.0.0/rust_core/src/gene_assignment.rs +196 -0
  26. isoforge-1.0.0/rust_core/src/genome_ref.rs +659 -0
  27. isoforge-1.0.0/rust_core/src/gtf_to_parquet.rs +1259 -0
  28. isoforge-1.0.0/rust_core/src/hyper_core.rs +738 -0
  29. isoforge-1.0.0/rust_core/src/hypergraph.rs +385 -0
  30. isoforge-1.0.0/rust_core/src/junction_groups.rs +484 -0
  31. isoforge-1.0.0/rust_core/src/junction_hmm.rs +553 -0
  32. isoforge-1.0.0/rust_core/src/lib.rs +57 -0
  33. isoforge-1.0.0/rust_core/src/microexon_repair.rs +328 -0
  34. isoforge-1.0.0/rust_core/src/model_hypergraph.rs +100 -0
  35. isoforge-1.0.0/rust_core/src/novel_sites.rs +449 -0
  36. isoforge-1.0.0/rust_core/src/parquet_io.rs +1315 -0
  37. isoforge-1.0.0/rust_core/src/post_processing.rs +4844 -0
  38. isoforge-1.0.0/rust_core/src/python_bindings.rs +874 -0
  39. isoforge-1.0.0/rust_core/src/quant_em.rs +422 -0
  40. isoforge-1.0.0/rust_core/src/reference_end_support.rs +302 -0
  41. isoforge-1.0.0/rust_core/src/small_rna.rs +324 -0
  42. isoforge-1.0.0/rust_core/src/splice_realignment.rs +295 -0
  43. isoforge-1.0.0/rust_core/src/splice_scores.rs +125 -0
  44. isoforge-1.0.0/rust_core/src/strand_evidence.rs +276 -0
  45. isoforge-1.0.0/rust_core/src/terminal_rescue.rs +284 -0
  46. isoforge-1.0.0/rust_core/src/transcript_classifier.rs +1393 -0
  47. isoforge-1.0.0/rust_core/src/transcript_utils.rs +128 -0
  48. isoforge-1.0.0/rust_core/src/tss_tes_clustering.rs +2323 -0
  49. isoforge-1.0.0/rust_core/src/types.rs +1354 -0
  50. isoforge-1.0.0/rust_core/src/vertex_matching.rs +900 -0
  51. isoforge-1.0.0/src/isoforge/__init__.py +0 -0
  52. isoforge-1.0.0/src/isoforge/cage_utils.py +158 -0
  53. isoforge-1.0.0/src/isoforge/cli.py +84 -0
  54. isoforge-1.0.0/src/isoforge/data/admission_v1.json +1 -0
  55. isoforge-1.0.0/src/isoforge/genome_fasta.py +56 -0
  56. isoforge-1.0.0/src/isoforge/isoforge_align.py +68 -0
  57. isoforge-1.0.0/src/isoforge/isoforge_export.py +175 -0
  58. isoforge-1.0.0/src/isoforge/isoforge_init.py +199 -0
  59. isoforge-1.0.0/src/isoforge/isoforge_main.py +848 -0
  60. isoforge-1.0.0/src/isoforge/isoforge_post.py +95 -0
  61. isoforge-1.0.0/src/isoforge/options.py +558 -0
  62. isoforge-1.0.0/src/isoforge_core/__init__.py +3 -0
  63. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/.cargo_vcs_info.json +6 -0
  64. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/Cargo.lock +270 -0
  65. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/Cargo.toml +94 -0
  66. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/Cargo.toml.orig +57 -0
  67. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/LICENSE +23 -0
  68. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/README.isoforge.md +7 -0
  69. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/README.md +93 -0
  70. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/build.rs +262 -0
  71. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/FAQ.md +46 -0
  72. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/LICENSE.txt +24 -0
  73. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/MANIFEST.in +10 -0
  74. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/Makefile +137 -0
  75. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/Makefile.simde +97 -0
  76. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/NEWS.md +989 -0
  77. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/README.md +428 -0
  78. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/align.c +1120 -0
  79. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/bseq.c +169 -0
  80. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/bseq.h +64 -0
  81. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/code_of_conduct.md +30 -0
  82. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/cookbook.md +243 -0
  83. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/esterr.c +64 -0
  84. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/example.c +63 -0
  85. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/format.c +682 -0
  86. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/hit.c +474 -0
  87. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/index.c +1074 -0
  88. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/jump.c +201 -0
  89. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kalloc.c +224 -0
  90. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kalloc.h +95 -0
  91. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kdq.h +132 -0
  92. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ketopt.h +120 -0
  93. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/khash.h +615 -0
  94. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/krmq.h +474 -0
  95. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kseq.h +256 -0
  96. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksort.h +153 -0
  97. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksw2.h +188 -0
  98. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksw2_dispatch.c +96 -0
  99. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksw2_extd2_sse.c +402 -0
  100. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksw2_exts2_sse.c +466 -0
  101. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksw2_extz2_sse.c +313 -0
  102. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/ksw2_ll_sse.c +152 -0
  103. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kthread.c +159 -0
  104. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kthread.h +15 -0
  105. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/kvec.h +105 -0
  106. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lchain.c +368 -0
  107. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/CONTRIBUTING.md +114 -0
  108. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/COPYING +20 -0
  109. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/README.md +333 -0
  110. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/amalgamate.py +58 -0
  111. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/meson.build +33 -0
  112. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/netlify.toml +20 -0
  113. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/float32x2.h +140 -0
  114. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/float32x4.h +137 -0
  115. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/float64x1.h +142 -0
  116. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/float64x2.h +145 -0
  117. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int16x4.h +140 -0
  118. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int16x8.h +145 -0
  119. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int32x2.h +140 -0
  120. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int32x4.h +143 -0
  121. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int64x1.h +137 -0
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  123. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int8x16.h +147 -0
  124. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/int8x8.h +141 -0
  125. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/uint16x4.h +134 -0
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  129. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/uint64x1.h +131 -0
  130. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/uint64x2.h +135 -0
  131. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/uint8x16.h +141 -0
  132. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/arm/neon/uint8x8.h +135 -0
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  134. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/check.h +267 -0
  135. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/debug-trap.h +83 -0
  136. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/hedley.h +1899 -0
  137. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/simde-arch.h +445 -0
  138. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/simde-common.h +697 -0
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  143. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/lib/simde/simde/x86/avx512vl.h +112 -0
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  185. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/hs38-simu.sh +10 -0
  186. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/minialign.eval +49 -0
  187. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/minimap2.bib +460 -0
  188. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/minimap2.tex +724 -0
  189. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/mm2-s3.sam.eval +62 -0
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  192. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/mm2.eval +13 -0
  193. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/natbib.bst +1288 -0
  194. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/natbib.sty +803 -0
  195. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/ngmlr.eval +38 -0
  196. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/roc.gp +60 -0
  197. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2/tex/snap-s3.sam.eval +62 -0
  198. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/minimap2.h +15 -0
  199. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/mm2-fast.h +15 -0
  200. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/mm2_fast_glue.c +8 -0
  201. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/src/bindings.rs +6107 -0
  202. isoforge-1.0.0/vendor/minimap2-sys-0.1.30-mm230/src/lib.rs +209 -0
  203. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/.cargo_vcs_info.json +6 -0
  204. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/CHANGELOG.md +504 -0
  205. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/Cargo.toml +134 -0
  206. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/Cargo.toml.orig +52 -0
  207. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/LICENSE.md +9 -0
  208. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/README.isoforge.md +7 -0
  209. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/README.md +77 -0
  210. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/buffer.rs +200 -0
  211. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/ext.rs +9673 -0
  212. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/header.rs +177 -0
  213. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/index.rs +89 -0
  214. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/mod.rs +3132 -0
  215. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/pileup.rs +207 -0
  216. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/record.rs +2993 -0
  217. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bam/record_serde.rs +350 -0
  218. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bcf/buffer.rs +213 -0
  219. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bcf/header.rs +542 -0
  220. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bcf/index.rs +100 -0
  221. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bcf/mod.rs +1589 -0
  222. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bcf/record.rs +1717 -0
  223. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/bgzf/mod.rs +607 -0
  224. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/errors.rs +143 -0
  225. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/faidx/mod.rs +331 -0
  226. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/htslib.rs +2 -0
  227. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/lib.rs +134 -0
  228. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/tbx/mod.rs +430 -0
  229. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/tpool.rs +55 -0
  230. isoforge-1.0.0/vendor/rust-htslib-0.47.1-patched/src/utils.rs +53 -0
isoforge-1.0.0/.gitignore ADDED
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+ # Build artefacts
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+ target/
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+ **/target/
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+ *.so
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+ *.rlib
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+ build/
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+ dist/
8
+ wheels/
9
+ *.egg-info/
10
+ .eggs/
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+ .Python
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+
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+ # Python
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+ __pycache__/
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+ *.py[cod]
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+ *$py.class
17
+ .venv/
18
+ venv/
19
+ .ipynb_checkpoints/
20
+ .pytest_cache/
21
+
22
+ # Run outputs
23
+ isoforge_index/
24
+ *_isoforge_index/
25
+ *_alignments/
26
+ *_isoforge_db/
27
+ *_TSS_TES_Clusters/
28
+ *.spill.parquet
29
+
30
+ # Alignment and reference data
31
+ *.bam
32
+ *.bai
33
+ *.sam
34
+ *.cram
35
+ *.fastq
36
+ *.fastq.gz
37
+ *.db
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+
39
+ # Local
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+ *.bundle
41
+ *.bak
42
+ nohup.out
43
+ .DS_Store
44
+ *.swp
45
+ *.swo
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+ *~
isoforge-1.0.0/CITATION.cff ADDED
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1
+ cff-version: 1.2.0
2
+ message: "If you use IsoForge, please cite it as below."
3
+ title: "IsoForge"
4
+ version: 1.0.0
5
+ type: software
6
+ authors:
7
+ - family-names: Elshani
8
+ given-names: Mustafa
9
+ - family-names: Zhang
10
+ given-names: Ying
11
+ - family-names: Harrison
12
+ given-names: David J.
13
+ repository-code: "https://github.com/MustafaElshani/IsoForge"
14
+ license: MIT