ORForise 1.6.2__py3-none-any.whl

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 (73) hide show
  1. ORForise/Aggregate_Compare.py +378 -0
  2. ORForise/Annotation_Compare.py +317 -0
  3. ORForise/Annotation_Intersector.py +726 -0
  4. ORForise/Aux/StORF_Undetected/Completely_Undetected/Completey_Undetected.py +53 -0
  5. ORForise/Aux/StORF_Undetected/Completely_Undetected/__init__.py +0 -0
  6. ORForise/Aux/StORF_Undetected/StORF_Undetected.py +35 -0
  7. ORForise/Aux/StORF_Undetected/__init__.py +0 -0
  8. ORForise/Aux/StORF_Undetected/unvitiated_Genes/__init__.py +0 -0
  9. ORForise/Aux/StORF_Undetected/unvitiated_Genes/unvitiated_Missed_Genes.py +46 -0
  10. ORForise/Aux/TabToGFF/TabToGFF.py +140 -0
  11. ORForise/Aux/TabToGFF/__init__.py +0 -0
  12. ORForise/Aux/__init__.py +0 -0
  13. ORForise/Comparator.py +882 -0
  14. ORForise/Convert_To_GFF.py +141 -0
  15. ORForise/GFF_Adder.py +543 -0
  16. ORForise/List_Tools.py +56 -0
  17. ORForise/ORForise_Analysis/__init__.py +0 -0
  18. ORForise/ORForise_Analysis/cds_checker.py +77 -0
  19. ORForise/ORForise_Analysis/gene_Lenghts.py +28 -0
  20. ORForise/ORForise_Analysis/genome_Metrics.py +258 -0
  21. ORForise/ORForise_Analysis/hypothetical_gene_predictions.py +88 -0
  22. ORForise/ORForise_Analysis/missed_Gene_Metrics.py +277 -0
  23. ORForise/ORForise_Analysis/parital_Match_Analysis.py +230 -0
  24. ORForise/ORForise_Analysis/result_File_Analysis.py +286 -0
  25. ORForise/ORForise_Analysis/start_Codon_Substitution.py +161 -0
  26. ORForise/StORForise.py +115 -0
  27. ORForise/Tools/Augustus/Augustus.py +54 -0
  28. ORForise/Tools/Augustus/__init__.py +0 -0
  29. ORForise/Tools/Balrog/Balrog.py +56 -0
  30. ORForise/Tools/Balrog/__init__.py +0 -0
  31. ORForise/Tools/EasyGene/EasyGene.py +55 -0
  32. ORForise/Tools/EasyGene/__init__.py +0 -0
  33. ORForise/Tools/FGENESB/FGENESB.py +57 -0
  34. ORForise/Tools/FGENESB/__init__.py +0 -0
  35. ORForise/Tools/FragGeneScan/FragGeneScan.py +54 -0
  36. ORForise/Tools/FragGeneScan/__init__.py +0 -0
  37. ORForise/Tools/GFF/GFF.py +77 -0
  38. ORForise/Tools/GFF/__init__.py +0 -0
  39. ORForise/Tools/GLIMMER3/GLIMMER3.py +59 -0
  40. ORForise/Tools/GLIMMER3/__init__.py +0 -0
  41. ORForise/Tools/GeneMark/GeneMark.py +135 -0
  42. ORForise/Tools/GeneMark/__init__.py +0 -0
  43. ORForise/Tools/GeneMarkHA/GeneMarkHA.py +54 -0
  44. ORForise/Tools/GeneMarkHA/__init__.py +0 -0
  45. ORForise/Tools/GeneMarkHMM/GeneMarkHMM.py +55 -0
  46. ORForise/Tools/GeneMarkHMM/__init__.py +0 -0
  47. ORForise/Tools/GeneMarkS/GeneMarkS.py +54 -0
  48. ORForise/Tools/GeneMarkS/__init__.py +0 -0
  49. ORForise/Tools/GeneMarkS2/GeneMarkS2.py +55 -0
  50. ORForise/Tools/GeneMarkS2/__init__.py +0 -0
  51. ORForise/Tools/MetaGene/MetaGene.py +54 -0
  52. ORForise/Tools/MetaGene/__init__.py +0 -0
  53. ORForise/Tools/MetaGeneAnnotator/MetaGeneAnnotator.py +55 -0
  54. ORForise/Tools/MetaGeneAnnotator/__init__.py +0 -0
  55. ORForise/Tools/MetaGeneMark/MetaGeneMark.py +55 -0
  56. ORForise/Tools/MetaGeneMark/__init__.py +0 -0
  57. ORForise/Tools/Prodigal/Prodigal.py +55 -0
  58. ORForise/Tools/Prodigal/__init__.py +0 -0
  59. ORForise/Tools/Prokka/Prokka.py +57 -0
  60. ORForise/Tools/Prokka/__init__.py +0 -0
  61. ORForise/Tools/StORF-Reporter/StORF-Reporter.py +56 -0
  62. ORForise/Tools/StORF-Reporter/__init__.py +0 -0
  63. ORForise/Tools/TransDecoder/TransDecoder.py +54 -0
  64. ORForise/Tools/TransDecoder/__init__.py +0 -0
  65. ORForise/Tools/__init__.py +0 -0
  66. ORForise/__init__.py +0 -0
  67. ORForise/utils.py +236 -0
  68. orforise-1.6.2.dist-info/METADATA +1038 -0
  69. orforise-1.6.2.dist-info/RECORD +73 -0
  70. orforise-1.6.2.dist-info/WHEEL +5 -0
  71. orforise-1.6.2.dist-info/entry_points.txt +15 -0
  72. orforise-1.6.2.dist-info/licenses/LICENSE +624 -0
  73. orforise-1.6.2.dist-info/top_level.txt +1 -0
orforise-1.6.2.dist-info/RECORD ADDED
@@ -0,0 +1,73 @@
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+ ORForise/Aggregate_Compare.py,sha256=T61SdH9cY6KE9HnoVMqEn_yt5GOiG6_GukoVCMiCXaA,22788
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+ ORForise/Annotation_Compare.py,sha256=kd0J6UpvYlppmjSBenp9-Zrwzu1p5fnfMs8CvofAtXA,18460
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+ ORForise/Annotation_Intersector.py,sha256=LvV5h4NTZzzkaa1N2tOU8Bz63Fi2kRCy9c4qrmwXdkM,34481
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+ ORForise/Comparator.py,sha256=59VfUS8d19Xa83o1AsCuowDhhe-iNr5wO4FutDpoQRs,48078
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+ ORForise/Convert_To_GFF.py,sha256=6HUiWQUGOyEohvWDJH3hGLBvCvzFy0MdyZK_K29ikA8,5898
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+ ORForise/GFF_Adder.py,sha256=dm4JjezKUKHDMINf_lWLtm2nj4uvziJhwp3YYi5wSCg,28560
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+ ORForise/List_Tools.py,sha256=g46MLl4XU4VDJHeZ7Ky-SwEU9hLTxQ6LCCHG2DasxM8,1519
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+ ORForise/StORForise.py,sha256=ZlI_wLUE6QFKtRtrAAIEmeYA04Pucl36ys_CHFRO1xE,5650
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+ ORForise/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ ORForise/utils.py,sha256=sEDOATM5v50g9sKbBf2QinaCnGel7EtnKiR-UebtTwQ,15751
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+ ORForise/Aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ ORForise/Aux/StORF_Undetected/StORF_Undetected.py,sha256=B7f9AxXD6j2ip4QtuOi7pwtfBCxkexE0XiDCJrKSX5U,1318
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+ ORForise/Aux/StORF_Undetected/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ ORForise/Aux/StORF_Undetected/Completely_Undetected/Completey_Undetected.py,sha256=PjCtqenheuofqTaWpfJa7VCiMK0s-9kMnOlGIBl9f7k,1860
15
+ ORForise/Aux/StORF_Undetected/Completely_Undetected/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
16
+ ORForise/Aux/StORF_Undetected/unvitiated_Genes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
17
+ ORForise/Aux/StORF_Undetected/unvitiated_Genes/unvitiated_Missed_Genes.py,sha256=notWaFx7AG8BZjBhnGuSyitxa1cRK_7rygOPp9keGfM,1863
18
+ ORForise/Aux/TabToGFF/TabToGFF.py,sha256=i9PnODPdIcsLBiCIntiq_3Z8_WeajB8ZE--DeLdRf24,5168
19
+ ORForise/Aux/TabToGFF/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
20
+ ORForise/ORForise_Analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
21
+ ORForise/ORForise_Analysis/cds_checker.py,sha256=x838-PDd8HxZ3uhfW7wPzaJdiVwomNaYOZzMe-09f_0,2643
22
+ ORForise/ORForise_Analysis/gene_Lenghts.py,sha256=eDmJqVjBJYkBMuLr4s4XDA-E-fv0eEITpWAPySOynow,939
23
+ ORForise/ORForise_Analysis/genome_Metrics.py,sha256=Vra7X6AVJoBvjT6EAO819dPpqAOnWMlwSkWhwTVWNZk,10417
24
+ ORForise/ORForise_Analysis/hypothetical_gene_predictions.py,sha256=6SRNrNKUOHOnwsP96s1nI25oCj2oY4_2NcONO0EXj0c,3479
25
+ ORForise/ORForise_Analysis/missed_Gene_Metrics.py,sha256=ir54WJ_UpY_1UQd9kz67tTDwZvt7NSb20Yz0yVKVX3w,10890
26
+ ORForise/ORForise_Analysis/parital_Match_Analysis.py,sha256=a-f5MejmQftgrCUDtWV69Tp-UOYyJlgM77zf4v-MEVY,9515
27
+ ORForise/ORForise_Analysis/result_File_Analysis.py,sha256=ZHKW6sRW45NEExBqLVDnxpBPwsZyGTU-vm1TjawFsgY,9886
28
+ ORForise/ORForise_Analysis/start_Codon_Substitution.py,sha256=x_I7EGR0KqV3uos_UEJI79JKnuhjwqD-1XlJ0SR82uA,6114
29
+ ORForise/Tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
30
+ ORForise/Tools/Augustus/Augustus.py,sha256=OkDf0arkdEJocVEygWIkem9GTY5heg2IgnMJigByF3k,2283
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+ ORForise/Tools/Augustus/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
32
+ ORForise/Tools/Balrog/Balrog.py,sha256=j7CFZ2ysBtg_vdsfDoGGXifAp1VVUcdO7cqONc_Bk2s,2310
33
+ ORForise/Tools/Balrog/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
34
+ ORForise/Tools/EasyGene/EasyGene.py,sha256=FCvcmL6w_ytefSNvWfWXIG6h0BKObPtTcCp0iGUSdH0,2330
35
+ ORForise/Tools/EasyGene/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
36
+ ORForise/Tools/FGENESB/FGENESB.py,sha256=E6vghsstDeYgmT1lT4DL2M7wreYeXx2s-N-scCu_snk,2437
37
+ ORForise/Tools/FGENESB/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
38
+ ORForise/Tools/FragGeneScan/FragGeneScan.py,sha256=koPby-VZZ7X6RA1OBc3-yr9axGlm82LVbFZJ-kyx1Kw,2365
39
+ ORForise/Tools/FragGeneScan/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
40
+ ORForise/Tools/GFF/GFF.py,sha256=OBm3UmgusisqV7deUMHkruO3PLdlzr3OAc4OsZmRMdo,3763
41
+ ORForise/Tools/GFF/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
42
+ ORForise/Tools/GLIMMER3/GLIMMER3.py,sha256=EddNu6M1NrWDbWjvByM9gvStuvWoD5lq5jz0M27oro8,2686
43
+ ORForise/Tools/GLIMMER3/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
44
+ ORForise/Tools/GeneMark/GeneMark.py,sha256=92XHJJLU3zuFa9-TgibuDjP5rWFzwuFgX4SuUBk5K0Q,6391
45
+ ORForise/Tools/GeneMark/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ ORForise/Tools/GeneMarkHA/GeneMarkHA.py,sha256=QRl51kW8RVmLRDUwzhBQlptZkokJ1OILb6h525BXGL4,2296
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+ ORForise/Tools/GeneMarkHA/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
48
+ ORForise/Tools/GeneMarkHMM/GeneMarkHMM.py,sha256=l51rIRGchkH-r07x5SPQrDvsiF9IAtnaFQyevPymUQI,2314
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+ ORForise/Tools/GeneMarkHMM/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ ORForise/Tools/GeneMarkS/GeneMarkS.py,sha256=dhgw7ftJvd8kLkhc-GoU_TEovIuvGQHi5WO84dWB6Eo,2283
51
+ ORForise/Tools/GeneMarkS/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
52
+ ORForise/Tools/GeneMarkS2/GeneMarkS2.py,sha256=PX3lPktmvBZStwTSot45Xxg49fD2GqcFDPquhQsqTvM,2346
53
+ ORForise/Tools/GeneMarkS2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ ORForise/Tools/MetaGene/MetaGene.py,sha256=j6ISuAie2u4MSCaSgszK0cQtFV8PdNUHTDVcqIJ_wsE,2293
55
+ ORForise/Tools/MetaGene/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
56
+ ORForise/Tools/MetaGeneAnnotator/MetaGeneAnnotator.py,sha256=WSA-A4CR7v8NTGzxB8GxyBUyt2b4BrO7YjLOkQVtZGY,2445
57
+ ORForise/Tools/MetaGeneAnnotator/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
58
+ ORForise/Tools/MetaGeneMark/MetaGeneMark.py,sha256=QDPTsb8QdJqfIphjLwWoxT7oMZ-SVLT2PlDUPYHmsFQ,2432
59
+ ORForise/Tools/MetaGeneMark/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
60
+ ORForise/Tools/Prodigal/Prodigal.py,sha256=1KVkTL3gHp8iSNFt_CvPnLZUr66x1AfE0ZKxo2w65IE,2330
61
+ ORForise/Tools/Prodigal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
62
+ ORForise/Tools/Prokka/Prokka.py,sha256=Kcl1ocVj6hPOfEEwf8bBAWhzWX_XAe55kwNUeM8EUKg,2468
63
+ ORForise/Tools/Prokka/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
64
+ ORForise/Tools/StORF-Reporter/StORF-Reporter.py,sha256=mbpoCuzVDVVFZgSd3TDzgjbp-JsrxIDB-DL2qjQwq-U,2647
65
+ ORForise/Tools/StORF-Reporter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
66
+ ORForise/Tools/TransDecoder/TransDecoder.py,sha256=l9y4OFxhSdPRBhUprs0yt2fxtSwyNCOv7oKO-aTvpDk,2381
67
+ ORForise/Tools/TransDecoder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
68
+ orforise-1.6.2.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
69
+ orforise-1.6.2.dist-info/METADATA,sha256=xqVn0TcMdZkrKeyVbjENidxxhN6PKuHZkb0WC2nx5pE,59554
70
+ orforise-1.6.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ orforise-1.6.2.dist-info/entry_points.txt,sha256=_HaBzKQFXCkxHIIgBH_XIOng92-GWJ5FC29LmNaSpR0,670
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+ orforise-1.6.2.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
73
+ orforise-1.6.2.dist-info/RECORD,,
orforise-1.6.2.dist-info/WHEEL ADDED
@@ -0,0 +1,5 @@
1
+ Wheel-Version: 1.0
2
+ Generator: setuptools (80.9.0)
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any
5
+
orforise-1.6.2.dist-info/entry_points.txt ADDED
@@ -0,0 +1,15 @@
1
+ [console_scripts]
2
+ Aggregate-Compare = ORForise.Aggregate_Compare:main
3
+ Annotation-Compare = ORForise.Annotation_Compare:main
4
+ Annotation-Intersector = ORForise.Annotation_Intersector:main
5
+ Convert-To-GFF = ORForise.Convert_To_GFF:main
6
+ GFF-Adder = ORForise.GFF_Adder:main
7
+ List-Tools = ORForise.List_Tools:main
8
+ StORForise = ORForise.StORForise:main
9
+ aggregate-compare = ORForise.Aggregate_Compare:main
10
+ annotation-compare = ORForise.Annotation_Compare:main
11
+ annotation-intersector = ORForise.Annotation_Intersector:main
12
+ convert-to-gff = ORForise.Convert_To_GFF:main
13
+ gff-adder = ORForise.GFF_Adder:main
14
+ list-tools = ORForise.List_Tools:main
15
+ storforise = ORForise.StORForise:main