lynxgwas 0.1.0__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 (167) hide show
  1. lynxgwas-0.1.0/LICENSE +21 -0
  2. lynxgwas-0.1.0/PKG-INFO +804 -0
  3. lynxgwas-0.1.0/README.md +783 -0
  4. lynxgwas-0.1.0/pyproject.toml +36 -0
  5. lynxgwas-0.1.0/python/lynxgwas/__init__.py +1 -0
  6. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/AlleleHarmonizer$Result.class +0 -0
  7. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/AlleleHarmonizer.class +0 -0
  8. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/AnalysisColumnProvider$1.class +0 -0
  9. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/AnalysisColumnProvider.class +0 -0
  10. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/BaseStepPipeline$PipelineResult.class +0 -0
  11. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/BaseStepPipeline.class +0 -0
  12. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/CojoAdapter.class +0 -0
  13. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ColocAdapter.class +0 -0
  14. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Config.class +0 -0
  15. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ContentHasher.class +0 -0
  16. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Exon.class +0 -0
  17. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/FinemapAdapter.class +0 -0
  18. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Gene.class +0 -0
  19. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/GenomeSkyline.class +0 -0
  20. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/GffParser.class +0 -0
  21. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/GwamaAdapter.class +0 -0
  22. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/GwasParser.class +0 -0
  23. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/GwasQc$Result.class +0 -0
  24. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/GwasQc.class +0 -0
  25. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/InputContractWriter$DatasetMeta.class +0 -0
  26. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/InputContractWriter.class +0 -0
  27. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/JsonExporter$Jb.class +0 -0
  28. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/JsonExporter.class +0 -0
  29. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdCalculator$LdResult.class +0 -0
  30. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdCalculator.class +0 -0
  31. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdGwasDiagnostic$DiagnosticResult.class +0 -0
  32. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdGwasDiagnostic$FlaggedSnp.class +0 -0
  33. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdGwasDiagnostic.class +0 -0
  34. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdMatrixComputer$Result.class +0 -0
  35. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LdMatrixComputer.class +0 -0
  36. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocalServer$LocusMatrixJobMeta.class +0 -0
  37. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocalServer$ProjectState.class +0 -0
  38. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocalServer$SusiexJob.class +0 -0
  39. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocalServer.class +0 -0
  40. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LociMutationService$JournalEntry.class +0 -0
  41. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LociMutationService$MutationResult.class +0 -0
  42. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LociMutationService.class +0 -0
  43. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LociParser.class +0 -0
  44. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Locus.class +0 -0
  45. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusGwasExtractor$Result.class +0 -0
  46. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusGwasExtractor.class +0 -0
  47. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusOutput$LdTriangle$LdSnp.class +0 -0
  48. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusOutput$LdTriangle.class +0 -0
  49. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusOutput$LocusContext.class +0 -0
  50. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusOutput$LocusRef.class +0 -0
  51. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusOutput.class +0 -0
  52. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusUpdater$LdViolation.class +0 -0
  53. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusUpdater$SplitRegion.class +0 -0
  54. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusUpdater$UpdateResult.class +0 -0
  55. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusUpdater$ValidationResult.class +0 -0
  56. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/LocusUpdater.class +0 -0
  57. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Main$1.class +0 -0
  58. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Main$PipelineResult.class +0 -0
  59. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Main.class +0 -0
  60. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusExcelWriter.class +0 -0
  61. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusMerger.class +0 -0
  62. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusProgress.class +0 -0
  63. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusResult$DatasetInfo.class +0 -0
  64. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusResult$DatasetLocusStat.class +0 -0
  65. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusResult$LocusRow.class +0 -0
  66. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusResult.class +0 -0
  67. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusScanner$LocusAgg.class +0 -0
  68. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusScanner$ScanOneResult.class +0 -0
  69. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/MultiLocusScanner.class +0 -0
  70. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/OutputContractValidator$ColumnDecl.class +0 -0
  71. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/OutputContractValidator$ValidationResult.class +0 -0
  72. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/OutputContractValidator.class +0 -0
  73. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/PlinkSubsetter$SubsetResult.class +0 -0
  74. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/PlinkSubsetter.class +0 -0
  75. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/PluginEngine$RunRequest.class +0 -0
  76. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/PluginEngine$RunResult.class +0 -0
  77. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/PluginEngine.class +0 -0
  78. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ProgressTracker.class +0 -0
  79. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ProjectMetadata$StaleReason.class +0 -0
  80. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ProjectMetadata.class +0 -0
  81. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Snp.class +0 -0
  82. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SnpAnnotator.class +0 -0
  83. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SnpMatcher$AlleleMatch.class +0 -0
  84. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SnpMatcher$BimEntry.class +0 -0
  85. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SnpMatcher$Result.class +0 -0
  86. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SnpMatcher.class +0 -0
  87. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/StableSnpId.class +0 -0
  88. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/StatsUtil.class +0 -0
  89. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/StepManifest.class +0 -0
  90. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SusieAdapter.class +0 -0
  91. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SusiexAdapter$Member.class +0 -0
  92. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SusiexAdapter$ResultRow.class +0 -0
  93. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SusiexAdapter$RunResult.class +0 -0
  94. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/SusiexAdapter.class +0 -0
  95. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ToolDescriptor$OutputColumn.class +0 -0
  96. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ToolDescriptor$Param.class +0 -0
  97. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/ToolDescriptor.class +0 -0
  98. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/Transcript.class +0 -0
  99. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ColumnSpec$ColType.class +0 -0
  100. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ColumnSpec.class +0 -0
  101. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExcelExporter$ExportProgress.class +0 -0
  102. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExcelExporter$GenePos.class +0 -0
  103. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExcelExporter.class +0 -0
  104. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$GwasPassthroughProvider.class +0 -0
  105. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LdWithLeadProvider.class +0 -0
  106. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LeadFlagsProvider.class +0 -0
  107. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LocusCoreProvider.class +0 -0
  108. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LocusCountsProvider.class +0 -0
  109. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LocusIdentitySnpProvider.class +0 -0
  110. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LocusLeadProvider.class +0 -0
  111. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$LocusNearestGeneProvider.class +0 -0
  112. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$NearestGeneSnpProvider.class +0 -0
  113. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry$RsidProvider.class +0 -0
  114. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/ExportRegistry.class +0 -0
  115. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/GwasSchema.class +0 -0
  116. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/LocusColumnProvider.class +0 -0
  117. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/LocusContext.class +0 -0
  118. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/SnpColumnProvider.class +0 -0
  119. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/SnpContext.class +0 -0
  120. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/XlsxWriter$Sheet.class +0 -0
  121. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/XlsxWriter$SheetData.class +0 -0
  122. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/export/XlsxWriter.class +0 -0
  123. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/loci/LociIdentifier$CandidateSnp.class +0 -0
  124. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/loci/LociIdentifier$ClumpInterval.class +0 -0
  125. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/loci/LociIdentifier$IdentifiedLocus.class +0 -0
  126. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/loci/LociIdentifier$Params.class +0 -0
  127. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/loci/LociIdentifier.class +0 -0
  128. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/loci/LociProgress.class +0 -0
  129. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/CrossFileLookup.class +0 -0
  130. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/DbSnpRecord.class +0 -0
  131. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/GlobalConfig$NcbiApiConfig.class +0 -0
  132. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/GlobalConfig$RefPanel.class +0 -0
  133. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/GlobalConfig$SnpDatabase.class +0 -0
  134. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/GlobalConfig.class +0 -0
  135. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/GnomadProvider.class +0 -0
  136. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/MatchResult.class +0 -0
  137. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/NcbiDbSnpProvider.class +0 -0
  138. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RateLimiter.class +0 -0
  139. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiCache.class +0 -0
  140. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiCompleter$CompletionResult.class +0 -0
  141. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiCompleter$Config.class +0 -0
  142. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiCompleter$UnmatchedSnp.class +0 -0
  143. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiCompleter.class +0 -0
  144. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiProvider$ApiResult.class +0 -0
  145. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidApiProvider.class +0 -0
  146. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidDetector$DetectionResult.class +0 -0
  147. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidDetector.class +0 -0
  148. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidMatcher.class +0 -0
  149. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidPipeline.class +0 -0
  150. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidProgress.class +0 -0
  151. lynxgwas-0.1.0/python/lynxgwas/_bundled/classes/rsid/RsidRecovery.class +0 -0
  152. lynxgwas-0.1.0/python/lynxgwas/_bundled/lib/htsjdk-5.0.0-all.jar +0 -0
  153. lynxgwas-0.1.0/python/lynxgwas/_bundled/tools/cojo_conditional.yaml +16 -0
  154. lynxgwas-0.1.0/python/lynxgwas/_bundled/tools/coloc.yaml +21 -0
  155. lynxgwas-0.1.0/python/lynxgwas/_bundled/tools/finemap.yaml +13 -0
  156. lynxgwas-0.1.0/python/lynxgwas/_bundled/tools/gwama_meta.yaml +18 -0
  157. lynxgwas-0.1.0/python/lynxgwas/_bundled/tools/susie_finemapping.yaml +16 -0
  158. lynxgwas-0.1.0/python/lynxgwas/_bundled/web/assets/lynxgwas-icon.svg +10 -0
  159. lynxgwas-0.1.0/python/lynxgwas/_bundled/web/index.html +2282 -0
  160. lynxgwas-0.1.0/python/lynxgwas/_bundled/web/viewer.html +4728 -0
  161. lynxgwas-0.1.0/python/lynxgwas/cli.py +246 -0
  162. lynxgwas-0.1.0/python/lynxgwas.egg-info/PKG-INFO +804 -0
  163. lynxgwas-0.1.0/python/lynxgwas.egg-info/SOURCES.txt +165 -0
  164. lynxgwas-0.1.0/python/lynxgwas.egg-info/dependency_links.txt +1 -0
  165. lynxgwas-0.1.0/python/lynxgwas.egg-info/entry_points.txt +2 -0
  166. lynxgwas-0.1.0/python/lynxgwas.egg-info/top_level.txt +1 -0
  167. lynxgwas-0.1.0/setup.cfg +4 -0
lynxgwas-0.1.0/LICENSE ADDED
@@ -0,0 +1,21 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2026 Alsamman Alsamman
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.