SigProfilerAssignment 0.1.1__tar.gz → 0.1.2__tar.gz

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Files changed (186) hide show
  1. {SigProfilerAssignment-0.1.1/SigProfilerAssignment.egg-info → SigProfilerAssignment-0.1.2}/PKG-INFO +1 -1
  2. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/decomposition.py +4 -0
  3. SigProfilerAssignment-0.1.2/SigProfilerAssignment/version.py +8 -0
  4. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2/SigProfilerAssignment.egg-info}/PKG-INFO +1 -1
  5. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/setup.py +2 -2
  6. SigProfilerAssignment-0.1.1/SigProfilerAssignment/version.py +0 -8
  7. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/LICENSE.txt +0 -0
  8. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/MANIFEST.in +0 -0
  9. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/README.md +0 -0
  10. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/Analyzer.py +0 -0
  11. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py +0 -0
  12. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py +0 -0
  13. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py +0 -0
  14. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py +0 -0
  15. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py +0 -0
  16. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py +0 -0
  17. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py +0 -0
  18. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Accolade_fermante.png +0 -0
  19. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/ReferenceFiles/CREDIT.md +0 -0
  20. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Fonts/Arial Bold.ttf +0 -0
  21. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/DecompositionPlots/SigProfilerPlottingMatrix.py +0 -0
  22. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/__init__.py +0 -0
  23. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/21_breast_WGS_substitutions.mat +0 -0
  24. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/CNV_features.tsv +0 -0
  25. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/CNV_signatures.txt +0 -0
  26. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/CN_classes_dictionary.txt +0 -0
  27. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/DBS_signatures_genome_builds.xlsx +0 -0
  28. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v1_SBS_GRCh37.txt +0 -0
  29. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v1_SBS_GRCh37_exome.txt +0 -0
  30. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v2_SBS_GRCh37.txt +0 -0
  31. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v2_SBS_GRCh37_exome.txt +0 -0
  32. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.1_DBS_GRCh37.txt +0 -0
  33. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.1_DBS_GRCh37_exome.txt +0 -0
  34. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.1_ID_GRCh37.txt +0 -0
  35. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.1_SBS_GRCh37.txt +0 -0
  36. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.1_SBS_GRCh37_exome.txt +0 -0
  37. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.2_DBS_GRCh37.txt +0 -0
  38. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.2_DBS_GRCh37_exome.txt +0 -0
  39. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.2_ID_GRCh37.txt +0 -0
  40. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.2_SBS288_GRCh37.txt +0 -0
  41. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.2_SBS_GRCh37.txt +0 -0
  42. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.2_SBS_GRCh37_exome.txt +0 -0
  43. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_CN_GRCh37.txt +0 -0
  44. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_DBS_GRCh37.txt +0 -0
  45. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_DBS_GRCh37_exome.txt +0 -0
  46. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_ID_GRCh37.txt +0 -0
  47. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_SBS_GRCh37.txt +0 -0
  48. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_SBS_GRCh37_exome.txt +0 -0
  49. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.4_CN_GRCh37.txt +0 -0
  50. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.4_DBS_GRCh37.txt +0 -0
  51. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.4_DBS_GRCh37_exome.txt +0 -0
  52. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.4_ID_GRCh37.txt +0 -0
  53. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.4_SBS_GRCh37.txt +0 -0
  54. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.4_SBS_GRCh37_exome.txt +0 -0
  55. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3_DBS_GRCh37.txt +0 -0
  56. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3_DBS_GRCh37_exome.txt +0 -0
  57. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3_ID_GRCh37.txt +0 -0
  58. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3_SBS_GRCh37.txt +0 -0
  59. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3_SBS_GRCh37_exome.txt +0 -0
  60. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v1_SBS_GRCh38.txt +0 -0
  61. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v1_SBS_GRCh38_exome.txt +0 -0
  62. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v2_SBS_GRCh38.txt +0 -0
  63. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v2_SBS_GRCh38_exome.txt +0 -0
  64. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.1_DBS_GRCh38.txt +0 -0
  65. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.1_DBS_GRCh38_exome.txt +0 -0
  66. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.1_SBS_GRCh38.txt +0 -0
  67. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.1_SBS_GRCh38_exome.txt +0 -0
  68. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.2_DBS_GRCh38.txt +0 -0
  69. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.2_DBS_GRCh38_exome.txt +0 -0
  70. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.2_SBS_GRCh38.txt +0 -0
  71. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.2_SBS_GRCh38_exome.txt +0 -0
  72. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.3_DBS_GRCh38.txt +0 -0
  73. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.3_DBS_GRCh38_exome.txt +0 -0
  74. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.3_SBS_GRCh38.txt +0 -0
  75. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.3_SBS_GRCh38_exome.txt +0 -0
  76. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.4_DBS_GRCh38.txt +0 -0
  77. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.4_DBS_GRCh38_exome.txt +0 -0
  78. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.4_SBS_GRCh38.txt +0 -0
  79. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.4_SBS_GRCh38_exome.txt +0 -0
  80. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3.4_SV_GRCh38.txt +0 -0
  81. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3_DBS_GRCh38.txt +0 -0
  82. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3_DBS_GRCh38_exome.txt +0 -0
  83. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3_SBS_GRCh38.txt +0 -0
  84. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/GRCh38/COSMIC_v3_SBS_GRCh38_exome.txt +0 -0
  85. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v1_SBS_mm10.txt +0 -0
  86. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v1_SBS_mm10_exome.txt +0 -0
  87. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v2_SBS_mm10.txt +0 -0
  88. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v2_SBS_mm10_exome.txt +0 -0
  89. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.1_DBS_mm10.txt +0 -0
  90. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.1_DBS_mm10_exome.txt +0 -0
  91. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.1_SBS_mm10.txt +0 -0
  92. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.1_SBS_mm10_exome.txt +0 -0
  93. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.2_DBS_mm10.txt +0 -0
  94. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.2_DBS_mm10_exome.txt +0 -0
  95. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.2_SBS_mm10.txt +0 -0
  96. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.2_SBS_mm10_exome.txt +0 -0
  97. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.3_DBS_mm10.txt +0 -0
  98. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.3_DBS_mm10_exome.txt +0 -0
  99. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.3_SBS_mm10.txt +0 -0
  100. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.3_SBS_mm10_exome.txt +0 -0
  101. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.4_DBS_mm10.txt +0 -0
  102. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.4_DBS_mm10_exome.txt +0 -0
  103. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.4_SBS_mm10.txt +0 -0
  104. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3.4_SBS_mm10_exome.txt +0 -0
  105. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3_DBS_mm10.txt +0 -0
  106. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3_DBS_mm10_exome.txt +0 -0
  107. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3_SBS_mm10.txt +0 -0
  108. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm10/COSMIC_v3_SBS_mm10_exome.txt +0 -0
  109. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v1_SBS_mm9.txt +0 -0
  110. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v1_SBS_mm9_exome.txt +0 -0
  111. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v2_SBS_mm9.txt +0 -0
  112. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v2_SBS_mm9_exome.txt +0 -0
  113. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.1_DBS_mm9.txt +0 -0
  114. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.1_DBS_mm9_exome.txt +0 -0
  115. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.1_SBS_mm9.txt +0 -0
  116. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.1_SBS_mm9_exome.txt +0 -0
  117. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.2_DBS_mm9.txt +0 -0
  118. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.2_DBS_mm9_exome.txt +0 -0
  119. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.2_SBS_mm9.txt +0 -0
  120. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.2_SBS_mm9_exome.txt +0 -0
  121. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.3_DBS_mm9.txt +0 -0
  122. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.3_DBS_mm9_exome.txt +0 -0
  123. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.3_SBS_mm9.txt +0 -0
  124. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.3_SBS_mm9_exome.txt +0 -0
  125. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.4_DBS_mm9.txt +0 -0
  126. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.4_DBS_mm9_exome.txt +0 -0
  127. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.4_SBS_mm9.txt +0 -0
  128. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3.4_SBS_mm9_exome.txt +0 -0
  129. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3_DBS_mm9.txt +0 -0
  130. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3_DBS_mm9_exome.txt +0 -0
  131. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3_SBS_mm9.txt +0 -0
  132. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/mm9/COSMIC_v3_SBS_mm9_exome.txt +0 -0
  133. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v1_SBS_rn6.txt +0 -0
  134. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v1_SBS_rn6_exome.txt +0 -0
  135. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v2_SBS_rn6.txt +0 -0
  136. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v2_SBS_rn6_exome.txt +0 -0
  137. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.1_DBS_rn6.txt +0 -0
  138. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.1_DBS_rn6_exome.txt +0 -0
  139. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.1_SBS_rn6.txt +0 -0
  140. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.1_SBS_rn6_exome.txt +0 -0
  141. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.2_DBS_rn6.txt +0 -0
  142. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.2_DBS_rn6_exome.txt +0 -0
  143. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.2_SBS_rn6.txt +0 -0
  144. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.2_SBS_rn6_exome.txt +0 -0
  145. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.3_DBS_rn6.txt +0 -0
  146. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.3_DBS_rn6_exome.txt +0 -0
  147. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.3_SBS_rn6.txt +0 -0
  148. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.3_SBS_rn6_exome.txt +0 -0
  149. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.4_DBS_rn6.txt +0 -0
  150. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.4_DBS_rn6_exome.txt +0 -0
  151. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.4_SBS_rn6.txt +0 -0
  152. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3.4_SBS_rn6_exome.txt +0 -0
  153. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3_DBS_rn6.txt +0 -0
  154. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3_DBS_rn6_exome.txt +0 -0
  155. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3_SBS_rn6.txt +0 -0
  156. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Reference_Signatures/rn6/COSMIC_v3_SBS_rn6_exome.txt +0 -0
  157. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/SBS_signatures_genome_builds.xlsx +0 -0
  158. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/Samples.txt +0 -0
  159. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/csvexample.csv +0 -0
  160. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/sigProfiler_DBS_signatures.csv +0 -0
  161. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/sigProfiler_ID_signatures.csv +0 -0
  162. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/sigProfiler_SBS_signatures_2018_03_28.csv +0 -0
  163. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/cnv_input/all.breast.ascat.summary.sample.tsv +0 -0
  164. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/CNV48_S3_Signatures.txt +0 -0
  165. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/DBS78_S3_Signatures.txt +0 -0
  166. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/ID83_S3_Signatures.txt +0 -0
  167. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/SBS96_S3_Signatures.txt +0 -0
  168. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/SV32_S3_Signatures.txt +0 -0
  169. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/sample_matrix_CNV48.txt +0 -0
  170. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/sample_matrix_DBS.txt +0 -0
  171. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/sample_matrix_ID.txt +0 -0
  172. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/sample_matrix_SBS.txt +0 -0
  173. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/txt_input/sample_matrix_SV32.txt +0 -0
  174. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/vcf_input/PD3851a.vcf +0 -0
  175. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/vcf_input/PD3890a.vcf +0 -0
  176. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/vcf_input/PD3904a.vcf +0 -0
  177. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/vcf_input/PD3945a.vcf +0 -0
  178. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/data/tests/vcf_input/PD4005a.vcf +0 -0
  179. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/decompose_subroutines.py +0 -0
  180. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/single_sample.py +0 -0
  181. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment.egg-info/SOURCES.txt +0 -0
  182. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment.egg-info/dependency_links.txt +0 -0
  183. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment.egg-info/not-zip-safe +0 -0
  184. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment.egg-info/requires.txt +0 -0
  185. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment.egg-info/top_level.txt +0 -0
  186. {SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/setup.cfg +0 -0
{SigProfilerAssignment-0.1.1/SigProfilerAssignment.egg-info → SigProfilerAssignment-0.1.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: SigProfilerAssignment
3
- Version: 0.1.1
3
+ Version: 0.1.2
4
4
  Summary: Mutational signatures attribution and decomposition tool
5
5
  Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
6
6
  Author: Raviteja Vangara
{SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/SigProfilerAssignment/decomposition.py RENAMED
@@ -24,6 +24,7 @@ from SigProfilerMatrixGenerator.scripts import (
24
24
  SigProfilerMatrixGeneratorFunc as datadump,
25
25
  )
26
26
  from SigProfilerMatrixGenerator.scripts import CNVMatrixGenerator as scna
27
+ from sigProfilerPlotting import sigProfilerPlotting as sigPlot
27
28
  import sigProfilerPlotting
28
29
  import os, sys
29
30
  from PyPDF2 import PdfMerger
@@ -302,6 +303,9 @@ def spa_analyze(
302
303
  mutation_type = str(genomes.shape[0])
303
304
  m = mutation_type
304
305
 
306
+ # Re-indexing the input matrix file by using process_input function from SigProfilePlotting
307
+ genomes = sigPlot.process_input(genomes, m)
308
+
305
309
  m_for_subgroups = ""
306
310
  if m == "96" or m == "288" or m == "1536":
307
311
  m_for_subgroups = "SBS"
SigProfilerAssignment-0.1.2/SigProfilerAssignment/version.py ADDED
@@ -0,0 +1,8 @@
1
+
2
+ # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
3
+ short_version = '0.1.2'
4
+ version = '0.1.2'
5
+ Update = 'v0.1.2: Add matrix input format processing'
6
+
7
+
8
+
{SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2/SigProfilerAssignment.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: SigProfilerAssignment
3
- Version: 0.1.1
3
+ Version: 0.1.2
4
4
  Summary: Mutational signatures attribution and decomposition tool
5
5
  Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
6
6
  Author: Raviteja Vangara
{SigProfilerAssignment-0.1.1 → SigProfilerAssignment-0.1.2}/setup.py RENAMED
@@ -6,7 +6,7 @@ import os
6
6
  if os.path.exists("dist"):
7
7
  shutil.rmtree("dist")
8
8
 
9
- VERSION = "0.1.1"
9
+ VERSION = "0.1.2"
10
10
 
11
11
 
12
12
  def write_version_py(filename="SigProfilerAssignment/version.py"):
@@ -15,7 +15,7 @@ def write_version_py(filename="SigProfilerAssignment/version.py"):
15
15
  # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
16
16
  short_version = '%(version)s'
17
17
  version = '%(version)s'
18
- Update = 'v0.1.1: Update cosmic fit and decompose fit to use SV COSMIC signatures.'
18
+ Update = 'v0.1.2: Add matrix input format processing'
19
19
 
20
20
 
21
21
  """
SigProfilerAssignment-0.1.1/SigProfilerAssignment/version.py DELETED
@@ -1,8 +0,0 @@
1
-
2
- # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
3
- short_version = '0.1.1'
4
- version = '0.1.1'
5
- Update = 'v0.1.1: Update cosmic fit and decompose fit to use SV COSMIC signatures.'
6
-
7
-
8
-