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cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
https://cumc.github.io/xqtl-protocol/
MIT License
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patch for fsusie #902

Closed hsun3163 closed 6 months ago

hsun3163 commented 6 months ago

Test on locally generated fsusie object, it can

  1. correctly identify all the item with the exhibited dataset
  2. add the new susie to PC based on specified parameters But the twas weight needs to be regenerated (I could disable this by forcing the inclusion of twas_weight in the output dataset)

Practically speaking, since all the files that actually required patching are

  1. the ROSMAP_mQTL and some MSBB_mQTL where no susie and twas are computed.
  2. the old ROSMAP result where no Susie and twas are computed. The two steps needs to be ran again anyway.

For the files that are named normaltop, they all have their correct counterpart so patching them is unnecessary. I will removed the normaltop from matching patterns and swaps in the old ROSMAP result as pattern afterward

(py3.11) [sunh14@lh06c33 fsusie_analysis]$ cat current_file | grep rds | grep -B1  normaltop
2024-03-03 18:18:37  180 Bytes MSBB_mQTL.chr8_107871128_114436939.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:00:56  180 Bytes MSBB_mQTL.chr8_107871128_114436939.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:19:10  180 Bytes MSBB_mQTL.chr8_111148742_115318911.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:12  180 Bytes MSBB_mQTL.chr8_111148742_115318911.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:28  180 Bytes MSBB_mQTL.chr8_123450819_126367120.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:03  180 Bytes MSBB_mQTL.chr8_123450819_126367120.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:45  180 Bytes MSBB_mQTL.chr8_123998496_127008930.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:00:56  180 Bytes MSBB_mQTL.chr8_123998496_127008930.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:19:18  180 Bytes MSBB_mQTL.chr8_124648326_128419050.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:06  180 Bytes MSBB_mQTL.chr8_124648326_128419050.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:28  180 Bytes MSBB_mQTL.chr8_138600838_141638283.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:03  180 Bytes MSBB_mQTL.chr8_138600838_141638283.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:53  180 Bytes MSBB_mQTL.chr8_138727725_142507230.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:10  180 Bytes MSBB_mQTL.chr8_138727725_142507230.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:19:02  180 Bytes MSBB_mQTL.chr8_140356470_145138636.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:00:56  180 Bytes MSBB_mQTL.chr8_140356470_145138636.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:19:02  180 Bytes MSBB_mQTL.chr8_142280161_145138636.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:00:56  180 Bytes MSBB_mQTL.chr8_142280161_145138636.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:45  176 Bytes MSBB_mQTL.chr8_6092101_10782346.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:00:56  176 Bytes MSBB_mQTL.chr8_6092101_10782346.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:37  180 Bytes MSBB_mQTL.chr8_67330954_71078032.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:00:56  180 Bytes MSBB_mQTL.chr8_67330954_71078032.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:19:10  176 Bytes MSBB_mQTL.chr8_68466623_72228629.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:12  176 Bytes MSBB_mQTL.chr8_68466623_72228629.fsusie_mixture_normaltop_pc_weights.rds
2024-03-03 18:18:53  176 Bytes MSBB_mQTL.chr8_8899871_13665588.fsusie_mixture_normal_top_pc_weights.rds
2024-03-03 18:01:10  176 Bytes MSBB_mQTL.chr8_8899871_13665588.fsusie_mixture_normaltop_pc_weights.rds
--
2024-03-03 20:37:09   39.8 MiB ROSMAP_haQTL.chr1_152533602_156209051.fsusie_mixture_normal_top_pc_weights.rds
2024-03-01 14:46:10   39.8 MiB ROSMAP_haQTL.chr1_152533602_156209051.fsusie_mixture_normaltop_pc_weights.rds
--
2024-03-03 19:48:43   41.0 MiB ROSMAP_haQTL.chr1_17871430_20819502.fsusie_mixture_normal_top_pc_weights.rds
2024-03-01 17:33:03   40.6 MiB ROSMAP_haQTL.chr1_17871430_20819502.fsusie_mixture_normaltop_pc_weights.rds
--
2024-03-03 20:11:06   67.3 MiB ROSMAP_haQTL.chr1_191167786_198067260.fsusie_mixture_normal_top_pc_weights.rds
2024-03-01 12:53:22   67.8 MiB ROSMAP_haQTL.chr1_191167786_198067260.fsusie_mixture_normaltop_pc_weights.rds
--
2024-03-03 19:55:04   52.5 MiB ROSMAP_haQTL.chr1_63833229_68259979.fsusie_mixture_normal_top_pc_weights.rds
2024-03-01 18:49:45   52.3 MiB ROSMAP_haQTL.chr1_63833229_68259979.fsusie_mixture_normaltop_pc_weights.rds
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