From 56ce88ad31dec3cece63e9370ca4e4c02139753b Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Tue, 16 Mar 2021 11:38:13 +0300 Subject: delete unwanted correlation stuff (#5) * delete unwanted correlation stuff * Refactor/clean up correlations (#4) * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz --- tests/integration/correlation_data.json | 18 - tests/integration/expected_corr_results.json | 1902 -------------------------- 2 files changed, 1920 deletions(-) delete mode 100644 tests/integration/correlation_data.json delete mode 100644 tests/integration/expected_corr_results.json (limited to 'tests/integration') diff --git a/tests/integration/correlation_data.json b/tests/integration/correlation_data.json deleted file mode 100644 index 87d24e3..0000000 --- a/tests/integration/correlation_data.json +++ /dev/null @@ -1,18 +0,0 @@ -{ - "primary_samples": "C57BL/6J,DBA/2J,B6D2F1,D2B6F1,BXD1,BXD2,BXD5,BXD6,BXD8,BXD9,BXD11,BXD12,BXD13,BXD14,BXD15,BXD16,BXD18,BXD19,BXD20,BXD21,BXD22,BXD23,BXD24,BXD24a,BXD25,BXD27,BXD28,BXD29,BXD30,BXD31,BXD32,BXD33,BXD34,BXD35,BXD36,BXD37,BXD38,BXD39,BXD40,BXD41,BXD42,BXD43,BXD44,BXD45,BXD48,BXD48a,BXD49,BXD50,BXD51,BXD52,BXD53,BXD54,BXD55,BXD56,BXD59,BXD60,BXD61,BXD62,BXD63,BXD64,BXD65,BXD65a,BXD65b,BXD66,BXD67,BXD68,BXD69,BXD70,BXD71,BXD72,BXD73,BXD73a,BXD73b,BXD74,BXD75,BXD76,BXD77,BXD78,BXD79,BXD81,BXD83,BXD84,BXD85,BXD86,BXD87,BXD88,BXD89,BXD90,BXD91,BXD93,BXD94,BXD95,BXD98,BXD99,BXD100,BXD101,BXD102,BXD104,BXD105,BXD106,BXD107,BXD108,BXD109,BXD110,BXD111,BXD112,BXD113,BXD114,BXD115,BXD116,BXD117,BXD119,BXD120,BXD121,BXD122,BXD123,BXD124,BXD125,BXD126,BXD127,BXD128,BXD128a,BXD130,BXD131,BXD132,BXD133,BXD134,BXD135,BXD136,BXD137,BXD138,BXD139,BXD141,BXD142,BXD144,BXD145,BXD146,BXD147,BXD148,BXD149,BXD150,BXD151,BXD152,BXD153,BXD154,BXD155,BXD156,BXD157,BXD160,BXD161,BXD162,BXD165,BXD168,BXD169,BXD170,BXD171,BXD172,BXD173,BXD174,BXD175,BXD176,BXD177,BXD178,BXD180,BXD181,BXD183,BXD184,BXD186,BXD187,BXD188,BXD189,BXD190,BXD191,BXD192,BXD193,BXD194,BXD195,BXD196,BXD197,BXD198,BXD199,BXD200,BXD201,BXD202,BXD203,BXD204,BXD205,BXD206,BXD207,BXD208,BXD209,BXD210,BXD211,BXD212,BXD213,BXD214,BXD215,BXD216,BXD217,BXD218,BXD219,BXD220", - 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"sample_p": "1.344e-03", - "lit_corr": "--", - "tissue_corr": "0.108", - "tissue_pvalue": "5.990e-01" - }, - { - "index": 4, - "trait_id": "1415740_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415740_at:HC_M2_0606_P:755cdc41d0d50a03b647", - "symbol": "Psmc5", - "description": "protease (prosome, macropain) 26S subunit, ATPase 5; exons 7, 8, 9", - "location": "Chr11: 106.123450", - "mean": "12.424", - "additive": "0.059", - "lod_score": "2.6", - "lrs_location": "Chr9: 34.013550", - "sample_r": "0.364", - "num_overlap": 67, - "sample_p": "2.476e-03", - "lit_corr": "--", - "tissue_corr": "0.333", - "tissue_pvalue": "9.696e-02" - }, - { - "index": 5, - "trait_id": "1415757_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415757_at:HC_M2_0606_P:8bbf06aa2e3aa5530934", - "symbol": "Gbf1", - "description": "Golgi-specific brefeldin A-resistance factor 1; last exon and proximal 3' UTR", - "location": "Chr19: 46.360410", - "mean": "9.800", - "additive": "-0.062", - "lod_score": "2.0", - "lrs_location": "Chr17: 52.750885", - "sample_r": "0.363", - "num_overlap": 67, - "sample_p": "2.539e-03", - "lit_corr": "--", - "tissue_corr": "-0.059", - "tissue_pvalue": "7.741e-01" - }, - { - "index": 6, - "trait_id": "1415768_a_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415768_a_at:HC_M2_0606_P:5e67109eee04f5da3393", - "symbol": "Ube2r2", - "description": "ubiquitin-conjugating enzyme E2R 2", - "location": "Chr4: 41.137929", - "mean": "9.811", - "additive": "-0.087", - "lod_score": "3.3", - "lrs_location": "Chr12: 114.553844", - "sample_r": "-0.312", - "num_overlap": 67, - "sample_p": "1.019e-02", - "lit_corr": "--", - "tissue_corr": "-0.007", - "tissue_pvalue": "9.711e-01" - }, - { - "index": 7, - "trait_id": "1415670_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415670_at:HC_M2_0606_P:4f82d7374f29ebfacaaf", - "symbol": "Copg", - "description": "coatomer protein complex, subunit gamma 1; two of the three last exons and proximal 3' UTR", - "location": "Chr6: 87.859681", - "mean": "11.199", - "additive": "-0.113", - 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"mean": "10.974", - "additive": "0.048", - "lod_score": "2.0", - "lrs_location": "Chr4: 5.606394", - "sample_r": "-0.258", - "num_overlap": 67, - "sample_p": "3.489e-02", - "lit_corr": "--", - "tissue_corr": "0.271", - "tissue_pvalue": "1.812e-01" - }, - { - "index": 14, - "trait_id": "1415725_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415725_at:HC_M2_0606_P:fbd6458be4f8ccbf1dc0", - "symbol": "Rrn3", - "description": "RRN3 RNA polymerase I transcription factor homolog (yeast)", - "location": "Chr16: 13.814359", - "mean": "9.195", - "additive": "-0.085", - "lod_score": "2.8", - "lrs_location": "Chr1: 148.717644", - "sample_r": "0.256", - "num_overlap": 67, - "sample_p": "3.636e-02", - "lit_corr": "--", - "tissue_corr": "0.587", - "tissue_pvalue": "1.621e-03" - }, - { - "index": 15, - "trait_id": "1415717_at", - "dataset": "HC_M2_0606_P", - "hmac": "1415717_at:HC_M2_0606_P:dd51438830e4033114f8", - "symbol": "Rnf220", - "description": "ring finger protein 220; mid 3' UTR", - "location": "Chr4: 116.944155", - 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