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-rw-r--r--tests/integration/correlation_data.json18
-rw-r--r--tests/integration/expected_corr_results.json1902
-rw-r--r--tests/integration/test_correlation.py57
-rw-r--r--tests/unit/correlation/__init__.py0
-rw-r--r--tests/unit/correlation/correlation_test_data.json18
-rw-r--r--tests/unit/correlation/dataset.json64
-rw-r--r--tests/unit/correlation/expected_correlation_results.json1902
-rw-r--r--tests/unit/correlation/group_data_test.json214
-rw-r--r--tests/unit/correlation/my_results.json388
-rw-r--r--tests/unit/correlation/test_correlation_computations.py65
-rw-r--r--tests/unit/correlation/test_show_corr_results.py226
-rw-r--r--tests/unit/utility/__init__.py0
-rw-r--r--tests/unit/utility/test_chunks.py19
-rw-r--r--tests/unit/utility/test_corr_result_helpers.py35
-rw-r--r--tests/unit/utility/test_hmac.py51
15 files changed, 4959 insertions, 0 deletions
diff --git a/tests/integration/correlation_data.json b/tests/integration/correlation_data.json
new file mode 100644
index 0000000..87d24e3
--- /dev/null
+++ b/tests/integration/correlation_data.json
@@ -0,0 +1,18 @@
+{
+ "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",
+ "trait_id": "1444666_at",
+ "dataset": "HC_M2_0606_P",
+ "sample_vals": "{\"C57BL/6J\":\"6.638\",\"DBA/2J\":\"6.266\",\"B6D2F1\":\"6.494\",\"D2B6F1\":\"6.565\",\"BXD1\":\"6.357\",\"BXD2\":\"6.456\",\"BXD5\":\"6.590\",\"BXD6\":\"6.568\",\"BXD8\":\"6.581\",\"BXD9\":\"6.322\",\"BXD11\":\"6.519\",\"BXD12\":\"6.543\",\"BXD13\":\"6.636\",\"BXD14\":\"x\",\"BXD15\":\"6.578\",\"BXD16\":\"6.636\",\"BXD18\":\"x\",\"BXD19\":\"6.562\",\"BXD20\":\"6.610\",\"BXD21\":\"6.668\",\"BXD22\":\"6.607\",\"BXD23\":\"6.513\",\"BXD24\":\"6.601\",\"BXD24a\":\"x\",\"BXD25\":\"x\",\"BXD27\":\"6.573\",\"BXD28\":\"6.639\",\"BXD29\":\"6.656\",\"BXD30\":\"x\",\"BXD31\":\"6.549\",\"BXD32\":\"6.502\",\"BXD33\":\"6.584\",\"BXD34\":\"6.261\",\"BXD35\":\"x\",\"BXD36\":\"x\",\"BXD37\":\"x\",\"BXD38\":\"6.646\",\"BXD39\":\"6.584\",\"BXD40\":\"6.790\",\"BXD41\":\"x\",\"BXD42\":\"6.536\",\"BXD43\":\"6.476\",\"BXD44\":\"6.545\",\"BXD45\":\"6.742\",\"BXD48\":\"6.393\",\"BXD48a\":\"6.618\",\"BXD49\":\"x\",\"BXD50\":\"6.496\",\"BXD51\":\"6.494\",\"BXD52\":\"x\",\"BXD53\":\"x\",\"BXD54\":\"x\",\"BXD55\":\"6.263\",\"BXD56\":\"x\",\"BXD59\":\"x\",\"BXD60\":\"6.541\",\"BXD61\":\"6.662\",\"BXD62\":\"6.628\",\"BXD63\":\"6.556\",\"BXD64\":\"6.572\",\"BXD65\":\"6.530\",\"BXD65a\":\"6.280\",\"BXD65b\":\"6.490\",\"BXD66\":\"6.608\",\"BXD67\":\"6.534\",\"BXD68\":\"6.352\",\"BXD69\":\"6.548\",\"BXD70\":\"6.520\",\"BXD71\":\"x\",\"BXD72\":\"x\",\"BXD73\":\"6.484\",\"BXD73a\":\"6.486\",\"BXD73b\":\"x\",\"BXD74\":\"6.639\",\"BXD75\":\"6.401\",\"BXD76\":\"6.452\",\"BXD77\":\"6.568\",\"BXD78\":\"x\",\"BXD79\":\"6.642\",\"BXD81\":\"x\",\"BXD83\":\"6.446\",\"BXD84\":\"6.582\",\"BXD85\":\"6.484\",\"BXD86\":\"6.877\",\"BXD87\":\"6.474\",\"BXD88\":\"x\",\"BXD89\":\"6.676\",\"BXD90\":\"6.644\",\"BXD91\":\"x\",\"BXD93\":\"6.620\",\"BXD94\":\"6.528\",\"BXD95\":\"x\",\"BXD98\":\"6.486\",\"BXD99\":\"6.530\",\"BXD100\":\"x\",\"BXD101\":\"x\",\"BXD102\":\"x\",\"BXD104\":\"x\",\"BXD105\":\"x\",\"BXD106\":\"x\",\"BXD107\":\"x\",\"BXD108\":\"x\",\"BXD109\":\"x\",\"BXD110\":\"x\",\"BXD111\":\"x\",\"BXD112\":\"x\",\"BXD113\":\"x\",\"BXD114\":\"x\",\"BXD115\":\"x\",\"BXD116\":\"x\",\"BXD117\":\"x\",\"BXD119\":\"x\",\"BXD120\":\"x\",\"BXD121\":\"x\",\"BXD122\":\"x\",\"BXD123\":\"x\",\"BXD124\":\"x\",\"BXD125\":\"x\",\"BXD126\":\"x\",\"BXD127\":\"x\",\"BXD128\":\"x\",\"BXD128a\":\"x\",\"BXD130\":\"x\",\"BXD131\":\"x\",\"BXD132\":\"x\",\"BXD133\":\"x\",\"BXD134\":\"x\",\"BXD135\":\"x\",\"BXD136\":\"x\",\"BXD137\":\"x\",\"BXD138\":\"x\",\"BXD139\":\"x\",\"BXD141\":\"x\",\"BXD142\":\"x\",\"BXD144\":\"x\",\"BXD145\":\"x\",\"BXD146\":\"x\",\"BXD147\":\"x\",\"BXD148\":\"x\",\"BXD149\":\"x\",\"BXD150\":\"x\",\"BXD151\":\"x\",\"BXD152\":\"x\",\"BXD153\":\"x\",\"BXD154\":\"x\",\"BXD155\":\"x\",\"BXD156\":\"x\",\"BXD157\":\"x\",\"BXD160\":\"x\",\"BXD161\":\"x\",\"BXD162\":\"x\",\"BXD165\":\"x\",\"BXD168\":\"x\",\"BXD169\":\"x\",\"BXD170\":\"x\",\"BXD171\":\"x\",\"BXD172\":\"x\",\"BXD173\":\"x\",\"BXD174\":\"x\",\"BXD175\":\"x\",\"BXD176\":\"x\",\"BXD177\":\"x\",\"BXD178\":\"x\",\"BXD180\":\"x\",\"BXD181\":\"x\",\"BXD183\":\"x\",\"BXD184\":\"x\",\"BXD186\":\"x\",\"BXD187\":\"x\",\"BXD188\":\"x\",\"BXD189\":\"x\",\"BXD190\":\"x\",\"BXD191\":\"x\",\"BXD192\":\"x\",\"BXD193\":\"x\",\"BXD194\":\"x\",\"BXD195\":\"x\",\"BXD196\":\"x\",\"BXD197\":\"x\",\"BXD198\":\"x\",\"BXD199\":\"x\",\"BXD200\":\"x\",\"BXD201\":\"x\",\"BXD202\":\"x\",\"BXD203\":\"x\",\"BXD204\":\"x\",\"BXD205\":\"x\",\"BXD206\":\"x\",\"BXD207\":\"x\",\"BXD208\":\"x\",\"BXD209\":\"x\",\"BXD210\":\"x\",\"BXD211\":\"x\",\"BXD212\":\"x\",\"BXD213\":\"x\",\"BXD214\":\"x\",\"BXD215\":\"x\",\"BXD216\":\"x\",\"BXD217\":\"x\",\"BXD218\":\"x\",\"BXD219\":\"x\",\"BXD220\":\"x\"}",
+ "corr_type": "lit",
+ "corr_dataset": "HC_M2_0606_P",
+ "corr_return_results": "100",
+ "corr_samples_group": "samples_primary",
+ "corr_sample_method": "pearson",
+ "min_expr": "",
+ "location_type": "gene",
+ "loc_chr": "",
+ "min_loc_mb": "",
+ "max_loc_mb": "",
+ "p_range_lower": "-0.60",
+ "p_range_upper": "0.74"
+} \ No newline at end of file
diff --git a/tests/integration/expected_corr_results.json b/tests/integration/expected_corr_results.json
new file mode 100644
index 0000000..b5bbc2d
--- /dev/null
+++ b/tests/integration/expected_corr_results.json
@@ -0,0 +1,1902 @@
+[
+ {
+ "index": 1,
+ "trait_id": "1415758_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415758_at:HC_M2_0606_P:da50fa1141a7d608ab20",
+ "symbol": "Fryl",
+ "description": "furry homolog-like; far 3' UTR",
+ "location": "Chr5: 72.964984",
+ "mean": "9.193",
+ "additive": "-0.081",
+ "lod_score": "4.4",
+ "lrs_location": "Chr1: 196.404284",
+ "sample_r": "-0.407",
+ "num_overlap": 67,
+ "sample_p": "6.234e-04",
+ "lit_corr": "--",
+ "tissue_corr": "-0.221",
+ "tissue_pvalue": "2.780e-01"
+ },
+ {
+ "index": 2,
+ "trait_id": "1415693_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415693_at:HC_M2_0606_P:0959e913366f559ea22b",
+ "symbol": "Derl1",
+ "description": "derlin 1; proximal to mid 3' UTR",
+ "location": "Chr15: 57.702171",
+ "mean": "9.445",
+ "additive": "0.056",
+ "lod_score": "2.1",
+ "lrs_location": "Chr1: 193.731996",
+ "sample_r": "0.398",
+ "num_overlap": 67,
+ "sample_p": "8.614e-04",
+ "lit_corr": "--",
+ "tissue_corr": "0.114",
+ "tissue_pvalue": "5.800e-01"
+ },
+ {
+ "index": 3,
+ "trait_id": "1415753_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415753_at:HC_M2_0606_P:d75ca42e7fa1613364bb",
+ "symbol": "Fam108a",
+ "description": "abhydrolase domain-containing protein FAM108A; last two exons and proximal 3' UTR",
+ "location": "Chr10: 80.046470",
+ "mean": "12.731",
+ "additive": "0.050",
+ "lod_score": "1.5",
+ "lrs_location": "ChrX: 103.404884",
+ "sample_r": "0.384",
+ "num_overlap": 67,
+ "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",
+ "lod_score": "3.7",
+ "lrs_location": "Chr1: 157.588921",
+ "sample_r": "0.305",
+ "num_overlap": 67,
+ "sample_p": "1.200e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.405",
+ "tissue_pvalue": "4.032e-02"
+ },
+ {
+ "index": 8,
+ "trait_id": "1415742_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415742_at:HC_M2_0606_P:b72a582a1f840a18c3e7",
+ "symbol": "Aup1",
+ "description": "ancient ubiquitous protein 1",
+ "location": "Chr6: 83.006784",
+ "mean": "9.529",
+ "additive": "-0.062",
+ "lod_score": "2.4",
+ "lrs_location": "Chr19: 16.955950",
+ "sample_r": "0.295",
+ "num_overlap": 67,
+ "sample_p": "1.523e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.033",
+ "tissue_pvalue": "8.716e-01"
+ },
+ {
+ "index": 9,
+ "trait_id": "1415743_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415743_at:HC_M2_0606_P:3187245a079e824b4236",
+ "symbol": "Hdac5",
+ "description": "histone deacetylase 5; last four exons",
+ "location": "Chr11: 102.057397",
+ "mean": "11.009",
+ "additive": "0.081",
+ "lod_score": "2.1",
+ "lrs_location": "Chr7: 125.263073",
+ "sample_r": "0.285",
+ "num_overlap": 67,
+ "sample_p": "1.950e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.005",
+ "tissue_pvalue": "9.823e-01"
+ },
+ {
+ "index": 10,
+ "trait_id": "1415690_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415690_at:HC_M2_0606_P:603b215ede00b6fe1104",
+ "symbol": "Mrp127",
+ "description": "39S ribosomal protein L27, mitochondrial; last three exons",
+ "location": "Chr11: 94.517922",
+ "mean": "12.569",
+ "additive": "0.063",
+ "lod_score": "1.9",
+ "lrs_location": "Chr2: 164.779024",
+ "sample_r": "0.266",
+ "num_overlap": 67,
+ "sample_p": "2.986e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 11,
+ "trait_id": "1415727_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415727_at:HC_M2_0606_P:cb40b8cba0eee75781a6",
+ "symbol": "Apoa1bp",
+ "description": "apolipoprotein A-I binding protein; exons 3 through 6",
+ "location": "Chr3: 87.860534",
+ "mean": "11.707",
+ "additive": "-0.076",
+ "lod_score": "2.8",
+ "lrs_location": "Chr3: 56.295375",
+ "sample_r": "0.263",
+ "num_overlap": 67,
+ "sample_p": "3.136e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.535",
+ "tissue_pvalue": "4.841e-03"
+ },
+ {
+ "index": 12,
+ "trait_id": "1415730_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415730_at:HC_M2_0606_P:a970e0610a56ac4aba27",
+ "symbol": "Cpsf7",
+ "description": "cleavage and polyadenylation specificity factor 7; distal 3' UTR (transQTL on Chr 4 in BXD eye data)",
+ "location": "Chr19: 10.621618",
+ "mean": "10.662",
+ "additive": "-0.048",
+ "lod_score": "2.1",
+ "lrs_location": "Chr1: 188.085707",
+ "sample_r": "-0.263",
+ "num_overlap": 67,
+ "sample_p": "3.164e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 13,
+ "trait_id": "1415741_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415741_at:HC_M2_0606_P:033752be361d32960c29",
+ "symbol": "Tmem165",
+ "description": "transmembrane protein 165; 3' UTR",
+ "location": "Chr5: 76.637708",
+ "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",
+ "mean": "10.778",
+ "additive": "-0.084",
+ "lod_score": "2.4",
+ "lrs_location": "Chr4: 122.536808",
+ "sample_r": "0.242",
+ "num_overlap": 67,
+ "sample_p": "4.816e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 16,
+ "trait_id": "1415703_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415703_at:HC_M2_0606_P:51ee8e47654845a546f0",
+ "symbol": "Huwe1",
+ "description": "HECT, UBA and WWE domain containing 1; last 3 exons and proximal 3' UTR",
+ "location": "ChrX: 148.367136",
+ "mean": "11.335",
+ "additive": "-0.094",
+ "lod_score": "2.3",
+ "lrs_location": "Chr1: 135.891043",
+ "sample_r": "0.235",
+ "num_overlap": 67,
+ "sample_p": "5.541e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.528",
+ "tissue_pvalue": "5.576e-03"
+ },
+ {
+ "index": 17,
+ "trait_id": "1415748_a_at",
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+ "mean": "11.447",
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+ "tissue_corr": "-0.559",
+ "tissue_pvalue": "3.015e-03"
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+ {
+ "index": 20,
+ "trait_id": "1415731_at",
+ "dataset": "HC_M2_0606_P",
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+ "tissue_pvalue": "2.544e-01"
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+ {
+ "index": 21,
+ "trait_id": "1415750_at",
+ "dataset": "HC_M2_0606_P",
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+ "mean": "8.703",
+ "additive": "-0.132",
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+ "tissue_pvalue": "1.211e-01"
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+ "trait_id": "1415680_at",
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+ "tissue_pvalue": "7.413e-01"
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+ "dataset": "HC_M2_0606_P",
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+ "index": 25,
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+ "dataset": "HC_M2_0606_P",
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+ "location": "Chr18: 12.314783",
+ "mean": "10.906",
+ "additive": "0.068",
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+ "tissue_pvalue": "1.628e-01"
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+ "trait_id": "1415682_at",
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+ "location": "Chr14: 71.064730",
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+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
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+ "dataset": "HC_M2_0606_P",
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+ "tissue_pvalue": "6.671e-02"
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+ "trait_id": "1415697_at",
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+ "additive": "0.137",
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+ "tissue_pvalue": "4.580e-01"
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+ "dataset": "HC_M2_0606_P",
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+ "additive": "-0.196",
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+ "dataset": "HC_M2_0606_P",
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+ "tissue_corr": "0.298",
+ "tissue_pvalue": "1.388e-01"
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+ "dataset": "HC_M2_0606_P",
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+ "location": "Chr14: 55.517242",
+ "mean": "10.510",
+ "additive": "0.150",
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+ "lrs_location": "Chr19: 53.933992",
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+ "dataset": "HC_M2_0606_P",
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+ "description": "dolichol-phosphate (beta-D) mannosyltransferase 2; last exon and proximal to mid 3' UTR",
+ "location": "Chr2: 32.428524",
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+ "additive": "-0.043",
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+ "lrs_location": "Chr13: 30.769380",
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+ "tissue_pvalue": "6.201e-01"
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+ "description": "N(alpha)-acetyltransferase 60, NatF catalytic subunit; distal 3' UTR",
+ "location": "Chr16: 3.904169",
+ "mean": "10.153",
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+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
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+ "dataset": "HC_M2_0606_P",
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+ "description": "Src homology 2 domain containing adaptor protein B; putative far 3' UTR (or intercalated neighbor)",
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+ "mean": "10.756",
+ "additive": "-0.044",
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+ "lrs_location": "Chr5: 69.527298",
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+ "tissue_corr": "0.149",
+ "tissue_pvalue": "4.678e-01"
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+ "description": "mitotic arrest deficient 2, homolog-like 1 (MAD2L1) binding protein; last exon and 3' UTR",
+ "location": "Chr17: 46.284624",
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+ "additive": "0.048",
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+ "lrs_location": "Chr8: 33.934048",
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+ "tissue_corr": "0.463",
+ "tissue_pvalue": "1.709e-02"
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+ "index": 39,
+ "trait_id": "1415767_at",
+ "dataset": "HC_M2_0606_P",
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+ "additive": "-0.051",
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+ "lrs_location": "Chr6: 145.406059",
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+ "tissue_corr": "0.382",
+ "tissue_pvalue": "5.396e-02"
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+ "index": 40,
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+ "dataset": "HC_M2_0606_P",
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+ "description": "mitochondrial ribosomal protein L52",
+ "location": "Chr14: 55.045789",
+ "mean": "10.926",
+ "additive": "0.086",
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+ "lrs_location": "Chr1: 190.087097",
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+ "tissue_corr": "0.395",
+ "tissue_pvalue": "4.585e-02"
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+ "index": 41,
+ "trait_id": "1415736_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415736_at:HC_M2_0606_P:c9bd62acd0c2cc087606",
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+ "description": "prefoldin 5",
+ "location": "Chr15: 102.156651",
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+ "lrs_location": "Chr10: 5.378622",
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+ "sample_p": "3.418e-01",
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+ "tissue_corr": "-0.261",
+ "tissue_pvalue": "1.975e-01"
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+ "trait_id": "1415704_a_at",
+ "dataset": "HC_M2_0606_P",
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+ "symbol": "Cdv3",
+ "description": "carnitine deficiency-associated gene expressed in ventricle 3",
+ "location": "Chr9: 103.255487",
+ "mean": "10.994",
+ "additive": "0.060",
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+ "lrs_location": "Chr3: 10.018672",
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+ "sample_p": "3.539e-01",
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+ "tissue_corr": "0.598",
+ "tissue_pvalue": "1.246e-03"
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+ "trait_id": "1415699_a_at",
+ "dataset": "HC_M2_0606_P",
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+ "mean": "12.033",
+ "additive": "0.065",
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+ "lrs_location": "Chr11: 62.910461",
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+ "num_overlap": 67,
+ "sample_p": "3.575e-01",
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+ "tissue_corr": "0.150",
+ "tissue_pvalue": "4.638e-01"
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+ "index": 44,
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+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415739_at:HC_M2_0606_P:c5e8b34713057f53dd07",
+ "symbol": "Rbm42",
+ "description": "RNA-binding motif protein 42; exon 7 and 3' UTR",
+ "location": "Chr7: 31.426055",
+ "mean": "10.926",
+ "additive": "-0.154",
+ "lod_score": "12.8",
+ "lrs_location": "Chr1: 174.792334",
+ "sample_r": "0.107",
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+ "sample_p": "3.898e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.550",
+ "tissue_pvalue": "3.580e-03"
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+ {
+ "index": 45,
+ "trait_id": "1415695_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415695_at:HC_M2_0606_P:44556cafdf6f5e38669b",
+ "symbol": "Psma1",
+ "description": "proteasome (prosome, macropain) subunit, alpha type 1; last four exons and proximal 3' UTR",
+ "location": "Chr7: 121.408358",
+ "mean": "12.346",
+ "additive": "-0.081",
+ "lod_score": "3.1",
+ "lrs_location": "Chr12: 29.344230",
+ "sample_r": "-0.106",
+ "num_overlap": 67,
+ "sample_p": "3.925e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.274",
+ "tissue_pvalue": "1.763e-01"
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+ {
+ "index": 46,
+ "trait_id": "1415745_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415745_a_at:HC_M2_0606_P:0178fc19ada3ba0179fb",
+ "symbol": "Dscr3",
+ "description": "Down syndrome critical region protein 3",
+ "location": "Chr16: 94.719451",
+ "mean": "9.329",
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+ "sample_p": "7.559e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.275",
+ "tissue_pvalue": "1.738e-01"
+ },
+ {
+ "index": 76,
+ "trait_id": "1415744_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415744_at:HC_M2_0606_P:38f9abcb635f29e5871c",
+ "symbol": "Pfdn6",
+ "description": "prefoldin subunit 6 (H2-K region expressed gene 2); 5' UTR, exons 1, 3, 4, and 3' UTR",
+ "location": "Chr17: 34.075883",
+ "mean": "11.324",
+ "additive": "-0.157",
+ "lod_score": "11.0",
+ "lrs_location": "Chr17: 33.247164",
+ "sample_r": "0.038",
+ "num_overlap": 67,
+ "sample_p": "7.626e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 77,
+ "trait_id": "1415700_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415700_a_at:HC_M2_0606_P:95582b9daa0776067713",
+ "symbol": "Ssr3",
+ "description": "signal sequence receptor, gamma (translocon-associated protein gamma); mid-distal 3' UTR",
+ "location": "Chr3: 65.183917",
+ "mean": "12.068",
+ "additive": "0.067",
+ "lod_score": "2.1",
+ "lrs_location": "Chr7: 27.852865",
+ "sample_r": "0.036",
+ "num_overlap": 67,
+ "sample_p": "7.742e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.354",
+ "tissue_pvalue": "7.623e-02"
+ },
+ {
+ "index": 78,
+ "trait_id": "1415687_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415687_a_at:HC_M2_0606_P:f15bcfef7839d22ca5a3",
+ "symbol": "Psap",
+ "description": "prosaposin; mid and distal 3' UTR",
+ "location": "Chr10: 59.764772",
+ "mean": "14.976",
+ "additive": "0.121",
+ "lod_score": "2.0",
+ "lrs_location": "Chr5: 4.468199",
+ "sample_r": "0.035",
+ "num_overlap": 67,
+ "sample_p": "7.777e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.078",
+ "tissue_pvalue": "7.058e-01"
+ },
+ {
+ "index": 79,
+ "trait_id": "1415729_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415729_at:HC_M2_0606_P:08dc70633663e17111dd",
+ "symbol": "Pdpk1",
+ "description": "3-phosphoinositide dependent protein kinase-1; distal 3' UTR",
+ "location": "Chr17: 24.210667",
+ "mean": "12.376",
+ "additive": "-0.081",
+ "lod_score": "3.0",
+ "lrs_location": "Chr2: 55.266330",
+ "sample_r": "-0.029",
+ "num_overlap": 67,
+ "sample_p": "8.147e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.290",
+ "tissue_pvalue": "1.506e-01"
+ },
+ {
+ "index": 80,
+ "trait_id": "1415672_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415672_at:HC_M2_0606_P:d6a7286d4957f3487196",
+ "symbol": "Golga7",
+ "description": "golgi autoantigen, golgin subfamily a, 7",
+ "location": "Chr8: 24.351869",
+ "mean": "13.218",
+ "additive": "0.063",
+ "lod_score": "2.6",
+ "lrs_location": "Chr13: 120.059030",
+ "sample_r": "-0.027",
+ "num_overlap": 67,
+ "sample_p": "8.305e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.456",
+ "tissue_pvalue": "1.919e-02"
+ },
+ {
+ "index": 81,
+ "trait_id": "1415713_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415713_a_at:HC_M2_0606_P:e22be15fd9ade623e3bb",
+ "symbol": "Ddx24",
+ "description": "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24; last two exons",
+ "location": "Chr12: 104.646500",
+ "mean": "11.808",
+ "additive": "0.052",
+ "lod_score": "3.1",
+ "lrs_location": "Chr9: 15.693672",
+ "sample_r": "-0.026",
+ "num_overlap": 67,
+ "sample_p": "8.322e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.338",
+ "tissue_pvalue": "9.077e-02"
+ },
+ {
+ "index": 82,
+ "trait_id": "1415683_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415683_at:HC_M2_0606_P:f544e88da2dd8adb0b3f",
+ "symbol": "Nmt1",
+ "description": "N-myristoyltransferase 1; exons 10 and 11, and 3' UTR",
+ "location": "Chr11: 102.926047",
+ "mean": "12.261",
+ "additive": "-0.070",
+ "lod_score": "2.6",
+ "lrs_location": "Chr6: 101.797292",
+ "sample_r": "0.026",
+ "num_overlap": 67,
+ "sample_p": "8.375e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.366",
+ "tissue_pvalue": "6.559e-02"
+ },
+ {
+ "index": 83,
+ "trait_id": "1415701_x_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415701_x_at:HC_M2_0606_P:8faa1e92ec8fc8cf33b5",
+ "symbol": "Rpl23",
+ "description": "ribosomal protein L23; spans exons 1, 2, 3, 4, and intron 4, and proximal 3' UTR",
+ "location": "Chr11: 97.639386",
+ "mean": "16.236",
+ "additive": "0.067",
+ "lod_score": "2.7",
+ "lrs_location": "Chr2: 162.502590",
+ "sample_r": "0.024",
+ "num_overlap": 67,
+ "sample_p": "8.474e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.036",
+ "tissue_pvalue": "8.630e-01"
+ },
+ {
+ "index": 84,
+ "trait_id": "1415681_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415681_at:HC_M2_0606_P:96ceed972f5f3da9d52d",
+ "symbol": "Mrpl43",
+ "description": "mitochondrial ribosomal protein L43",
+ "location": "Chr19: 45.079983",
+ "mean": "10.604",
+ "additive": "-0.058",
+ "lod_score": "2.1",
+ "lrs_location": "Chr7: 90.186486",
+ "sample_r": "-0.021",
+ "num_overlap": 67,
+ "sample_p": "8.669e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.362",
+ "tissue_pvalue": "6.958e-02"
+ },
+ {
+ "index": 85,
+ "trait_id": "1415691_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415691_at:HC_M2_0606_P:c6a3213115c205f73f86",
+ "symbol": "Dlg1",
+ "description": "discs, large homolog 1 (presynaptic protein SAP97); distal 3' UTR",
+ "location": "Chr16: 31.872849",
+ "mean": "11.782",
+ "additive": "0.088",
+ "lod_score": "2.9",
+ "lrs_location": "Chr17: 55.490261",
+ "sample_r": "-0.020",
+ "num_overlap": 67,
+ "sample_p": "8.731e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.015",
+ "tissue_pvalue": "9.426e-01"
+ },
+ {
+ "index": 86,
+ "trait_id": "1415715_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415715_at:HC_M2_0606_P:8c7d719635beb0f7a9f5",
+ "symbol": "Slbp",
+ "description": "stem-loop binding protein",
+ "location": "Chr5: 33.995959",
+ "mean": "9.003",
+ "additive": "0.051",
+ "lod_score": "2.2",
+ "lrs_location": "Chr11: 69.415410",
+ "sample_r": "-0.020",
+ "num_overlap": 67,
+ "sample_p": "8.749e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.090",
+ "tissue_pvalue": "6.621e-01"
+ },
+ {
+ "index": 87,
+ "trait_id": "1415751_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415751_at:HC_M2_0606_P:d0d8a9fa8a2b142d4374",
+ "symbol": "Hb1bp3",
+ "description": "heterochromatin protein 1-binding protein 3",
+ "location": "Chr4: 137.798500",
+ "mean": "12.239",
+ "additive": "-0.168",
+ "lod_score": "14.7",
+ "lrs_location": "Chr4: 138.152371",
+ "sample_r": "0.019",
+ "num_overlap": 67,
+ "sample_p": "8.773e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 88,
+ "trait_id": "1415764_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415764_at:HC_M2_0606_P:8a23b78d5d55a0026ceb",
+ "symbol": "Cpsf7",
+ "description": "cleavage and polyadenylation specificity factor 7",
+ "location": "Chr1: 135.516541",
+ "mean": "11.499",
+ "additive": "-0.352",
+ "lod_score": "28.8",
+ "lrs_location": "Chr1: 135.115363",
+ "sample_r": "-0.019",
+ "num_overlap": 67,
+ "sample_p": "8.787e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 89,
+ "trait_id": "1415724_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415724_a_at:HC_M2_0606_P:4ff4b2d244043dc3b03e",
+ "symbol": "Cdc42",
+ "description": "cell division cycle 42 (activator of Rac); mid-distal 3' UTR",
+ "location": "Chr4: 136.876012",
+ "mean": "11.795",
+ "additive": "-0.120",
+ "lod_score": "5.5",
+ "lrs_location": "Chr1: 172.981863",
+ "sample_r": "0.019",
+ "num_overlap": 67,
+ "sample_p": "8.792e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.073",
+ "tissue_pvalue": "7.233e-01"
+ },
+ {
+ "index": 90,
+ "trait_id": "1415737_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415737_at:HC_M2_0606_P:c667a35a9b2b78172117",
+ "symbol": "Rfk",
+ "description": "riboflavin kinase; distal 3' UTR",
+ "location": "Chr19: 17.475267",
+ "mean": "11.552",
+ "additive": "0.414",
+ "lod_score": "35.4",
+ "lrs_location": "Chr19: 16.955950",
+ "sample_r": "0.019",
+ "num_overlap": 67,
+ "sample_p": "8.810e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.117",
+ "tissue_pvalue": "5.681e-01"
+ },
+ {
+ "index": 91,
+ "trait_id": "1415738_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415738_at:HC_M2_0606_P:304349c531fb99926720",
+ "symbol": "Txndc12",
+ "description": "thioredoxin domain-containing protein 12; 3' UTR",
+ "location": "Chr4: 108.534146",
+ "mean": "9.375",
+ "additive": "-0.103",
+ "lod_score": "3.2",
+ "lrs_location": "Chr1: 172.981863",
+ "sample_r": "-0.016",
+ "num_overlap": 67,
+ "sample_p": "9.004e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.135",
+ "tissue_pvalue": "5.114e-01"
+ },
+ {
+ "index": 92,
+ "trait_id": "1415735_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415735_at:HC_M2_0606_P:f30f5a5f571c8c61d459",
+ "symbol": "Ddb1",
+ "description": "damage-specific DNA binding protein 1, 127 kDa",
+ "location": "Chr19: 10.703737",
+ "mean": "10.647",
+ "additive": "-0.085",
+ "lod_score": "5.1",
+ "lrs_location": "Chr16: 28.990480",
+ "sample_r": "0.016",
+ "num_overlap": 67,
+ "sample_p": "9.008e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.248",
+ "tissue_pvalue": "2.217e-01"
+ },
+ {
+ "index": 93,
+ "trait_id": "1415684_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415684_at:HC_M2_0606_P:710753b49f7e38406e4b",
+ "symbol": "Atg5",
+ "description": "autophagy related 5; mid 3' UTR",
+ "location": "Chr10: 44.083511",
+ "mean": "8.854",
+ "additive": "-0.068",
+ "lod_score": "2.2",
+ "lrs_location": "Chr6: 145.406059",
+ "sample_r": "-0.014",
+ "num_overlap": 67,
+ "sample_p": "9.086e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.109",
+ "tissue_pvalue": "5.954e-01"
+ },
+ {
+ "index": 94,
+ "trait_id": "1415686_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415686_at:HC_M2_0606_P:455a84fffcd7a0997580",
+ "symbol": "Rab14",
+ "description": "Rab GTPase family member 14",
+ "location": "Chr2: 35.036216",
+ "mean": "12.112",
+ "additive": "0.110",
+ "lod_score": "3.6",
+ "lrs_location": "Chr14: 124.508018",
+ "sample_r": "-0.013",
+ "num_overlap": 67,
+ "sample_p": "9.139e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.056",
+ "tissue_pvalue": "7.850e-01"
+ },
+ {
+ "index": 95,
+ "trait_id": "1415685_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415685_at:HC_M2_0606_P:60c84786fe2f4a62d13d",
+ "symbol": "Mtif2",
+ "description": "mitochondrial translational initiation factor 2",
+ "location": "Chr11: 29.442428",
+ "mean": "9.271",
+ "additive": "-0.367",
+ "lod_score": "23.1",
+ "lrs_location": "Chr11: 28.975002",
+ "sample_r": "0.012",
+ "num_overlap": 67,
+ "sample_p": "9.259e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.358",
+ "tissue_pvalue": "7.272e-02"
+ },
+ {
+ "index": 96,
+ "trait_id": "1415679_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415679_at:HC_M2_0606_P:513339a6b22faab7d8f6",
+ "symbol": "Psenen",
+ "description": "presenilin enhancer 2; 5' UTR, all exons, and 3' UTR",
+ "location": "Chr7: 31.346914",
+ "mean": "11.480",
+ "additive": "-0.283",
+ "lod_score": "19.1",
+ "lrs_location": "Chr7: 31.505577",
+ "sample_r": "-0.011",
+ "num_overlap": 67,
+ "sample_p": "9.286e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.002",
+ "tissue_pvalue": "9.929e-01"
+ },
+ {
+ "index": 97,
+ "trait_id": "1415710_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415710_at:HC_M2_0606_P:4b8e32a96cf0e9bb30d3",
+ "symbol": "Cox18",
+ "description": "cytochrome c oxidase assembly protein 18; last three exons and proximal 3' UTR",
+ "location": "Chr5: 90.644087",
+ "mean": "9.513",
+ "additive": "0.402",
+ "lod_score": "33.4",
+ "lrs_location": "Chr5: 90.500265",
+ "sample_r": "0.010",
+ "num_overlap": 67,
+ "sample_p": "9.360e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.420",
+ "tissue_pvalue": "3.257e-02"
+ },
+ {
+ "index": 98,
+ "trait_id": "1415702_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415702_a_at:HC_M2_0606_P:7ef725f27498e294d14a",
+ "symbol": "Ctbp1",
+ "description": "C-terminal binding protein 1; 3' UTR",
+ "location": "Chr5: 33.590456",
+ "mean": "12.530",
+ "additive": "-0.056",
+ "lod_score": "2.3",
+ "lrs_location": "Chr12: 76.993653",
+ "sample_r": "-0.010",
+ "num_overlap": 67,
+ "sample_p": "9.372e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.514",
+ "tissue_pvalue": "7.288e-03"
+ },
+ {
+ "index": 99,
+ "trait_id": "1415711_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415711_at:HC_M2_0606_P:f71bb40cdefd07ae95d6",
+ "symbol": "Arfgef1",
+ "description": "ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited); 3' UTR",
+ "location": "Chr18: 22.122655",
+ "mean": "11.617",
+ "additive": "-0.055",
+ "lod_score": "3.3",
+ "lrs_location": "Chr2: 50.500580",
+ "sample_r": "-0.003",
+ "num_overlap": 67,
+ "sample_p": "9.802e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.020",
+ "tissue_pvalue": "9.216e-01"
+ },
+ {
+ "index": 100,
+ "trait_id": "1415726_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415726_at:HC_M2_0606_P:89e8ab5b988a202a2fb0",
+ "symbol": "Ankrd17",
+ "description": "ankyrin repeat domain protein 17; last exon and proximal 3' UTR",
+ "location": "Chr5: 90.657781",
+ "mean": "11.533",
+ "additive": "0.046",
+ "lod_score": "2.0",
+ "lrs_location": "Chr14: 42.819085",
+ "sample_r": "0.000",
+ "num_overlap": 67,
+ "sample_p": "9.991e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.530",
+ "tissue_pvalue": "5.382e-03"
+ }
+] \ No newline at end of file
diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py
new file mode 100644
index 0000000..b94487a
--- /dev/null
+++ b/tests/integration/test_correlation.py
@@ -0,0 +1,57 @@
+"""Integration tests for correlation api"""
+
+import os
+import json
+import pickle
+import unittest
+from unittest import mock
+
+from gn3.app import create_app
+
+
+def file_path(relative_path):
+ """getting abs path for file """
+ dir_name = os.path.dirname(os.path.abspath(__file__))
+ split_path = relative_path.split("/")
+ new_path = os.path.join(dir_name, *split_path)
+ return new_path
+
+
+class CorrelationAPITest(unittest.TestCase):
+ # currently disable
+ """Test cases for the Correlation API"""
+
+ def setUp(self):
+ self.app = create_app().test_client()
+
+ with open(file_path("correlation_data.json")) as json_file:
+ self.correlation_data = json.load(json_file)
+
+ with open(file_path("expected_corr_results.json")) as results_file:
+ self.correlation_results = json.load(results_file)
+
+ def tearDown(self):
+ self.correlation_data = ""
+
+ self.correlation_results = ""
+
+ @mock.patch("gn3.api.correlation.compute_correlation")
+ def test_corr_compute(self, compute_corr):
+ """Test that the correct response in correlation"""
+
+ compute_corr.return_value = self.correlation_results
+ response = self.app.post(
+ "/api/correlation/corr_compute", json=self.correlation_data, follow_redirects=True)
+
+ self.assertEqual(response.status_code, 200)
+
+ @mock.patch("gn3.api.correlation.compute_correlation")
+ def test_corr_compute_failed_request(self,compute_corr):
+ """test taht cormpute requests fails """
+
+ compute_corr.return_value = self.correlation_results
+
+ response = self.app.post(
+ "/api/correlation/corr_compute", json=None, follow_redirects=True)
+
+ self.assertEqual(response.status_code,400)
diff --git a/tests/unit/correlation/__init__.py b/tests/unit/correlation/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tests/unit/correlation/__init__.py
diff --git a/tests/unit/correlation/correlation_test_data.json b/tests/unit/correlation/correlation_test_data.json
new file mode 100644
index 0000000..87d24e3
--- /dev/null
+++ b/tests/unit/correlation/correlation_test_data.json
@@ -0,0 +1,18 @@
+{
+ "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",
+ "trait_id": "1444666_at",
+ "dataset": "HC_M2_0606_P",
+ "sample_vals": "{\"C57BL/6J\":\"6.638\",\"DBA/2J\":\"6.266\",\"B6D2F1\":\"6.494\",\"D2B6F1\":\"6.565\",\"BXD1\":\"6.357\",\"BXD2\":\"6.456\",\"BXD5\":\"6.590\",\"BXD6\":\"6.568\",\"BXD8\":\"6.581\",\"BXD9\":\"6.322\",\"BXD11\":\"6.519\",\"BXD12\":\"6.543\",\"BXD13\":\"6.636\",\"BXD14\":\"x\",\"BXD15\":\"6.578\",\"BXD16\":\"6.636\",\"BXD18\":\"x\",\"BXD19\":\"6.562\",\"BXD20\":\"6.610\",\"BXD21\":\"6.668\",\"BXD22\":\"6.607\",\"BXD23\":\"6.513\",\"BXD24\":\"6.601\",\"BXD24a\":\"x\",\"BXD25\":\"x\",\"BXD27\":\"6.573\",\"BXD28\":\"6.639\",\"BXD29\":\"6.656\",\"BXD30\":\"x\",\"BXD31\":\"6.549\",\"BXD32\":\"6.502\",\"BXD33\":\"6.584\",\"BXD34\":\"6.261\",\"BXD35\":\"x\",\"BXD36\":\"x\",\"BXD37\":\"x\",\"BXD38\":\"6.646\",\"BXD39\":\"6.584\",\"BXD40\":\"6.790\",\"BXD41\":\"x\",\"BXD42\":\"6.536\",\"BXD43\":\"6.476\",\"BXD44\":\"6.545\",\"BXD45\":\"6.742\",\"BXD48\":\"6.393\",\"BXD48a\":\"6.618\",\"BXD49\":\"x\",\"BXD50\":\"6.496\",\"BXD51\":\"6.494\",\"BXD52\":\"x\",\"BXD53\":\"x\",\"BXD54\":\"x\",\"BXD55\":\"6.263\",\"BXD56\":\"x\",\"BXD59\":\"x\",\"BXD60\":\"6.541\",\"BXD61\":\"6.662\",\"BXD62\":\"6.628\",\"BXD63\":\"6.556\",\"BXD64\":\"6.572\",\"BXD65\":\"6.530\",\"BXD65a\":\"6.280\",\"BXD65b\":\"6.490\",\"BXD66\":\"6.608\",\"BXD67\":\"6.534\",\"BXD68\":\"6.352\",\"BXD69\":\"6.548\",\"BXD70\":\"6.520\",\"BXD71\":\"x\",\"BXD72\":\"x\",\"BXD73\":\"6.484\",\"BXD73a\":\"6.486\",\"BXD73b\":\"x\",\"BXD74\":\"6.639\",\"BXD75\":\"6.401\",\"BXD76\":\"6.452\",\"BXD77\":\"6.568\",\"BXD78\":\"x\",\"BXD79\":\"6.642\",\"BXD81\":\"x\",\"BXD83\":\"6.446\",\"BXD84\":\"6.582\",\"BXD85\":\"6.484\",\"BXD86\":\"6.877\",\"BXD87\":\"6.474\",\"BXD88\":\"x\",\"BXD89\":\"6.676\",\"BXD90\":\"6.644\",\"BXD91\":\"x\",\"BXD93\":\"6.620\",\"BXD94\":\"6.528\",\"BXD95\":\"x\",\"BXD98\":\"6.486\",\"BXD99\":\"6.530\",\"BXD100\":\"x\",\"BXD101\":\"x\",\"BXD102\":\"x\",\"BXD104\":\"x\",\"BXD105\":\"x\",\"BXD106\":\"x\",\"BXD107\":\"x\",\"BXD108\":\"x\",\"BXD109\":\"x\",\"BXD110\":\"x\",\"BXD111\":\"x\",\"BXD112\":\"x\",\"BXD113\":\"x\",\"BXD114\":\"x\",\"BXD115\":\"x\",\"BXD116\":\"x\",\"BXD117\":\"x\",\"BXD119\":\"x\",\"BXD120\":\"x\",\"BXD121\":\"x\",\"BXD122\":\"x\",\"BXD123\":\"x\",\"BXD124\":\"x\",\"BXD125\":\"x\",\"BXD126\":\"x\",\"BXD127\":\"x\",\"BXD128\":\"x\",\"BXD128a\":\"x\",\"BXD130\":\"x\",\"BXD131\":\"x\",\"BXD132\":\"x\",\"BXD133\":\"x\",\"BXD134\":\"x\",\"BXD135\":\"x\",\"BXD136\":\"x\",\"BXD137\":\"x\",\"BXD138\":\"x\",\"BXD139\":\"x\",\"BXD141\":\"x\",\"BXD142\":\"x\",\"BXD144\":\"x\",\"BXD145\":\"x\",\"BXD146\":\"x\",\"BXD147\":\"x\",\"BXD148\":\"x\",\"BXD149\":\"x\",\"BXD150\":\"x\",\"BXD151\":\"x\",\"BXD152\":\"x\",\"BXD153\":\"x\",\"BXD154\":\"x\",\"BXD155\":\"x\",\"BXD156\":\"x\",\"BXD157\":\"x\",\"BXD160\":\"x\",\"BXD161\":\"x\",\"BXD162\":\"x\",\"BXD165\":\"x\",\"BXD168\":\"x\",\"BXD169\":\"x\",\"BXD170\":\"x\",\"BXD171\":\"x\",\"BXD172\":\"x\",\"BXD173\":\"x\",\"BXD174\":\"x\",\"BXD175\":\"x\",\"BXD176\":\"x\",\"BXD177\":\"x\",\"BXD178\":\"x\",\"BXD180\":\"x\",\"BXD181\":\"x\",\"BXD183\":\"x\",\"BXD184\":\"x\",\"BXD186\":\"x\",\"BXD187\":\"x\",\"BXD188\":\"x\",\"BXD189\":\"x\",\"BXD190\":\"x\",\"BXD191\":\"x\",\"BXD192\":\"x\",\"BXD193\":\"x\",\"BXD194\":\"x\",\"BXD195\":\"x\",\"BXD196\":\"x\",\"BXD197\":\"x\",\"BXD198\":\"x\",\"BXD199\":\"x\",\"BXD200\":\"x\",\"BXD201\":\"x\",\"BXD202\":\"x\",\"BXD203\":\"x\",\"BXD204\":\"x\",\"BXD205\":\"x\",\"BXD206\":\"x\",\"BXD207\":\"x\",\"BXD208\":\"x\",\"BXD209\":\"x\",\"BXD210\":\"x\",\"BXD211\":\"x\",\"BXD212\":\"x\",\"BXD213\":\"x\",\"BXD214\":\"x\",\"BXD215\":\"x\",\"BXD216\":\"x\",\"BXD217\":\"x\",\"BXD218\":\"x\",\"BXD219\":\"x\",\"BXD220\":\"x\"}",
+ "corr_type": "lit",
+ "corr_dataset": "HC_M2_0606_P",
+ "corr_return_results": "100",
+ "corr_samples_group": "samples_primary",
+ "corr_sample_method": "pearson",
+ "min_expr": "",
+ "location_type": "gene",
+ "loc_chr": "",
+ "min_loc_mb": "",
+ "max_loc_mb": "",
+ "p_range_lower": "-0.60",
+ "p_range_upper": "0.74"
+} \ No newline at end of file
diff --git a/tests/unit/correlation/dataset.json b/tests/unit/correlation/dataset.json
new file mode 100644
index 0000000..8a53ed5
--- /dev/null
+++ b/tests/unit/correlation/dataset.json
@@ -0,0 +1,64 @@
+{
+ "name":"HC_M2_0606_P",
+ "id":112,
+ "shortname":"Hippocampus M430v2 BXD 06/06 PDNN",
+ "fullname":"Hippocampus Consortium M430v2 (Jun06) PDNN",
+ "type":"ProbeSet",
+ "data_scale":"log2",
+ "search_fields":[
+ "Name",
+ "Description",
+ "Probe_Target_Description",
+ "Symbol",
+ "Alias",
+ "GenbankId",
+ "UniGeneId",
+ "RefSeq_TranscriptId"
+ ],
+ "display_fields":[
+ "name",
+ "symbol",
+ "description",
+ "probe_target_description",
+ "chr",
+ "mb",
+ "alias",
+ "geneid",
+ "genbankid",
+ "unigeneid",
+ "omim",
+ "refseq_transcriptid",
+ "blatseq",
+ "targetseq",
+ "chipid",
+ "comments",
+ "strand_probe",
+ "strand_gene",
+ "proteinid",
+ "uniprotid",
+ "probe_set_target_region",
+ "probe_set_specificity",
+ "probe_set_blat_score",
+ "probe_set_blat_mb_start",
+ "probe_set_blat_mb_end",
+ "probe_set_strand",
+ "probe_set_note_by_rw",
+ "flag"
+ ],
+ "header_fields":[
+ "Index",
+ "Record",
+ "Symbol",
+ "Description",
+ "Location",
+ "Mean",
+ "Max LRS",
+ "Max LRS Location",
+ "Additive Effect"
+ ],
+ "query_for_group":"\n SELECT\n InbredSet.Name, InbredSet.Id, InbredSet.GeneticType\n FROM\n InbredSet, ProbeSetFreeze, ProbeFreeze\n WHERE\n ProbeFreeze.InbredSetId = InbredSet.Id AND\n ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND\n ProbeSetFreeze.Name = \"HC_M2_0606_P\"\n ",
+ "tissue":"Hippocampus mRNA",
+ "group":"None",
+ "accession_id":"None",
+ "species":"None"
+} \ No newline at end of file
diff --git a/tests/unit/correlation/expected_correlation_results.json b/tests/unit/correlation/expected_correlation_results.json
new file mode 100644
index 0000000..b5bbc2d
--- /dev/null
+++ b/tests/unit/correlation/expected_correlation_results.json
@@ -0,0 +1,1902 @@
+[
+ {
+ "index": 1,
+ "trait_id": "1415758_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415758_at:HC_M2_0606_P:da50fa1141a7d608ab20",
+ "symbol": "Fryl",
+ "description": "furry homolog-like; far 3' UTR",
+ "location": "Chr5: 72.964984",
+ "mean": "9.193",
+ "additive": "-0.081",
+ "lod_score": "4.4",
+ "lrs_location": "Chr1: 196.404284",
+ "sample_r": "-0.407",
+ "num_overlap": 67,
+ "sample_p": "6.234e-04",
+ "lit_corr": "--",
+ "tissue_corr": "-0.221",
+ "tissue_pvalue": "2.780e-01"
+ },
+ {
+ "index": 2,
+ "trait_id": "1415693_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415693_at:HC_M2_0606_P:0959e913366f559ea22b",
+ "symbol": "Derl1",
+ "description": "derlin 1; proximal to mid 3' UTR",
+ "location": "Chr15: 57.702171",
+ "mean": "9.445",
+ "additive": "0.056",
+ "lod_score": "2.1",
+ "lrs_location": "Chr1: 193.731996",
+ "sample_r": "0.398",
+ "num_overlap": 67,
+ "sample_p": "8.614e-04",
+ "lit_corr": "--",
+ "tissue_corr": "0.114",
+ "tissue_pvalue": "5.800e-01"
+ },
+ {
+ "index": 3,
+ "trait_id": "1415753_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415753_at:HC_M2_0606_P:d75ca42e7fa1613364bb",
+ "symbol": "Fam108a",
+ "description": "abhydrolase domain-containing protein FAM108A; last two exons and proximal 3' UTR",
+ "location": "Chr10: 80.046470",
+ "mean": "12.731",
+ "additive": "0.050",
+ "lod_score": "1.5",
+ "lrs_location": "ChrX: 103.404884",
+ "sample_r": "0.384",
+ "num_overlap": 67,
+ "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",
+ "lod_score": "3.7",
+ "lrs_location": "Chr1: 157.588921",
+ "sample_r": "0.305",
+ "num_overlap": 67,
+ "sample_p": "1.200e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.405",
+ "tissue_pvalue": "4.032e-02"
+ },
+ {
+ "index": 8,
+ "trait_id": "1415742_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415742_at:HC_M2_0606_P:b72a582a1f840a18c3e7",
+ "symbol": "Aup1",
+ "description": "ancient ubiquitous protein 1",
+ "location": "Chr6: 83.006784",
+ "mean": "9.529",
+ "additive": "-0.062",
+ "lod_score": "2.4",
+ "lrs_location": "Chr19: 16.955950",
+ "sample_r": "0.295",
+ "num_overlap": 67,
+ "sample_p": "1.523e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.033",
+ "tissue_pvalue": "8.716e-01"
+ },
+ {
+ "index": 9,
+ "trait_id": "1415743_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415743_at:HC_M2_0606_P:3187245a079e824b4236",
+ "symbol": "Hdac5",
+ "description": "histone deacetylase 5; last four exons",
+ "location": "Chr11: 102.057397",
+ "mean": "11.009",
+ "additive": "0.081",
+ "lod_score": "2.1",
+ "lrs_location": "Chr7: 125.263073",
+ "sample_r": "0.285",
+ "num_overlap": 67,
+ "sample_p": "1.950e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.005",
+ "tissue_pvalue": "9.823e-01"
+ },
+ {
+ "index": 10,
+ "trait_id": "1415690_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415690_at:HC_M2_0606_P:603b215ede00b6fe1104",
+ "symbol": "Mrp127",
+ "description": "39S ribosomal protein L27, mitochondrial; last three exons",
+ "location": "Chr11: 94.517922",
+ "mean": "12.569",
+ "additive": "0.063",
+ "lod_score": "1.9",
+ "lrs_location": "Chr2: 164.779024",
+ "sample_r": "0.266",
+ "num_overlap": 67,
+ "sample_p": "2.986e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 11,
+ "trait_id": "1415727_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415727_at:HC_M2_0606_P:cb40b8cba0eee75781a6",
+ "symbol": "Apoa1bp",
+ "description": "apolipoprotein A-I binding protein; exons 3 through 6",
+ "location": "Chr3: 87.860534",
+ "mean": "11.707",
+ "additive": "-0.076",
+ "lod_score": "2.8",
+ "lrs_location": "Chr3: 56.295375",
+ "sample_r": "0.263",
+ "num_overlap": 67,
+ "sample_p": "3.136e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.535",
+ "tissue_pvalue": "4.841e-03"
+ },
+ {
+ "index": 12,
+ "trait_id": "1415730_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415730_at:HC_M2_0606_P:a970e0610a56ac4aba27",
+ "symbol": "Cpsf7",
+ "description": "cleavage and polyadenylation specificity factor 7; distal 3' UTR (transQTL on Chr 4 in BXD eye data)",
+ "location": "Chr19: 10.621618",
+ "mean": "10.662",
+ "additive": "-0.048",
+ "lod_score": "2.1",
+ "lrs_location": "Chr1: 188.085707",
+ "sample_r": "-0.263",
+ "num_overlap": 67,
+ "sample_p": "3.164e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 13,
+ "trait_id": "1415741_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415741_at:HC_M2_0606_P:033752be361d32960c29",
+ "symbol": "Tmem165",
+ "description": "transmembrane protein 165; 3' UTR",
+ "location": "Chr5: 76.637708",
+ "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",
+ "mean": "10.778",
+ "additive": "-0.084",
+ "lod_score": "2.4",
+ "lrs_location": "Chr4: 122.536808",
+ "sample_r": "0.242",
+ "num_overlap": 67,
+ "sample_p": "4.816e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 16,
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+ "dataset": "HC_M2_0606_P",
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+ "tissue_pvalue": "--"
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+ "additive": "0.150",
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+ "additive": "0.048",
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+ "dataset": "HC_M2_0606_P",
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+ "location": "Chr14: 55.045789",
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+ "tissue_corr": "0.395",
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+ "dataset": "HC_M2_0606_P",
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+ "sample_p": "3.418e-01",
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+ "tissue_pvalue": "1.975e-01"
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+ "location": "Chr9: 103.255487",
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+ "additive": "0.060",
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+ "lrs_location": "Chr3: 10.018672",
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+ "dataset": "HC_M2_0606_P",
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+ "additive": "0.065",
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+ "sample_p": "3.575e-01",
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+ "tissue_corr": "0.150",
+ "tissue_pvalue": "4.638e-01"
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+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415739_at:HC_M2_0606_P:c5e8b34713057f53dd07",
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+ "location": "Chr7: 31.426055",
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+ "additive": "-0.154",
+ "lod_score": "12.8",
+ "lrs_location": "Chr1: 174.792334",
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+ "sample_p": "3.898e-01",
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+ "tissue_corr": "0.550",
+ "tissue_pvalue": "3.580e-03"
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+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415695_at:HC_M2_0606_P:44556cafdf6f5e38669b",
+ "symbol": "Psma1",
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+ "location": "Chr7: 121.408358",
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+ },
+ {
+ "index": 75,
+ "trait_id": "1415694_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415694_at:HC_M2_0606_P:38c96bb74d8916f0c519",
+ "symbol": "Wars",
+ "description": "tryptophanyl-tRNA synthetase; alternative 3' UTR (short form, test Mendelian 12.109, BXD hippocampus, B high)",
+ "location": "Chr12: 110.098698",
+ "mean": "8.523",
+ "additive": "-0.938",
+ "lod_score": "32.3",
+ "lrs_location": "Chr12: 110.136559",
+ "sample_r": "-0.039",
+ "num_overlap": 67,
+ "sample_p": "7.559e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.275",
+ "tissue_pvalue": "1.738e-01"
+ },
+ {
+ "index": 76,
+ "trait_id": "1415744_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415744_at:HC_M2_0606_P:38f9abcb635f29e5871c",
+ "symbol": "Pfdn6",
+ "description": "prefoldin subunit 6 (H2-K region expressed gene 2); 5' UTR, exons 1, 3, 4, and 3' UTR",
+ "location": "Chr17: 34.075883",
+ "mean": "11.324",
+ "additive": "-0.157",
+ "lod_score": "11.0",
+ "lrs_location": "Chr17: 33.247164",
+ "sample_r": "0.038",
+ "num_overlap": 67,
+ "sample_p": "7.626e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 77,
+ "trait_id": "1415700_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415700_a_at:HC_M2_0606_P:95582b9daa0776067713",
+ "symbol": "Ssr3",
+ "description": "signal sequence receptor, gamma (translocon-associated protein gamma); mid-distal 3' UTR",
+ "location": "Chr3: 65.183917",
+ "mean": "12.068",
+ "additive": "0.067",
+ "lod_score": "2.1",
+ "lrs_location": "Chr7: 27.852865",
+ "sample_r": "0.036",
+ "num_overlap": 67,
+ "sample_p": "7.742e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.354",
+ "tissue_pvalue": "7.623e-02"
+ },
+ {
+ "index": 78,
+ "trait_id": "1415687_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415687_a_at:HC_M2_0606_P:f15bcfef7839d22ca5a3",
+ "symbol": "Psap",
+ "description": "prosaposin; mid and distal 3' UTR",
+ "location": "Chr10: 59.764772",
+ "mean": "14.976",
+ "additive": "0.121",
+ "lod_score": "2.0",
+ "lrs_location": "Chr5: 4.468199",
+ "sample_r": "0.035",
+ "num_overlap": 67,
+ "sample_p": "7.777e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.078",
+ "tissue_pvalue": "7.058e-01"
+ },
+ {
+ "index": 79,
+ "trait_id": "1415729_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415729_at:HC_M2_0606_P:08dc70633663e17111dd",
+ "symbol": "Pdpk1",
+ "description": "3-phosphoinositide dependent protein kinase-1; distal 3' UTR",
+ "location": "Chr17: 24.210667",
+ "mean": "12.376",
+ "additive": "-0.081",
+ "lod_score": "3.0",
+ "lrs_location": "Chr2: 55.266330",
+ "sample_r": "-0.029",
+ "num_overlap": 67,
+ "sample_p": "8.147e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.290",
+ "tissue_pvalue": "1.506e-01"
+ },
+ {
+ "index": 80,
+ "trait_id": "1415672_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415672_at:HC_M2_0606_P:d6a7286d4957f3487196",
+ "symbol": "Golga7",
+ "description": "golgi autoantigen, golgin subfamily a, 7",
+ "location": "Chr8: 24.351869",
+ "mean": "13.218",
+ "additive": "0.063",
+ "lod_score": "2.6",
+ "lrs_location": "Chr13: 120.059030",
+ "sample_r": "-0.027",
+ "num_overlap": 67,
+ "sample_p": "8.305e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.456",
+ "tissue_pvalue": "1.919e-02"
+ },
+ {
+ "index": 81,
+ "trait_id": "1415713_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415713_a_at:HC_M2_0606_P:e22be15fd9ade623e3bb",
+ "symbol": "Ddx24",
+ "description": "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24; last two exons",
+ "location": "Chr12: 104.646500",
+ "mean": "11.808",
+ "additive": "0.052",
+ "lod_score": "3.1",
+ "lrs_location": "Chr9: 15.693672",
+ "sample_r": "-0.026",
+ "num_overlap": 67,
+ "sample_p": "8.322e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.338",
+ "tissue_pvalue": "9.077e-02"
+ },
+ {
+ "index": 82,
+ "trait_id": "1415683_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415683_at:HC_M2_0606_P:f544e88da2dd8adb0b3f",
+ "symbol": "Nmt1",
+ "description": "N-myristoyltransferase 1; exons 10 and 11, and 3' UTR",
+ "location": "Chr11: 102.926047",
+ "mean": "12.261",
+ "additive": "-0.070",
+ "lod_score": "2.6",
+ "lrs_location": "Chr6: 101.797292",
+ "sample_r": "0.026",
+ "num_overlap": 67,
+ "sample_p": "8.375e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.366",
+ "tissue_pvalue": "6.559e-02"
+ },
+ {
+ "index": 83,
+ "trait_id": "1415701_x_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415701_x_at:HC_M2_0606_P:8faa1e92ec8fc8cf33b5",
+ "symbol": "Rpl23",
+ "description": "ribosomal protein L23; spans exons 1, 2, 3, 4, and intron 4, and proximal 3' UTR",
+ "location": "Chr11: 97.639386",
+ "mean": "16.236",
+ "additive": "0.067",
+ "lod_score": "2.7",
+ "lrs_location": "Chr2: 162.502590",
+ "sample_r": "0.024",
+ "num_overlap": 67,
+ "sample_p": "8.474e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.036",
+ "tissue_pvalue": "8.630e-01"
+ },
+ {
+ "index": 84,
+ "trait_id": "1415681_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415681_at:HC_M2_0606_P:96ceed972f5f3da9d52d",
+ "symbol": "Mrpl43",
+ "description": "mitochondrial ribosomal protein L43",
+ "location": "Chr19: 45.079983",
+ "mean": "10.604",
+ "additive": "-0.058",
+ "lod_score": "2.1",
+ "lrs_location": "Chr7: 90.186486",
+ "sample_r": "-0.021",
+ "num_overlap": 67,
+ "sample_p": "8.669e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.362",
+ "tissue_pvalue": "6.958e-02"
+ },
+ {
+ "index": 85,
+ "trait_id": "1415691_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415691_at:HC_M2_0606_P:c6a3213115c205f73f86",
+ "symbol": "Dlg1",
+ "description": "discs, large homolog 1 (presynaptic protein SAP97); distal 3' UTR",
+ "location": "Chr16: 31.872849",
+ "mean": "11.782",
+ "additive": "0.088",
+ "lod_score": "2.9",
+ "lrs_location": "Chr17: 55.490261",
+ "sample_r": "-0.020",
+ "num_overlap": 67,
+ "sample_p": "8.731e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.015",
+ "tissue_pvalue": "9.426e-01"
+ },
+ {
+ "index": 86,
+ "trait_id": "1415715_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415715_at:HC_M2_0606_P:8c7d719635beb0f7a9f5",
+ "symbol": "Slbp",
+ "description": "stem-loop binding protein",
+ "location": "Chr5: 33.995959",
+ "mean": "9.003",
+ "additive": "0.051",
+ "lod_score": "2.2",
+ "lrs_location": "Chr11: 69.415410",
+ "sample_r": "-0.020",
+ "num_overlap": 67,
+ "sample_p": "8.749e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.090",
+ "tissue_pvalue": "6.621e-01"
+ },
+ {
+ "index": 87,
+ "trait_id": "1415751_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415751_at:HC_M2_0606_P:d0d8a9fa8a2b142d4374",
+ "symbol": "Hb1bp3",
+ "description": "heterochromatin protein 1-binding protein 3",
+ "location": "Chr4: 137.798500",
+ "mean": "12.239",
+ "additive": "-0.168",
+ "lod_score": "14.7",
+ "lrs_location": "Chr4: 138.152371",
+ "sample_r": "0.019",
+ "num_overlap": 67,
+ "sample_p": "8.773e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 88,
+ "trait_id": "1415764_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415764_at:HC_M2_0606_P:8a23b78d5d55a0026ceb",
+ "symbol": "Cpsf7",
+ "description": "cleavage and polyadenylation specificity factor 7",
+ "location": "Chr1: 135.516541",
+ "mean": "11.499",
+ "additive": "-0.352",
+ "lod_score": "28.8",
+ "lrs_location": "Chr1: 135.115363",
+ "sample_r": "-0.019",
+ "num_overlap": 67,
+ "sample_p": "8.787e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 89,
+ "trait_id": "1415724_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415724_a_at:HC_M2_0606_P:4ff4b2d244043dc3b03e",
+ "symbol": "Cdc42",
+ "description": "cell division cycle 42 (activator of Rac); mid-distal 3' UTR",
+ "location": "Chr4: 136.876012",
+ "mean": "11.795",
+ "additive": "-0.120",
+ "lod_score": "5.5",
+ "lrs_location": "Chr1: 172.981863",
+ "sample_r": "0.019",
+ "num_overlap": 67,
+ "sample_p": "8.792e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.073",
+ "tissue_pvalue": "7.233e-01"
+ },
+ {
+ "index": 90,
+ "trait_id": "1415737_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415737_at:HC_M2_0606_P:c667a35a9b2b78172117",
+ "symbol": "Rfk",
+ "description": "riboflavin kinase; distal 3' UTR",
+ "location": "Chr19: 17.475267",
+ "mean": "11.552",
+ "additive": "0.414",
+ "lod_score": "35.4",
+ "lrs_location": "Chr19: 16.955950",
+ "sample_r": "0.019",
+ "num_overlap": 67,
+ "sample_p": "8.810e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.117",
+ "tissue_pvalue": "5.681e-01"
+ },
+ {
+ "index": 91,
+ "trait_id": "1415738_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415738_at:HC_M2_0606_P:304349c531fb99926720",
+ "symbol": "Txndc12",
+ "description": "thioredoxin domain-containing protein 12; 3' UTR",
+ "location": "Chr4: 108.534146",
+ "mean": "9.375",
+ "additive": "-0.103",
+ "lod_score": "3.2",
+ "lrs_location": "Chr1: 172.981863",
+ "sample_r": "-0.016",
+ "num_overlap": 67,
+ "sample_p": "9.004e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.135",
+ "tissue_pvalue": "5.114e-01"
+ },
+ {
+ "index": 92,
+ "trait_id": "1415735_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415735_at:HC_M2_0606_P:f30f5a5f571c8c61d459",
+ "symbol": "Ddb1",
+ "description": "damage-specific DNA binding protein 1, 127 kDa",
+ "location": "Chr19: 10.703737",
+ "mean": "10.647",
+ "additive": "-0.085",
+ "lod_score": "5.1",
+ "lrs_location": "Chr16: 28.990480",
+ "sample_r": "0.016",
+ "num_overlap": 67,
+ "sample_p": "9.008e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.248",
+ "tissue_pvalue": "2.217e-01"
+ },
+ {
+ "index": 93,
+ "trait_id": "1415684_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415684_at:HC_M2_0606_P:710753b49f7e38406e4b",
+ "symbol": "Atg5",
+ "description": "autophagy related 5; mid 3' UTR",
+ "location": "Chr10: 44.083511",
+ "mean": "8.854",
+ "additive": "-0.068",
+ "lod_score": "2.2",
+ "lrs_location": "Chr6: 145.406059",
+ "sample_r": "-0.014",
+ "num_overlap": 67,
+ "sample_p": "9.086e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.109",
+ "tissue_pvalue": "5.954e-01"
+ },
+ {
+ "index": 94,
+ "trait_id": "1415686_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415686_at:HC_M2_0606_P:455a84fffcd7a0997580",
+ "symbol": "Rab14",
+ "description": "Rab GTPase family member 14",
+ "location": "Chr2: 35.036216",
+ "mean": "12.112",
+ "additive": "0.110",
+ "lod_score": "3.6",
+ "lrs_location": "Chr14: 124.508018",
+ "sample_r": "-0.013",
+ "num_overlap": 67,
+ "sample_p": "9.139e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.056",
+ "tissue_pvalue": "7.850e-01"
+ },
+ {
+ "index": 95,
+ "trait_id": "1415685_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415685_at:HC_M2_0606_P:60c84786fe2f4a62d13d",
+ "symbol": "Mtif2",
+ "description": "mitochondrial translational initiation factor 2",
+ "location": "Chr11: 29.442428",
+ "mean": "9.271",
+ "additive": "-0.367",
+ "lod_score": "23.1",
+ "lrs_location": "Chr11: 28.975002",
+ "sample_r": "0.012",
+ "num_overlap": 67,
+ "sample_p": "9.259e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.358",
+ "tissue_pvalue": "7.272e-02"
+ },
+ {
+ "index": 96,
+ "trait_id": "1415679_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415679_at:HC_M2_0606_P:513339a6b22faab7d8f6",
+ "symbol": "Psenen",
+ "description": "presenilin enhancer 2; 5' UTR, all exons, and 3' UTR",
+ "location": "Chr7: 31.346914",
+ "mean": "11.480",
+ "additive": "-0.283",
+ "lod_score": "19.1",
+ "lrs_location": "Chr7: 31.505577",
+ "sample_r": "-0.011",
+ "num_overlap": 67,
+ "sample_p": "9.286e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.002",
+ "tissue_pvalue": "9.929e-01"
+ },
+ {
+ "index": 97,
+ "trait_id": "1415710_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415710_at:HC_M2_0606_P:4b8e32a96cf0e9bb30d3",
+ "symbol": "Cox18",
+ "description": "cytochrome c oxidase assembly protein 18; last three exons and proximal 3' UTR",
+ "location": "Chr5: 90.644087",
+ "mean": "9.513",
+ "additive": "0.402",
+ "lod_score": "33.4",
+ "lrs_location": "Chr5: 90.500265",
+ "sample_r": "0.010",
+ "num_overlap": 67,
+ "sample_p": "9.360e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.420",
+ "tissue_pvalue": "3.257e-02"
+ },
+ {
+ "index": 98,
+ "trait_id": "1415702_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415702_a_at:HC_M2_0606_P:7ef725f27498e294d14a",
+ "symbol": "Ctbp1",
+ "description": "C-terminal binding protein 1; 3' UTR",
+ "location": "Chr5: 33.590456",
+ "mean": "12.530",
+ "additive": "-0.056",
+ "lod_score": "2.3",
+ "lrs_location": "Chr12: 76.993653",
+ "sample_r": "-0.010",
+ "num_overlap": 67,
+ "sample_p": "9.372e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.514",
+ "tissue_pvalue": "7.288e-03"
+ },
+ {
+ "index": 99,
+ "trait_id": "1415711_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415711_at:HC_M2_0606_P:f71bb40cdefd07ae95d6",
+ "symbol": "Arfgef1",
+ "description": "ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited); 3' UTR",
+ "location": "Chr18: 22.122655",
+ "mean": "11.617",
+ "additive": "-0.055",
+ "lod_score": "3.3",
+ "lrs_location": "Chr2: 50.500580",
+ "sample_r": "-0.003",
+ "num_overlap": 67,
+ "sample_p": "9.802e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.020",
+ "tissue_pvalue": "9.216e-01"
+ },
+ {
+ "index": 100,
+ "trait_id": "1415726_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415726_at:HC_M2_0606_P:89e8ab5b988a202a2fb0",
+ "symbol": "Ankrd17",
+ "description": "ankyrin repeat domain protein 17; last exon and proximal 3' UTR",
+ "location": "Chr5: 90.657781",
+ "mean": "11.533",
+ "additive": "0.046",
+ "lod_score": "2.0",
+ "lrs_location": "Chr14: 42.819085",
+ "sample_r": "0.000",
+ "num_overlap": 67,
+ "sample_p": "9.991e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.530",
+ "tissue_pvalue": "5.382e-03"
+ }
+] \ No newline at end of file
diff --git a/tests/unit/correlation/group_data_test.json b/tests/unit/correlation/group_data_test.json
new file mode 100644
index 0000000..9a73a46
--- /dev/null
+++ b/tests/unit/correlation/group_data_test.json
@@ -0,0 +1,214 @@
+{
+ "name":"BXD",
+ "id":1,
+ "genetic_type":"riset",
+ "f1list":"None",
+ "parlist":"None",
+ "mapping_id":"1",
+ "mapping_names":[
+ "GEMMA",
+ "QTLReaper",
+ "R/qtl"
+ ],
+ "species":"mouse",
+ "samplelist":[
+ "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"
+ ]
+} \ No newline at end of file
diff --git a/tests/unit/correlation/my_results.json b/tests/unit/correlation/my_results.json
new file mode 100644
index 0000000..2061c6e
--- /dev/null
+++ b/tests/unit/correlation/my_results.json
@@ -0,0 +1,388 @@
+[
+
+ {
+ "sample_r_correlation_using_genenetwork3":"Results",
+
+ },
+
+ {
+ "index": 1,
+ "trait_id": "1445813_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1445813_at:HC_M2_0606_P:ca1b85915ccba7198af3",
+ "symbol": "0610012K18Rik",
+ "description": "RIKEN cDNA 0610012H03 (no human homolog defined)",
+ "location": "Chr17: 14.966404",
+ "mean": "6.643",
+ "additive": "0.042",
+ "lod_score": "2.6",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.694",
+ "num_overlap": 67,
+ "sample_p": "7.244e-11",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 2,
+ "trait_id": "1439910_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1439910_a_at:HC_M2_0606_P:0c4c7a3cb088699af36c",
+ "symbol": "Tradd",
+ "description": "TNFRSF1A-associated via death domain",
+ "location": "Chr8: 107.783836",
+ "mean": "7.449",
+ "additive": "0.039",
+ "lod_score": "1.7",
+ "lrs_location": "Chr1: 195.987783",
+ "sample_r": "-0.692",
+ "num_overlap": 67,
+ "sample_p": "9.012e-11",
+ "lit_corr": "--",
+ "tissue_corr": "-0.285",
+ "tissue_pvalue": "1.575e-01"
+ },
+ {
+ "index": 3,
+ "trait_id": "1421499_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1421499_a_at:HC_M2_0606_P:b807253e0829c2592ceb",
+ "symbol": "Ptpn14",
+ "description": "protein tyrosine phosphatase, non-receptor type 14",
+ "location": "Chr1: 191.689356",
+ "mean": "6.655",
+ "additive": "0.049",
+ "lod_score": "2.4",
+ "lrs_location": "Chr1: 197.014645",
+ "sample_r": "-0.691",
+ "num_overlap": 67,
+ "sample_p": "1.009e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.242",
+ "tissue_pvalue": "2.337e-01"
+ },
+ {
+ "index": 4,
+ "trait_id": "1421167_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1421167_at:HC_M2_0606_P:d7b29d02c306e1ae105a",
+ "symbol": "Atp11a",
+ "description": "ATPase, class VI, type 11A; last four exons and 3' UTR",
+ "location": "Chr8: 12.856932",
+ "mean": "7.341",
+ "additive": "0.050",
+ "lod_score": "1.7",
+ "lrs_location": "Chr9: 62.226499",
+ "sample_r": "-0.690",
+ "num_overlap": 67,
+ "sample_p": "1.059e-10",
+ "lit_corr": "--",
+ "tissue_corr": "0.154",
+ "tissue_pvalue": "4.522e-01"
+ },
+ {
+ "index": 5,
+ "trait_id": "1436525_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1436525_at:HC_M2_0606_P:b36b6c4053c40cc5b25b",
+ "symbol": "Ap3s2",
+ "description": "adaptor-related protein complex 3, sigma 2 subunit",
+ "location": "Chr7: 87.022674",
+ "mean": "8.227",
+ "additive": "-0.070",
+ "lod_score": "3.0",
+ "lrs_location": "Chr4: 63.346622",
+ "sample_r": "-0.679",
+ "num_overlap": 67,
+ "sample_p": "2.627e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.059",
+ "tissue_pvalue": "7.750e-01"
+ },
+ {
+ "index": 6,
+ "trait_id": "1450824_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1450824_at:HC_M2_0606_P:fa9b15d1d4a2d629decb",
+ "symbol": "Ptch1",
+ "description": "patched homolog 1",
+ "location": "Chr13: 63.612887",
+ "mean": "7.105",
+ "additive": "0.070",
+ "lod_score": "3.9",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.679",
+ "num_overlap": 67,
+ "sample_p": "2.771e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.360",
+ "tissue_pvalue": "7.075e-02"
+ },
+ {
+ "index": 7,
+ "trait_id": "1450540_x_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1450540_x_at:HC_M2_0606_P:0836630187705e0a98ed",
+ "symbol": "Krtap5-1",
+ "description": "keratin associated protein 5-1",
+ "location": "Chr7: 149.482282",
+ "mean": "7.584",
+ "additive": "0.059",
+ "lod_score": "2.2",
+ "lrs_location": "Chr5: 140.893042",
+ "sample_r": "-0.678",
+ "num_overlap": 67,
+ "sample_p": "2.828e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.486",
+ "tissue_pvalue": "1.174e-02"
+ },
+ {
+ "index": 8,
+ "trait_id": "1454403_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1454403_at:HC_M2_0606_P:d6625a44bb78d0c9a7bc",
+ "symbol": "Fgd5",
+ "description": "FYVE, RhoGEF and PH domain containing 5",
+ "location": "Chr6: 91.964079",
+ "mean": "6.447",
+ "additive": "-0.036",
+ "lod_score": "1.8",
+ "lrs_location": "Chr8: 7.701081",
+ "sample_r": "-0.669",
+ "num_overlap": 67,
+ "sample_p": "5.895e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.209",
+ "tissue_pvalue": "3.062e-01"
+ },
+ {
+ "index": 9,
+ "trait_id": "1444162_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1444162_at:HC_M2_0606_P:fea27946a4ed1ee2b47a",
+ "symbol": "Frs2",
+ "description": "fibroblast growth factor receptor substrate 2",
+ "location": "Chr10: 116.521472",
+ "mean": "5.677",
+ "additive": "-0.040",
+ "lod_score": "1.8",
+ "lrs_location": "Chr4: 66.843058",
+ "sample_r": "-0.666",
+ "num_overlap": 67,
+ "sample_p": "7.946e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.241",
+ "tissue_pvalue": "2.352e-01"
+ },
+ {
+ "index": 10,
+ "trait_id": "1451876_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1451876_a_at:HC_M2_0606_P:eb879785591c3c2addeb",
+ "symbol": "Trp63",
+ "description": "transformation related protein 63",
+ "location": "Chr16: 25.884897",
+ "mean": "6.207",
+ "additive": "0.059",
+ "lod_score": "2.0",
+ "lrs_location": "Chr9: 74.382952",
+ "sample_r": "-0.664",
+ "num_overlap": 67,
+ "sample_p": "8.743e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.187",
+ "tissue_pvalue": "3.601e-01"
+ },
+ {
+ "index": 11,
+ "trait_id": "1457795_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1457795_at:HC_M2_0606_P:617d62e702f1f04b065d",
+ "symbol": "Scamp4",
+ "description": "secretory carrier membrane protein 4",
+ "location": "Chr10: 80.076487",
+ "mean": "7.060",
+ "additive": "-0.042",
+ "lod_score": "2.4",
+ "lrs_location": "Chr11: 58.923978",
+ "sample_r": "-0.663",
+ "num_overlap": 67,
+ "sample_p": "9.806e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.040",
+ "tissue_pvalue": "8.462e-01"
+ },
+ {
+ "index": 12,
+ "trait_id": "1439472_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1439472_at:HC_M2_0606_P:f52f356bf5d00add1ba9",
+ "symbol": "Gcn1l1",
+ "description": "general control of amino-acid synthesis 1-like 1",
+ "location": "Chr5: 116.033483",
+ "mean": "7.325",
+ "additive": "0.058",
+ "lod_score": "3.1",
+ "lrs_location": "Chr1: 196.404284",
+ "sample_r": "-0.662",
+ "num_overlap": 67,
+ "sample_p": "1.075e-09",
+ "lit_corr": "--",
+ "tissue_corr": "-0.205",
+ "tissue_pvalue": "3.157e-01"
+ },
+ {
+ "index": 13,
+ "trait_id": "1422074_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1422074_at:HC_M2_0606_P:4acd73cfd3d194327d79",
+ "symbol": "Cdx2",
+ "description": "caudal type homeo box 2",
+ "location": "Chr5: 148.113293",
+ "mean": "6.415",
+ "additive": "-0.037",
+ "lod_score": "1.8",
+ "lrs_location": "Chr2: 180.825581",
+ "sample_r": "-0.661",
+ "num_overlap": 67,
+ "sample_p": "1.140e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.002",
+ "tissue_pvalue": "9.926e-01"
+ },
+ {
+ "index": 14,
+ "trait_id": "1429140_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1429140_at:HC_M2_0606_P:16116d150fd7a8d09687",
+ "symbol": "Spns3",
+ "description": "spinster homolog 3; exons 10, 12, and proximal 3' UTR",
+ "location": "Chr11: 72.311676",
+ "mean": "7.194",
+ "additive": "0.050",
+ "lod_score": "2.1",
+ "lrs_location": "Chr9: 69.810185",
+ "sample_r": "-0.661",
+ "num_overlap": 67,
+ "sample_p": "1.175e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.557",
+ "tissue_pvalue": "3.116e-03"
+ },
+ {
+ "index": 15,
+ "trait_id": "1437477_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1437477_at:HC_M2_0606_P:990d16df933d7bb03428",
+ "symbol": "Lrrfip1",
+ "description": "leucine rich repeat (in FLII) interacting protein 1",
+ "location": "Chr1: 93.011523",
+ "mean": "7.597",
+ "additive": "0.068",
+ "lod_score": "2.3",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.658",
+ "num_overlap": 67,
+ "sample_p": "1.393e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.132",
+ "tissue_pvalue": "5.204e-01"
+ },
+ {
+ "index": 16,
+ "trait_id": "1440212_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1440212_at:HC_M2_0606_P:01ae82e4856177dd9d89",
+ "symbol": "Slc12a1",
+ "description": "solute carrier family 12, member 1",
+ "location": "Chr2: 124.990152",
+ "mean": "7.061",
+ "additive": "0.038",
+ "lod_score": "2.2",
+ "lrs_location": "Chr1: 193.731996",
+ "sample_r": "-0.655",
+ "num_overlap": 67,
+ "sample_p": "1.769e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.028",
+ "tissue_pvalue": "8.923e-01"
+ },
+ {
+ "index": 17,
+ "trait_id": "1419755_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1419755_at:HC_M2_0606_P:15fea7c69b0d5faa1298",
+ "symbol": "Mfi2",
+ "description": "antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5",
+ "location": "Chr16: 31.898518",
+ "mean": "6.697",
+ "additive": "-0.038",
+ "lod_score": "2.0",
+ "lrs_location": "Chr4: 50.881071",
+ "sample_r": "-0.654",
+ "num_overlap": 67,
+ "sample_p": "1.950e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.244",
+ "tissue_pvalue": "2.305e-01"
+ },
+ {
+ "index": 18,
+ "trait_id": "1425457_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1425457_a_at:HC_M2_0606_P:669c485b158c0207026c",
+ "symbol": "Grb10",
+ "description": "growth factor receptor bound protein 10",
+ "location": "Chr11: 11.833500",
+ "mean": "6.515",
+ "additive": "0.081",
+ "lod_score": "3.9",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.652",
+ "num_overlap": 67,
+ "sample_p": "2.295e-09",
+ "lit_corr": "--",
+ "tissue_corr": "-0.090",
+ "tissue_pvalue": "6.617e-01"
+ },
+ {
+ "index": 19,
+ "trait_id": "1431329_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1431329_at:HC_M2_0606_P:a6df7ed818ea0042c550",
+ "symbol": "Nphp4",
+ "description": "nephronophthisis 4 (renal tubular development and function)",
+ "location": "Chr4: 151.863271",
+ "mean": "6.191",
+ "additive": "0.039",
+ "lod_score": "1.9",
+ "lrs_location": "ChrX: 112.637353",
+ "sample_r": "-0.652",
+ "num_overlap": 67,
+ "sample_p": "2.330e-09",
+ "lit_corr": "--",
+ "tissue_corr": "-0.104",
+ "tissue_pvalue": "6.144e-01"
+ },
+ {
+ "index": 20,
+ "trait_id": "1443987_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1443987_at:HC_M2_0606_P:681e6c787b4d652d0c07",
+ "symbol": "Klhl18",
+ "description": "kelch-like 18 (Drosophila)",
+ "location": "Chr9: 110.330597",
+ "mean": "7.244",
+ "additive": "-0.070",
+ "lod_score": "2.1",
+ "lrs_location": "Chr15: 13.149248",
+ "sample_r": "-0.650",
+ "num_overlap": 67,
+ "sample_p": "2.561e-09",
+ "lit_corr": "--",
+ "tissue_corr": "-0.200",
+ "tissue_pvalue": "3.270e-01"
+ }
+] \ No newline at end of file
diff --git a/tests/unit/correlation/test_correlation_computations.py b/tests/unit/correlation/test_correlation_computations.py
new file mode 100644
index 0000000..dbb2587
--- /dev/null
+++ b/tests/unit/correlation/test_correlation_computations.py
@@ -0,0 +1,65 @@
+"""module for testing correlation/correlation_computations"""
+
+import unittest
+from gn3.correlation.correlation_computations import compute_correlation
+
+
+# mock for calculating correlation function
+
+def mock_get_loading_page_data(initial_start_vars):
+ """function to mock filtering input"""
+ results = {'start_vars':
+ {'genofile': 'SAMPLE:X', 'dataset': 'HC_M2_0606_P',
+ 'sample_vals': '{"C57BL/6J":"7.197","DBA/2J":"7.148","B6D2F1":"6.999"}',
+ 'primary_samples': 'C57BL/6J,DBA/2J,B6D2F1',
+ 'n_samples': 3,
+ 'wanted_inputs': "sample_vals,dataset,genofile,primary_samples"}}
+
+ return results
+
+
+class MockCorrelationResults:
+ """mock class for CorrelationResults"""
+
+ def __init__(self, start_vars):
+ for _key, value in start_vars.items():
+ self.value = value
+
+ self.assert_start_vars(start_vars)
+
+ @staticmethod
+ def assert_start_vars(start_vars):
+ """assert data required is supplied"""
+ assert "wanted_inputs" in start_vars
+
+ def do_correlation(self, start_vars):
+ """mock method for doing correlation"""
+
+ return {
+ "results": "success"
+ }
+
+
+class TestCorrelationUtility(unittest.TestCase):
+ """tests for correlation computations"""
+
+ def test_compute_correlation(self):
+ """test function for doing correlation"""
+
+ sample_vals = """{"C57BL/6J":"7.197","DBA/2J":"7.148","B6D2F1":"6.999"}"""
+
+ correlation_input_data = {
+ "wanted_inputs": "sample_vals,dataset,genofile,primary_samples",
+ "genofile": "SAMPLE:X",
+ "dataset": "HC_M2_0606_P",
+
+ "sample_vals": sample_vals,
+ "primary_samples": "C57BL/6J,DBA/2J,B6D2F1"
+
+ }
+ correlation_results = compute_correlation(
+ correlation_input_data=correlation_input_data,
+ correlation_results=MockCorrelationResults)
+ results = {"results": "success"}
+
+ self.assertEqual(results,correlation_results)
diff --git a/tests/unit/correlation/test_show_corr_results.py b/tests/unit/correlation/test_show_corr_results.py
new file mode 100644
index 0000000..4846f5e
--- /dev/null
+++ b/tests/unit/correlation/test_show_corr_results.py
@@ -0,0 +1,226 @@
+"""module contains code for testing creating show correlation object"""
+
+import unittest
+import json
+import os
+from unittest import mock
+from types import SimpleNamespace
+from gn3.correlation.show_corr_results import CorrelationResults
+from gn3.correlation.show_corr_results import get_header_fields
+from gn3.correlation.show_corr_results import generate_corr_json
+# pylint: disable=unused-argument
+
+
+
+class ObjectMixin:
+ """object for adding other methods"""
+ def __str__(self):
+ raise NotImplementedError
+
+ def get_dict(self):
+ raise NotImplementedError
+
+class MockGroup(ObjectMixin):
+ """mock class for Group"""
+
+ def __init__(self):
+ self.samplelist = "add a mock for this"
+ self.parlist = None
+
+ self.filist = None
+
+class MockCreateTrait(ObjectMixin):
+ """mock class for create trait"""
+
+ def __init__(self):
+ pass
+
+ def get_dict(self):
+ """class for getting dict items"""
+ return self.__dict__
+
+ def __str__(self):
+ return self.__class__.__name__
+
+
+class MockCreateDataset:
+ """mock class for create dataset"""
+
+ def __init__(self):
+
+ self.group = MockGroup()
+
+ def get_trait_data(self, sample_keys):
+ """method for getting trait data"""
+ raise NotImplementedError()
+
+ def retrieve_genes(self, symbol):
+ """method for retrieving genes"""
+ raise NotImplementedError()
+
+
+def file_path(relative_path):
+ """getting abs path for file """
+ # adopted from github
+ dir_name = os.path.dirname(os.path.abspath(__file__))
+ split_path = relative_path.split("/")
+ new_path = os.path.join(dir_name, *split_path)
+ return new_path
+
+
+def create_trait(dataset="Temp", name=None, cellid=None):
+ """mock function for creating trait"""
+ return "trait results"
+
+
+def create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=None):
+ """mock function to create dataset """
+ return "dataset results"
+
+
+def get_species(self, start_vars):
+ """
+ how this function works is that it sets the self.dataset and self.species and self.this_trait
+ """
+
+ with open(file_path("./dataset.json")) as dataset_file:
+ results = json.load(dataset_file)
+ self.dataset = SimpleNamespace(**results)
+
+ with open(file_path("./group_data_test.json")) as group_file:
+ results = json.load(group_file)
+ self.group = SimpleNamespace(**results)
+
+ self.dataset.group = self.group
+
+ trait_dict = {'name': '1434568_at', 'dataset': self.dataset, 'cellid': None,
+ 'identification': 'un-named trait', 'haveinfo': True, 'sequence': None}
+
+ trait_obj = SimpleNamespace(**trait_dict)
+
+ self.this_trait = trait_obj
+
+ self.species = "this species data"
+
+
+class TestCorrelationResults(unittest.TestCase):
+ """unittests for Correlation Results"""
+
+ def setUp(self):
+
+ with open(file_path("./correlation_test_data.json")) as json_file:
+ self.correlation_data = json.load(json_file)
+
+ def tearDown(self):
+
+ self.correlation_data = ""
+
+ def test_for_assertion(self):
+ """test for assertion failures"""
+ with self.assertRaises(AssertionError):
+ _corr_results_object = CorrelationResults(start_vars={})
+
+ @mock.patch("gn3.correlation.show_corr_results.CorrelationResults.process_samples")
+ def test_do_correlation(self, process_samples):
+ """test for doing correlation"""
+ process_samples.return_value = None
+ corr_object = CorrelationResults(start_vars=self.correlation_data)
+
+ with self.assertRaises(Exception) as _error:
+
+ # xtodo;to be completed
+
+ _corr_results = corr_object.do_correlation(start_vars=self.correlation_data,
+ create_dataset=create_dataset,
+ create_trait=None,
+ get_species_dataset_trait=get_species)
+
+
+
+ def test_get_header_fields(self):
+ expected = [
+ ['Index',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)',
+ 'Lit rho',
+ 'Tissue rho',
+ 'Tissue p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect'],
+
+ ['Index',
+ 'ID',
+ 'Location',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)']
+
+ ]
+ result1 = get_header_fields("ProbeSet", "spearman")
+ result2 = get_header_fields("Other", "Other")
+ self.assertEqual(result1, expected[0])
+ self.assertEqual(result2, expected[1])
+
+
+
+ @mock.patch("gn3.utility.hmac.data_hmac")
+ def test_generate_corr_json(self, mock_data_hmac):
+ mock_data_hmac.return_value = "hajsdiau"
+
+ dataset = SimpleNamespace(**{"name": "the_name"})
+ this_trait = SimpleNamespace(**{"name": "trait_test", "dataset": dataset})
+ target_dataset = SimpleNamespace(**{"type": "Publish"})
+ corr_trait_1 = SimpleNamespace(**{
+ "name": "trait_1",
+ "dataset": SimpleNamespace(**{"name": "dataset_1"}),
+ "view": True,
+ "abbreviation": "T1",
+ "description_display": "Trait I description",
+ "authors": "JM J,JYEW",
+ "pubmed_id": "34n4nn31hn43",
+ "pubmed_text": "2016",
+ "pubmed_link": "https://www.load",
+ "lod_score": "",
+ "mean": "",
+ "LRS_location_repr": "BXBS",
+ "additive": "",
+ "sample_r": 10.5,
+ "num_overlap": 2,
+ "sample_p": 5
+
+
+
+
+ })
+ corr_results = [corr_trait_1]
+
+ dataset_type_other = {
+ "location": "cx-3-4",
+ "sample_4": 12.32,
+ "num_overlap": 3,
+ "sample_p": 10.34
+ }
+
+ expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
+
+ results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
+ dataset=dataset, target_dataset=target_dataset, for_api=True)
+ self.assertEqual(expected_results, results1)
+
+
+ def test_generate_corr_json_view_false(self):
+ trait = SimpleNamespace(**{"view": False})
+ corr_results = [trait]
+ this_trait = SimpleNamespace(**{"name": "trait_test"})
+ dataset = SimpleNamespace(**{"name": "the_name"})
+
+ results_where_view_is_false = generate_corr_json(
+ corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False)
+ self.assertEqual(results_where_view_is_false, "[]") \ No newline at end of file
diff --git a/tests/unit/utility/__init__.py b/tests/unit/utility/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tests/unit/utility/__init__.py
diff --git a/tests/unit/utility/test_chunks.py b/tests/unit/utility/test_chunks.py
new file mode 100644
index 0000000..7c42b44
--- /dev/null
+++ b/tests/unit/utility/test_chunks.py
@@ -0,0 +1,19 @@
+"""Test chunking"""
+
+import unittest
+
+from gn3.utility.chunks import divide_into_chunks
+
+
+class TestChunks(unittest.TestCase):
+ "Test Utility method for chunking"
+ def test_divide_into_chunks(self):
+ "Check that a list is chunked correctly"
+ self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
+ [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+ self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4),
+ [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+ self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5),
+ [[1, 2], [7, 3], [22, 8], [5, 22], [333]])
+ self.assertEqual(divide_into_chunks([], 5),
+ [[]])
diff --git a/tests/unit/utility/test_corr_result_helpers.py b/tests/unit/utility/test_corr_result_helpers.py
new file mode 100644
index 0000000..ce5891f
--- /dev/null
+++ b/tests/unit/utility/test_corr_result_helpers.py
@@ -0,0 +1,35 @@
+""" Test correlation helper methods """
+
+import unittest
+from gn3.utility.corr_result_helpers import normalize_values
+from gn3.utility.corr_result_helpers import common_keys
+from gn3.utility.corr_result_helpers import normalize_values_with_samples
+
+
+class TestCorrelationHelpers(unittest.TestCase):
+ """Test methods for normalising lists"""
+
+ def test_normalize_values(self):
+ """Test that a list is normalised correctly"""
+ self.assertEqual(
+ normalize_values([2.3, None, None, 3.2, 4.1, 5],\
+ [3.4, 7.2, 1.3, None, 6.2, 4.1]),
+ ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
+ )
+
+ def test_common_keys(self):
+ """Test that common keys are returned as a list"""
+ test_a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300)
+ test_b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)
+ self.assertEqual(sorted(common_keys(test_a, test_b)),
+ ['BXD1', 'BXD14'])
+
+ def test_normalize_values_with_samples(self):
+ """Test that a sample(dict) is normalised correctly"""
+ self.assertEqual(
+ normalize_values_with_samples(
+ dict(BXD1=9.113, BXD2=9.825, BXD14=8.985,
+ BXD15=9.300, BXD20=9.300),
+ dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)),
+ (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2))
+ )
diff --git a/tests/unit/utility/test_hmac.py b/tests/unit/utility/test_hmac.py
new file mode 100644
index 0000000..eba25a3
--- /dev/null
+++ b/tests/unit/utility/test_hmac.py
@@ -0,0 +1,51 @@
+"""Test hmac utility functions"""
+# pylint: disable-all
+import unittest
+from unittest import mock
+
+from gn3.utility.hmac import data_hmac
+from gn3.utility.hmac import url_for_hmac
+from gn3.utility.hmac import hmac_creation
+
+
+class TestHmacUtil():
+ """Test Utility method for hmac creation"""
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ def test_hmac_creation(self):
+ """Test hmac creation with a utf-8 string"""
+ self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
+
+ @mock.patch("utility.hmac.app.config",
+ {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80'
+ '\xd9\\H@\\\x9f`\x98d^'
+ '\xb4a;\xc6OM\x946a\xbc'
+ '\xfc\x80:*\xebc')})
+ def test_hmac_creation_with_cookie(self):
+ """Test hmac creation with a cookie"""
+ cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce"
+ uuid_, _, signature = cookie.partition(":")
+ self.assertEqual(
+ hmac_creation(uuid_),
+ "af4fcf5eace9e7c864ce")
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ def test_data_hmac(self):
+ """Test data_hmac fn with a utf-8 string"""
+ self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ @mock.patch("utility.hmac.url_for")
+ def test_url_for_hmac_with_plain_url(self, mock_url):
+ """Test url_for_hmac without params"""
+ mock_url.return_value = "https://mock_url.com/ファイ/"
+ self.assertEqual(url_for_hmac("ファイ"),
+ "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ @mock.patch("utility.hmac.url_for")
+ def test_url_for_hmac_with_param_in_url(self, mock_url):
+ """Test url_for_hmac with params"""
+ mock_url.return_value = "https://mock_url.com/?ファイ=1"
+ self.assertEqual(url_for_hmac("ファイ"),
+ "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 15:06:54 +0000