diff options
| author | Alexander Kabui | 2021-03-16 11:38:13 +0300 |
|---|---|---|
| committer | GitHub | 2021-03-16 11:38:13 +0300 |
| commit | 56ce88ad31dec3cece63e9370ca4e4c02139753b (patch) | |
| tree | 766504dfaca75a14cc91fc3d88c41d1e775d415f /tests/unit/correlation | |
| parent | 43d1bb7f6cd2b5890d5b3eb7c357caafda25a35c (diff) | |
| download | genenetwork3-56ce88ad31dec3cece63e9370ca4e4c02139753b.tar.gz | |
delete unwanted correlation stuff (#5)
* delete unwanted correlation stuff
* Refactor/clean up correlations (#4)
* initial commit for Refactor/clean-up-correlation
* add python scipy dependency
* initial commit for sample correlation
* initial commit for sample correlation endpoint
* initial commit for integration and unittest
* initial commit for registering correlation blueprint
* add and modify unittest and integration tests for correlation
* Add compute compute_all_sample_corr method for correlation
* add scipy to requirement txt file
* add tissue correlation for trait list
* add unittest for tissue correlation
* add lit correlation for trait list
* add unittests for lit correlation for trait list
* modify lit correlarion for trait list
* add unittests for lit correlation for trait list
* add correlation metho in dynamic url
* add file format for expected structure input while doing sample correlation
* modify input data structure -> add trait id
* update tests for sample r correlation
* add compute all lit correlation method
* add endpoint for computing lit_corr
* add unit and integration tests for computing lit corr
* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation
* add unittest and integration tests for tissue correlation
Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
* update guix scm file
* fix pylint error for correlations api
Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
Diffstat (limited to 'tests/unit/correlation')
| -rw-r--r-- | tests/unit/correlation/__init__.py | 0 | ||||
| -rw-r--r-- | tests/unit/correlation/correlation_test_data.json | 18 | ||||
| -rw-r--r-- | tests/unit/correlation/dataset.json | 64 | ||||
| -rw-r--r-- | tests/unit/correlation/expected_correlation_results.json | 1902 | ||||
| -rw-r--r-- | tests/unit/correlation/group_data_test.json | 214 | ||||
| -rw-r--r-- | tests/unit/correlation/my_results.json | 388 | ||||
| -rw-r--r-- | tests/unit/correlation/test_correlation_computations.py | 65 | ||||
| -rw-r--r-- | tests/unit/correlation/test_show_corr_results.py | 226 |
8 files changed, 0 insertions, 2877 deletions
diff --git a/tests/unit/correlation/__init__.py b/tests/unit/correlation/__init__.py deleted file mode 100644 index e69de29..0000000 --- a/tests/unit/correlation/__init__.py +++ /dev/null diff --git a/tests/unit/correlation/correlation_test_data.json b/tests/unit/correlation/correlation_test_data.json deleted file mode 100644 index 87d24e3..0000000 --- a/tests/unit/correlation/correlation_test_data.json +++ /dev/null @@ -1,18 +0,0 @@ -{ - "primary_samples": "C57BL/6J,DBA/2J,B6D2F1,D2B6F1,BXD1,BXD2,BXD5,BXD6,BXD8,BXD9,BXD11,BXD12,BXD13,BXD14,BXD15,BXD16,BXD18,BXD19,BXD20,BXD21,BXD22,BXD23,BXD24,BXD24a,BXD25,BXD27,BXD28,BXD29,BXD30,BXD31,BXD32,BXD33,BXD34,BXD35,BXD36,BXD37,BXD38,BXD39,BXD40,BXD41,BXD42,BXD43,BXD44,BXD45,BXD48,BXD48a,BXD49,BXD50,BXD51,BXD52,BXD53,BXD54,BXD55,BXD56,BXD59,BXD60,BXD61,BXD62,BXD63,BXD64,BXD65,BXD65a,BXD65b,BXD66,BXD67,BXD68,BXD69,BXD70,BXD71,BXD72,BXD73,BXD73a,BXD73b,BXD74,BXD75,BXD76,BXD77,BXD78,BXD79,BXD81,BXD83,BXD84,BXD85,BXD86,BXD87,BXD88,BXD89,BXD90,BXD91,BXD93,BXD94,BXD95,BXD98,BXD99,BXD100,BXD101,BXD102,BXD104,BXD105,BXD106,BXD107,BXD108,BXD109,BXD110,BXD111,BXD112,BXD113,BXD114,BXD115,BXD116,BXD117,BXD119,BXD120,BXD121,BXD122,BXD123,BXD124,BXD125,BXD126,BXD127,BXD128,BXD128a,BXD130,BXD131,BXD132,BXD133,BXD134,BXD135,BXD136,BXD137,BXD138,BXD139,BXD141,BXD142,BXD144,BXD145,BXD146,BXD147,BXD148,BXD149,BXD150,BXD151,BXD152,BXD153,BXD154,BXD155,BXD156,BXD157,BXD160,BXD161,BXD162,BXD165,BXD168,BXD169,BXD170,BXD171,BXD172,BXD173,BXD174,BXD175,BXD176,BXD177,BXD178,BXD180,BXD181,BXD183,BXD184,BXD186,BXD187,BXD188,BXD189,BXD190,BXD191,BXD192,BXD193,BXD194,BXD195,BXD196,BXD197,BXD198,BXD199,BXD200,BXD201,BXD202,BXD203,BXD204,BXD205,BXD206,BXD207,BXD208,BXD209,BXD210,BXD211,BXD212,BXD213,BXD214,BXD215,BXD216,BXD217,BXD218,BXD219,BXD220", - "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 deleted file mode 100644 index 8a53ed5..0000000 --- a/tests/unit/correlation/dataset.json +++ /dev/null @@ -1,64 +0,0 @@ -{ - "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 deleted file mode 100644 index b5bbc2d..0000000 --- a/tests/unit/correlation/expected_correlation_results.json +++ /dev/null @@ -1,1902 +0,0 @@ -[ - { - "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; 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"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 deleted file mode 100644 index dbb2587..0000000 --- a/tests/unit/correlation/test_correlation_computations.py +++ /dev/null @@ -1,65 +0,0 @@ -"""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 deleted file mode 100644 index 4846f5e..0000000 --- a/tests/unit/correlation/test_show_corr_results.py +++ /dev/null @@ -1,226 +0,0 @@ -"""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 |