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| author | Alexander Kabui | 2021-03-13 13:04:33 +0300 |
|---|---|---|
| committer | GitHub | 2021-03-13 13:04:33 +0300 |
| commit | 236ca06dc4c84baecb7b090b8724db997a5d988a (patch) | |
| tree | 7fce724ae007dacfe3cf0f7511756b6064026ea3 /tests/integration/expected_corr_results.json | |
| parent | 7f9a293929be021eb73aec35defe254351557dcb (diff) | |
| download | genenetwork3-236ca06dc4c84baecb7b090b8724db997a5d988a.tar.gz | |
Correlation api (#2)
* add file for correlation api
* register initial correlation api
* add correlation package
* add function for getting page data
* delete loading page api
* modify code for correlation
* add tests folder for correlations
* fix error in correlation api
* add tests for correlation
* add tests for correlation loading data
* add module for correlation computations
* modify api to return json when computing correlation
* add tests for computing correlation
* modify code for loading correlation data
* modify tests for correlation computation
* test loading correlation data using api endpoint
* add tests for asserting error in creating Correlation object
* add do correlation method
* add dummy tests for do_correlation method
* delete unused modules
* add tests for creating trait and dataset
* add intergration test for correlation api
* add tests for correlation api
* edit docorrelation method
* modify integration tests for correlation api
* modify tests for show_corr_results
* add create dataset function
* pep8 formatting and fix return value for api
* add more test data for doing correlation
* modify tests for correlation
* pep8 formatting
* add getting formatted corr type method
* import json library
add process samples method for correlation
* fix issue with sample_vals key_error
* create utility module for correlation
* refactor endpoint for /corr_compute
* add test and mocks for compute_correlation function
* add compute correlation function and pep8 formatting
* move get genofile samplelist to utility module
* refactor code for CorrelationResults object
* pep8 formatting for module
* remove CorrelationResults from Api
* add base package
initialize data_set module with create_dataset,redis and Dataset_Getter
* set dataset_structure if redis is empty
* add callable for DatsetType
* add set_dataset_key method If name is not in the object's dataset dictionary
* add Dataset object and MrnaAssayDataSet
* add db_tools
* add mysql client
* add DatasetGroup object
* add species module
* get mapping method
* import helper functions and new dataset
* add connection to db before request
* add helper functions
* add logger module
* add get_group_samplelists module
* add logger for debug
* add code for adding sample_data
* pep8 formatting
* Add chunks module
* add correlation helper module
* add get_sample_r_and_p_values method
add get_header_fields function
* add generate corr json method
* add function to retrieve_trait_info
* remove comments and clean up code in show_corr_results
* remove comments and clean up code for data_set module
* pep8 formatting for helper_functions module
* pep8 formatting for trait module
* add module for species
* add Temp Dataset Object
* add Phenotype Dataset
* add Genotype Dataset
* add rettrieve sample_sample_data method
* add webqtlUtil module
* add do lit correlation for all traits
* add webqtlCaseData:Settings not ported
* return the_trait for create trait method
* add correlation_test json data
* add tests fore show corr results
* add dictfier package
* add tests for show_corr_results
* add assertion for trait_id
* refactor code for show_corr_results
* add test file for compute_corr intergration tests
* add scipy dependency
* refactor show_corr_results object
add do lit correlation for trait_list
* add hmac module
* add bunch module:Dictionary using object notation
* add correlation functions
* add rpy2 dependency
* add hmac module
* add MrnaAssayTissueData object and get_symbol_values_pairs function
* add config module
* add get json_results method
* pep8 formatting remove comments
* add config file
* add db package
* refactor correlatio compuatation module
* add do tissue correlation for trait list
* add do lit correlation for all traits
* add do tissue correlation for all traits
* add do_bicor for bicor method
* raise error for when initital start vars is None
* add support for both form and json data when for correlation input
* remove print statement and pep8 formatting
* add default settings file
* add tools module for locate_ignore_error
* refactor code remove comments for trait module
* Add new test data for computing correlation
* pep8 formatting and use pickle
* refactor function for filtering form/json data
* remove unused imports
* remove mock functions in correlation_utility module
* refactor tests for compute correlation and pep8 formatting
* add tests for show_correlation results
* modify tests for show_corr_results
* add json files for tests
* pep8 formatting for show_corr_results
* Todo:Lint base files
* pylint for intergration tests
* add test module for test_corr_helpers
* Add test chunk module
* lint utility package
* refactoring and pep8 formatting
* implement simple metric for correlation
* add hmac utility file
* add correlation prefix
* fix merge conflict
* minor fixes for endpoints
* import:python-scipy,python-sqlalchemy from guix
* add python mysqlclient
* remove pkg-resources from requirements
* add python-rpy3 from guix
* refactor code for species module
* pep8 formatting and refactor code
* add tests for genereating correlation results
* lint correlation functions
* fix failing tests for show_corr_results
* add new correlation test data fix errors
* fix issues related to getting group samplelists
* refactor intergration tests for correlation
* add todo for refactoring_wanted_inputs
* replace custom Attribute setter with SimpleNamespace
* comparison of sample r correlation results btwn genenenetwork2 and genenetwork3
* delete AttributeSetter
* test request for /api/correlation/compute_correlation took 18.55710196495056 Seconds
* refactor tests and show_correlation results
* remove unneccessary comments and print statements
* edit requirement txt file
* api/correlation took 114.29814600944519 Seconds for correlation resullts:20000
- corr-type:lit
- corr-method:pearson
corr-dataset:corr_dataset:HC_M2_0606_P
* capture SQL_URI and GENENETWORK FILES path
* pep8 formatting edit && remove print statements
* delete filter_input function
update test and data for correlation
* add docstring for required correlation_input
* /api/correlation took 12.905632972717285 Seconds
* pearson
* lit
*dataset:HX_M2_0606_P
trait_id :1444666
p_range:(lower->-0.60,uppper->0.74)
corr_return_results: 100
* update integration and unittest for correlation
* add simple markdown docs for correlation
* update docs
* add tests and catch for invalid correlation_input
* minor fix for api
* Remove jupyter from deps
* guix.scm: Remove duplicate entry
* guix.scm: Add extra action items as comments
* Trim requirements.txt file
Co-authored-by: BonfaceKilz <me@bonfacemunyoki.com>
Diffstat (limited to 'tests/integration/expected_corr_results.json')
| -rw-r--r-- | tests/integration/expected_corr_results.json | 1902 |
1 files changed, 1902 insertions, 0 deletions
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", + "dataset": "HC_M2_0606_P", + "hmac": "1415748_a_at:HC_M2_0606_P:749a2279081b54e89885", + "symbol": "Dctn5", + "description": "dynactin 5; last exon and proximal half of 3' UTR", + "location": "Chr7: 129.291923", + "mean": "11.250", + "additive": "0.071", + "lod_score": "3.4", + "lrs_location": "Chr5: 138.337847", + "sample_r": "0.230", + "num_overlap": 67, + "sample_p": "6.133e-02", + "lit_corr": "--", + "tissue_corr": "0.064", + "tissue_pvalue": "7.557e-01" + }, + { + "index": 18, + "trait_id": "1415706_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415706_at:HC_M2_0606_P:ddfffdb78d0ff84d6a1a", + "symbol": "Copa", + "description": "coatomer protein complex, subunit alpha; 3' UTR", + "location": "Chr1: 174.051912", + "mean": "12.577", + "additive": "-0.143", + "lod_score": "8.7", + "lrs_location": "Chr1: 172.981863", + "sample_r": "0.224", + "num_overlap": 67, + "sample_p": "6.829e-02", + "lit_corr": "--", + "tissue_corr": "-0.147", + "tissue_pvalue": "4.739e-01" + }, + { + "index": 19, + "trait_id": "1415696_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415696_at:HC_M2_0606_P:da00b2667d7c27dc76a2", + "symbol": "Sar1a", + "description": "SAR1 gene homolog A; distal 3' UTR", + "location": "Chr10: 61.155492", + "mean": "11.447", + "additive": "-0.051", + "lod_score": "2.4", + "lrs_location": "Chr15: 87.788313", + "sample_r": "0.220", + "num_overlap": 67, + "sample_p": "7.356e-02", + "lit_corr": "--", + "tissue_corr": "-0.559", + "tissue_pvalue": "3.015e-03" + }, + { + "index": 20, + "trait_id": "1415731_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415731_at:HC_M2_0606_P:9e91e97ca1001091a5f3", + "symbol": "Angel2", + "description": "angel homolog 2; distal 3' UTR", + "location": "Chr1: 192.769800", + "mean": "9.490", + "additive": "0.062", + "lod_score": "2.6", + "lrs_location": "Chr14: 124.508018", + "sample_r": "0.218", + "num_overlap": 67, + "sample_p": "7.623e-02", + "lit_corr": "--", + "tissue_corr": "0.232", + "tissue_pvalue": "2.544e-01" + }, + { + "index": 21, + "trait_id": "1415750_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415750_at:HC_M2_0606_P:c9f757736d57e5f23aa5", + "symbol": "Tbl3", + "description": "transducin (beta)-like 3", + "location": "Chr17: 24.838067", + "mean": "8.703", + "additive": "-0.132", + "lod_score": "10.0", + "lrs_location": "Chr17: 23.322636", + "sample_r": "0.213", + "num_overlap": 67, + "sample_p": "8.332e-02", + "lit_corr": "--", + "tissue_corr": "0.312", + "tissue_pvalue": "1.211e-01" + }, + { + "index": 22, + "trait_id": "1415680_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415680_at:HC_M2_0606_P:22e90a54261cb373975e", + "symbol": "Anapc1", + "description": "anaphase promoting complex subunit 1; last 3 exons and 3' UTR", + "location": "Chr2: 128.438499", + "mean": "9.180", + "additive": "-0.102", + "lod_score": "8.7", + "lrs_location": "Chr2: 125.304784", + "sample_r": "-0.210", + "num_overlap": 67, + "sample_p": "8.734e-02", + "lit_corr": "--", + "tissue_corr": "0.367", + "tissue_pvalue": "6.539e-02" + }, + { + "index": 23, + "trait_id": "1415712_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415712_at:HC_M2_0606_P:48e284402cb79a5fbede", + "symbol": "Zranb1", + "description": "zinc finger, RAN-binding domain containing 1 (ubiquitin thioesterase, TRAF-binding protein); far 3' UTR (M430AB control duplicate)", + "location": "Chr7: 140.175988", + "mean": "9.923", + "additive": "-0.079", + "lod_score": "2.8", + "lrs_location": "Chr5: 143.642242", + "sample_r": "-0.208", + "num_overlap": 67, + "sample_p": "9.125e-02", + "lit_corr": "--", + "tissue_corr": "-0.068", + "tissue_pvalue": "7.413e-01" + }, + { + "index": 24, + "trait_id": "1415674_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415674_a_at:HC_M2_0606_P:c8e7fb1fcad21d73fcfd", + "symbol": "Trappc4", + "description": "trafficking protein particle complex 4; 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\ No newline at end of file |