diff options
| -rw-r--r-- | gn3/computations/biweight.py | 25 | ||||
| -rw-r--r-- | gn3/computations/correlations.py | 9 | ||||
| -rw-r--r-- | gn3/settings.py | 6 | ||||
| -rw-r--r-- | guix.scm | 4 | ||||
| -rw-r--r-- | scripts/calculate_biweight.R | 42 | ||||
| -rw-r--r-- | tests/unit/computations/test_biweight.py | 21 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 6 |
7 files changed, 107 insertions, 6 deletions
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py new file mode 100644 index 0000000..6d031ad --- /dev/null +++ b/gn3/computations/biweight.py @@ -0,0 +1,25 @@ +"""module contains script to call biweight midcorrelation in R""" +import subprocess + +from typing import List +from typing import Tuple + +from gn3.settings import BIWEIGHT_RSCRIPT + + +def calculate_biweight_corr(trait_vals: List, + target_vals: List, + path_to_script: str = BIWEIGHT_RSCRIPT, + command: str = "Rscript" + ) -> Tuple[float, float]: + """biweight function""" + + args_1 = ' '.join(str(trait_val) for trait_val in trait_vals) + args_2 = ' '.join(str(target_val) for target_val in target_vals) + cmd = [command, path_to_script] + [args_1] + [args_2] + + results = subprocess.check_output(cmd, universal_newlines=True) + + (corr_coeff, p_val) = tuple([float(y) for y in results.split()]) + + return (corr_coeff, p_val) diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index 0fe46ab..bc738a7 100644 --- a/gn3/computations/correlations.py +++ b/gn3/computations/correlations.py @@ -7,6 +7,7 @@ from typing import Optional from typing import Callable import scipy.stats +from gn3.computations.biweight import calculate_biweight_corr def map_shared_keys_to_values(target_sample_keys: List, @@ -99,8 +100,12 @@ def do_bicor(x_val, y_val) -> Tuple[float, float]: package :not packaged in guix """ - x_val, y_val = 0, 0 - return (x_val, y_val) + + try: + results = calculate_biweight_corr(x_val, y_val) + return results + except Exception as error: + raise error def filter_shared_sample_keys(this_samplelist, diff --git a/gn3/settings.py b/gn3/settings.py index ecfd502..770ba3d 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -14,9 +14,13 @@ TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) RQTL_WRAPPER = "rqtl_wrapper.R" # SQL confs -SQL_URI = os.environ.get("SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") +SQL_URI = os.environ.get( + "SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") SECRET_KEY = "password" SQLALCHEMY_TRACK_MODIFICATIONS = False # gn2 results only used in fetching dataset info GN2_BASE_URL = "http://www.genenetwork.org/" + +# biweight script +BIWEIGHT_RSCRIPT = "~/genenetwork3/script/calculate_biweight.R" @@ -30,6 +30,7 @@ (gnu packages cran) (gnu packages databases) (gnu packages statistics) + (gnu packages bioconductor) (gnu packages python) (gnu packages python-check) (gnu packages python-crypto) @@ -89,7 +90,8 @@ ("r-optparse" ,r-optparse) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) - ; ("r-wgcna" ,r-wgcna) + ("r-testthat" ,r-testthat) + ("r-wgcna" ,r-wgcna) )) (build-system python-build-system) (home-page "https://github.com/genenetwork/genenetwork3") diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R new file mode 100644 index 0000000..bad93cb --- /dev/null +++ b/scripts/calculate_biweight.R @@ -0,0 +1,42 @@ + +library(testthat) +library(WGCNA) + +arg_values <- commandArgs(trailingOnly = TRUE) +ParseArgs <- function(args){ + + trait_vals <- as.numeric(unlist(strsplit(args[1], split=" "))) + target_vals <- as.numeric(unlist(strsplit(args[2], split=" "))) + + return(list(trait_vals= c(trait_vals),target_vals = c(target_vals))) + +} +BiweightMidCorrelation <- function(trait_val,target_val){ + + results <- bicorAndPvalue(c(trait_val),c(target_val)) + return ((c(c(results$bicor)[1],c(results$p)[1]))) + +} + + + +test_that("biweight results"),{ + vec_1 <- c(1,2,3,4) + vec_2 <- c(1,2,3,4) + + results <- BiweightMidCorrelation(vec_1,vec_2) + expect_equal(c(1.0,0.0),results) +} + + +test_that("parsing args "),{ + my_args <- c("1 2 3 4","5 6 7 8") + results <- ParseArgs(my_args) + + expect_equal(results[1],c(1,2,3,4)) + expect_equal(results[2],c(5,6,7,8)) +} + +parsed_values <- ParseArgs(arg_values) + +cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
\ No newline at end of file diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py new file mode 100644 index 0000000..ad404f1 --- /dev/null +++ b/tests/unit/computations/test_biweight.py @@ -0,0 +1,21 @@ +"""test for biweight script""" +from unittest import TestCase +from unittest import mock + +from gn3.computations.biweight import calculate_biweight_corr + + +class TestBiweight(TestCase): + """test class for biweight""" + + @mock.patch("gn3.computations.biweight.subprocess.check_output") + def test_calculate_biweight_corr(self, mock_check_output): + """test for calculate_biweight_corr func""" + mock_check_output.return_value = "0.1 0.5" + results = calculate_biweight_corr(command="Rscript", + path_to_script="./r_script.R", + trait_vals=[ + 1.2, 1.1, 1.9], + target_vals=[1.9, 0.4, 1.1]) + + self.assertEqual(results, (0.1, 0.5)) diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 5746adf..b1bc6ef 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -98,12 +98,14 @@ class TestCorrelation(TestCase): self.assertEqual(results, expected_results) - def test_bicor(self): + @mock.patch("gn3.computations.correlations.calculate_biweight_corr") + def test_bicor(self, mock_biweight): """Test for doing biweight mid correlation """ + mock_biweight.return_value = (1.0, 0.0) results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6]) - self.assertEqual(results, (0.0, 0.0) + self.assertEqual(results, (1.0, 0.0) ) @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value") |