diff options
| -rw-r--r-- | gn3/computations/biweight.R | 15 | ||||
| -rw-r--r-- | gn3/computations/biweight.py | 22 | ||||
| -rw-r--r-- | gn3/computations/correlations.py | 10 | ||||
| -rw-r--r-- | tests/unit/computations/test_biweight.py | 21 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 6 |
5 files changed, 70 insertions, 4 deletions
diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R new file mode 100644 index 0000000..d0d8de4 --- /dev/null +++ b/gn3/computations/biweight.R @@ -0,0 +1,15 @@ + +library(WGCNA) + + +myArgs <- commandArgs(trailingOnly = TRUE) +trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" "))) +target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" "))) + +BiweightMidCorrelation <- function(trait_val,target_val){ + # results <- bicorAndPvalue(x,y) + return (list(c(results$bicor)[1],c(results$p)[1])) +} +cat(BiweightMidCorrelation(trait_vals,target_vals)) + + diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py new file mode 100644 index 0000000..c17de8e --- /dev/null +++ b/gn3/computations/biweight.py @@ -0,0 +1,22 @@ + + +"""module contains script to call biweight mid\ +correlation in R""" + +import subprocess +from typing import List + + +def call_biweight_script(trait_vals: List, + target_vals: List, + path_to_script: str = "./biweight_R", + command: str = "Rscript" + ): + '''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) + + return tuple([float(y) for y in results.split()]) diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index f0ce502..89d37fc 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 call_biweight_script def map_shared_keys_to_values(target_sample_keys: List, @@ -99,8 +100,13 @@ 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 = call_biweight_script(x_val, y_val) + except Exception as error: + raise error + + return results def filter_shared_sample_keys(this_samplelist, diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py new file mode 100644 index 0000000..3045f78 --- /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 call_biweight_script + + +class TestBiweight(TestCase): + """test class for biweight""" + + @mock.patch("gn3.computations.biweight.subprocess.check_output") + def test_call_biweight_script(self, mock_check_output): + """test for call_biweight_script func""" + mock_check_output.return_value = "0.1 0.5" + results = call_biweight_script(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..606f96d 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.call_biweight_script") + 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") |