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| author | Alexander Kabui | 2021-06-23 10:18:54 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-06-23 10:18:54 +0300 |
| commit | fed7009b5eec9cc8b9370d4fb8486c7e4136b3d4 (patch) | |
| tree | 6e1decbe45fe98d212ab976a57cbba246c8a54a3 | |
| parent | 3cc3cf68c2dcbdc2cd496f8e2728a59fbb6614e6 (diff) | |
| download | genenetwork3-fed7009b5eec9cc8b9370d4fb8486c7e4136b3d4.tar.gz | |
minor fixes for biweight script
| -rw-r--r-- | gn3/computations/biweight.py | 10 | ||||
| -rw-r--r-- | gn3/settings.py | 2 | ||||
| -rw-r--r-- | scripts/calculate_biweight.R | 5 |
3 files changed, 10 insertions, 7 deletions
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py index 6d031ad..0377bdf 100644 --- a/gn3/computations/biweight.py +++ b/gn3/computations/biweight.py @@ -19,7 +19,9 @@ def calculate_biweight_corr(trait_vals: List, 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) + try: + (corr_coeff, p_val) = tuple( + [float(y.strip()) for y in results.split()]) + return (corr_coeff, p_val) + except Exception as e: + raise e diff --git a/gn3/settings.py b/gn3/settings.py index 770ba3d..f4866d5 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -23,4 +23,4 @@ SQLALCHEMY_TRACK_MODIFICATIONS = False GN2_BASE_URL = "http://www.genenetwork.org/" # biweight script -BIWEIGHT_RSCRIPT = "~/genenetwork3/script/calculate_biweight.R" +BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R" diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R index bad93cb..8d8366e 100644 --- a/scripts/calculate_biweight.R +++ b/scripts/calculate_biweight.R @@ -13,7 +13,7 @@ ParseArgs <- function(args){ } BiweightMidCorrelation <- function(trait_val,target_val){ - results <- bicorAndPvalue(c(trait_val),c(target_val)) + results <-bicorAndPvalue(as.numeric(unlist(trait_val)),as.numeric(unlist(target_val))) return ((c(c(results$bicor)[1],c(results$p)[1]))) } @@ -39,4 +39,5 @@ test_that("parsing args "),{ parsed_values <- ParseArgs(arg_values) -cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
\ No newline at end of file + +cat(BiweightMidCorrelation(parsed_values[1],parsed_values[2]))
\ No newline at end of file |