Fixes the tests to match the new, fixed, version

VensinMa · Aug 2, 2021 · 56d10dd · 56d10dd
1 parent 7cf6cfb
commit 56d10dd
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Showing 5 changed files with 19 additions and 19 deletions.
diff --git a/pyRona/file_parser.py b/pyRona/file_parser.py
@@ -122,7 +122,7 @@ def lfmm_results_parser(lfmm_results_filename, assoc_threshold,
  imut_indeces = [int(x) - 1 for x in immutables]
  results = open(lfmm_results_filename, "r")
  for snp, line in enumerate(results):
-
+ line = line.strip()
  # line = [float(y) for x, y in enumerate(line.split(","))
  # if x not in imut_indeces]
  snp_assocs = [(str(snp + 1), covar_names[i]) for i, j in

diff --git a/tests/data/jar/LFMM_envdata.pickle b/tests/data/jar/LFMM_envdata.pickle
diff --git a/tests/data/jar/file_parser.lfmm_results_parser.pickle b/tests/data/jar/file_parser.lfmm_results_parser.pickle
diff --git a/tests/test_file_parser.py b/tests/test_file_parser.py
@@ -58,7 +58,7 @@ def test_baypass_s_b_p():
  """
  test_betai = fp.baypass_summary_betai_parser(
  "../tests/data/Qsuber_GBS_mcmc_aux_summary_betai.out", 20,
- ["1", "2", "3"])
+ ["1", "2", "3"], [str(x + 1) for x in range(16)])
 
  with open("../tests/data/jar/"
  "file_parser.baypass_summary_betai_parser.pickle", "rb") as fle:
@@ -75,7 +75,7 @@ def test_baypass_pij_parser():
  "../tests/data/Qsuber_GBS_mcmc_aux_summary_pij.out",
  fp.baypass_summary_betai_parser(
  "../tests/data/Qsuber_GBS_mcmc_aux_summary_betai.out",
- 20, ["1", "2", "3"]))
+ 20, ["1", "2", "3"], [str(x + 1) for x in range(16)]))
 
  with open("../tests/data/jar/"
  "file_parser.baypass_pij_parser.pickle", "rb") as fle:
@@ -91,12 +91,13 @@ def test_lfmm_res_parser():
  lfmm_results = fp.lfmm_results_parser(
  "../tests/data/Qsuber_lfmm_results.csv",
  0.01,
- ["1", "2", "3"])
+ ["1", "2", "3"],
+ [str(x) for x in range(16)])
  with open("../tests/data/jar/file_parser.lfmm_results_parser.pickle",
  "rb") as fle:
  control_pvalues = pickle.load(fle)
 
- assert str(lfmm_results) == str(control_pvalues)
+ assert lfmm_results == control_pvalues
 
 
 def test_lfmm_to_pop_allele_freqs():

diff --git a/tests/test_pyRona.py b/tests/test_pyRona.py
@@ -670,17 +670,16 @@ def test_argument_parser():
 
  test_arguments = pr.argument_parser(args)
 
- control_arguments = (
- "Namespace(bayes_factor=20.0, "
- "baypass_pij_file='..tests/data/Qsuber_GBS_mcmc_aux_summary_pij.out',"
- " baypass_summary_betai_file="
- "'..tests/data/Qsuber_GBS_mcmc_aux_summary_betai.out',"
- " future_covars_file='..tests/data/ENVFILE_rpc85',"
- " immutables=[], map_filename=None, num_covars=3,"
- " outfile='/home/baptista/Music/LOL',"
- " outliers=True, plots='/tmp/indplots',"
- " popnames_file='..tests/data/popnames_single_GEO.txt',"
- " present_covars_file='..tests/data/ENVFILE', rtype='absdiff',"
- " upstream='baypass', use_weights=True)")
-
- assert str(test_arguments) == control_arguments
+ control_arguments = [
+ "Namespace(upstream='baypass'", " bayes_factor=20.0",
+ " baypass_pij_file='..tests/data/Qsuber_GBS_mcmc_aux_summary_pij.out')",
+ " baypass_summary_betai_file='..tests/data/Qsuber_GBS_mcmc_aux_summary_betai.out'",
+ " future_covars_file='..tests/data/ENVFILE_rpc85'",
+ " immutables=[]", " map_filename=None", " num_covars=3",
+ " outfile='/home/baptista/Music/LOL'",
+ " outliers=True", " plots='/tmp/indplots'",
+ " popnames_file='..tests/data/popnames_single_GEO.txt'",
+ " present_covars_file='..tests/data/ENVFILE'", " rtype='absdiff'",
+ " use_weights=True", " covar_names_file=None"]
+
+ assert sorted(str(test_arguments).strip().split(",")) == sorted(control_arguments)