Provide fixtures for test. Fix error to pass test.

Provide the following (empty) files to be used for the test
* wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
* wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt

Rework the paths in
`wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py`
such that they point to the files added above for testing.

Do not require that the phenotype file exists in
`wqflask/wqflask/marker_regression/gemma_mapping.py` before attempting
the mapping.

4 files changed, 6 insertions, 3 deletions

diff --git a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt b/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
diff --git a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt b/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 43051828..24400b33 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -1,4 +1,5 @@
 # test for wqflask/marker_regression/gemma_mapping.py
+import os
 import unittest
 import random
 from unittest import mock
@@ -40,7 +41,8 @@ class TestGemmaMapping(unittest.TestCase):
     @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
     @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
     @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR",
+                os.path.join(os.path.dirname(__file__), "user/data"))
     @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
     @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
     @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
@@ -64,7 +66,8 @@ class TestGemmaMapping(unittest.TestCase):
         mock_os.path.isfile.return_value = True
         mock_gen_covar.return_value = None
         mock_choice.return_value = "R"
-        mock_flat_files.return_value = "/home/genotype/bimbam"
+        mock_flat_files.return_value = os.path.join(
+            os.path.dirname(__file__), "genotype/bimbam")
         mock_parse_loco.return_value = []
         results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
         ], vals=[], covariates="", use_loco=True)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index fa7f0beb..cc063d03 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -58,7 +58,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
             bimbam_dir = flat_files('genotype/bimbam')
             geno_filepath = assert_file(
                 f"{bimbam_dir}/{genofile_name}_geno.txt")
-            pheno_filepath = assert_file(f"{TEMPDIR}/gn2/{pheno_filename}.txt")
+            pheno_filepath = f"{TEMPDIR}/gn2/{pheno_filename}.txt"
             snps_filepath = assert_file(
                 f"{bimbam_dir}/{genofile_name}_snps.txt")
             k_json_output_filepath = f"{TEMPDIR}/gn2/{k_output_filename}.json"