added the remaining tests to plasmid components

Author: tiagofilipe12

flowcraft/templates/mashscreen2json.py

@@ -99,7 +99,7 @@ def main(mash_output, sample_id):
             # estimated copy number
             copy_number = int(float(v[1]) / median_cutoff)
             # assure that plasmid as at least twice the median coverage depth
-            if float(v[1]) > median_cutoff:
+            if float(v[1]) >= median_cutoff:
                 filtered_dic["_".join(k.split("_")[0:3])] = [
                     round(float(v[0]),2),
                     copy_number

flowcraft/tests/template_tests/test_mapping2json.py

@@ -1,4 +1,5 @@
 import os
+import json
 import flowcraft.templates.mapping2json as mapping2json
 
 depth_dict_coverage = {
@@ -96,3 +97,48 @@ def test_generate_file(tmpdir):
     assert not assert_message, "errors occurred:\n{}".format(
         "\n".join(assert_message)
     )
+
+
+def test_generated_dict(tmpdir):
+    """
+    This function tests if the files generated by this template script are
+    created
+    """
+
+    # create a temporary file depth txt file
+    depth_file = tmpdir.join("test_depth_file.txt")
+    depth_file.write("ACC1\t1\t30")
+
+    # creates a temporary file with the json_dict
+    json_dict = tmpdir.join("test_json_dict.json")
+    json_dict.write('{"ACC1": 2000}')
+
+    expected_dict = {"ACC1": 0.0}
+
+    # executes the function to be tested
+    mapping2json.main(str(depth_file), str(json_dict), "0", "test")
+
+    result_dict = json.load(open("{}_mapping.json".format(str(depth_file))))
+
+    assert_message = []
+
+    # checks if result_dict is indeed a dictionary
+    if not isinstance(result_dict, dict):
+        assert_message.append("Contents of the generated file must be a "
+                              "dictionary.")
+
+    if not result_dict == expected_dict:
+        assert_message.append("The expected dictionary must be equal to the "
+                              "one present in the generated file.\n"
+                              "Expected: {}\n"
+                              "Result: {}". format(
+            json.dumps(expected_dict),
+            json.dumps(result_dict)
+        ))
+
+    # remove the .report.json file
+    os.remove(".report.json")
+
+    assert not assert_message, "Errors occurred:\n{}".format(
+        "\n".join(assert_message)
+    )

flowcraft/tests/template_tests/test_mashdist2json.py

@@ -1,4 +1,5 @@
 import os
+import json
 import flowcraft.templates.mashdist2json as mashdist2json
 
 
@@ -10,7 +11,7 @@ def test_generate_file(tmpdir):
 
     # create a temporary file mash screen txt file
     mash_file = tmpdir.join("test_depth_file.txt")
-    mash_file.write("NC_ACC_1_seq\tseq1\t100\t900/1000")
+    mash_file.write("ACC1\tseq1\t0\t900/1000")
 
     mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
 
@@ -28,3 +29,45 @@ def test_generate_file(tmpdir):
     assert not assert_message, "errors occurred:\n{}".format(
         "\n".join(assert_message)
     )
+
+
+def test_generated_dict(tmpdir):
+    """
+    This function tests if the files generated by this template script are
+    created
+    """
+
+    # create a temporary file mash screen txt file
+    mash_file = tmpdir.join("test_depth_file.txt")
+    mash_file.write("ACC1\tseq1\t0\t900/1000")
+
+    # the expected result from loading the dictionary in the generated file
+    expected_dict = {"ACC1": [1.0, 0.9, "seq1"]}
+
+    mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
+
+    result_dict = json.load(open("{}.json".format(
+            str(mash_file).split(".")[0])))
+
+    assert_message = []
+
+    # checks if result_dict is indeed a dictionary
+    if not isinstance(result_dict, dict):
+        assert_message.append("Contents of the generated file must be a "
+                              "dictionary.")
+
+    if not result_dict == expected_dict:
+        assert_message.append("The expected dictionary must be equal to the "
+                              "one present in the generated file.\n"
+                              "Expected: {}\n"
+                              "Result: {}". format(
+            json.dumps(expected_dict),
+            json.dumps(result_dict)
+        ))
+
+    # remove the .report.json file
+    os.remove(".report.json")
+
+    assert not assert_message, "Errors occurred:\n{}".format(
+        "\n".join(assert_message)
+    )

flowcraft/tests/template_tests/test_mashscreen2json.py

@@ -1,4 +1,5 @@
 import os
+import json
 import flowcraft.templates.mashscreen2json as mashscreen2json
 
 
@@ -28,3 +29,46 @@ def test_generate_file(tmpdir):
     assert not assert_message, "errors occurred:\n{}".format(
         "\n".join(assert_message)
     )
+
+
+def test_generated_dict(tmpdir):
+    """
+    This function tests if the files generated by this template script are
+    created
+    """
+
+    # create a temporary file mash screen txt file
+    mash_file = tmpdir.join("test_depth_file.txt")
+    mash_file.write("100\tNA\t30\tNA\tACC1")
+
+    # the expected result from loading the dictionary in the generated file
+    expected_dict = {"ACC1": [100.0, 1]}
+
+    mashscreen2json.main(str(mash_file), "test")
+
+    result_dict = json.load(open("{}.json".format(
+            str(mash_file).split(".")[0])))
+
+    assert_message = []
+
+    # checks if result_dict is indeed a dictionary
+    if not isinstance(result_dict, dict):
+        assert_message.append("Contents of the generated file must be a "
+                              "dictionary.")
+
+    if not result_dict == expected_dict:
+        assert_message.append("The expected dictionary must be equal to the "
+                              "one present in the generated file.\n"
+                              "Expected: {}\n"
+                              "Result: {}". format(
+            json.dumps(expected_dict),
+            json.dumps(result_dict)
+        ))
+
+    # remove the .report.json file
+    os.remove(".report.json")
+
+    assert not assert_message, "Errors occurred:\n{}".format(
+        "\n".join(assert_message)
+    )
+

flowcraft/tests/template_tests/test_pATLAS_consensus_json.py

@@ -1,5 +1,4 @@
 import os
-import re
 import json
 import flowcraft.templates.pATLAS_consensus_json as pATLAS_consensus_json
 
@@ -103,6 +102,10 @@ def test_generated_dict(tmpdir):
             [str(x + 1) for x, el in enumerate(list_of_checks) if not el]
         )))
 
+    # remove the .report.json file
+    os.remove(".report.json")
+    os.remove("consensus_file.json")
+
     assert not assert_message, "Errors occurred:\n{}".format(
         "\n".join(assert_message)
     )