Creating log files (#76)

bioforensics · Jul 10, 2024 · aac73a4 · aac73a4
1 parent 3c2b19b
commit aac73a4
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Showing 5 changed files with 106 additions and 19 deletions.
diff --git a/lusSTR/tests/test_filters.py b/lusSTR/tests/test_filters.py
@@ -183,7 +183,7 @@ def test_EFMoutput_format(outputdir, datatype, software, tmp_path):
         "--str-type",
         datatype,
         "--input",
-        "WD",
+        str(inputfile),
     ]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "test_output.csv"))
@@ -208,7 +208,7 @@ def test_STRmixoutput_format(outputdir, datatype, tmp_path):
         "-w",
         str_path,
         "--input",
-        "WD",
+        str(inputfile),
         "-o",
         "STRmix_Files",
         "--str-type",
@@ -230,7 +230,16 @@ def test_STRmixoutput_customranges(tmp_path):
     exp_info_out = data_file("NGS_stutter_test/custom/test_stutter_sequence_info.csv")
     obs_out = str(tmp_path / f"WD/test_stutter/Sample1_evidence_ngs.csv")
     obs_info_out = str(tmp_path / f"WD/test_stutter/test_stutter_sequence_info.csv")
-    arglist = ["config", "-w", str_path, "--input", "WD", "-o", "test_stutter", "--custom"]
+    arglist = [
+        "config",
+        "-w",
+        str_path,
+        "--input",
+        str(inputfile),
+        "-o",
+        "test_stutter",
+        "--custom",
+    ]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "test_stutter.csv"))
     shutil.copyfile(inputfile, os.path.join(str_path, "test_stutter.txt"))
@@ -247,7 +256,7 @@ def test_nofilters(tmp_path):
     inputfile = data_file("test_stutter.txt")
     exp_out = data_file("NGS_stutter_test/Sample1_nofilter.csv")
     obs_out = str(tmp_path / "WD/lusstr_output/Sample1_evidence_ngs.csv")
-    arglist = ["config", "-w", str_path, "--input", "WD", "--nofilter"]
+    arglist = ["config", "-w", str_path, "--input", str(inputfile), "--nofilter"]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "lusstr_output.csv"))
     shutil.copyfile(inputfile, os.path.join(str_path, "lusstr_output.txt"))
@@ -261,7 +270,7 @@ def test_flags(tmp_path):
     inputfile = data_file("test_stutter.txt")
     exp_out = data_file("RU_stutter_test/Flagged_Loci.csv")
     obs_out = str(tmp_path / "WD/lusstr_output/lusstr_output_Flagged_Loci.csv")
-    arglist = ["config", "-w", str_path, "--input", "WD"]
+    arglist = ["config", "-w", str_path, "--input", str(inputfile)]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "lusstr_output.csv"))
     shutil.copyfile(inputfile, os.path.join(str_path, "lusstr_output.txt"))
@@ -288,7 +297,7 @@ def test_efm_reference(outputdir, datatype, software, tmp_path):
         "-w",
         str_path,
         "--input",
-        "WD",
+        str(inputfile),
         "--software",
         software,
         "--reference",
@@ -316,7 +325,7 @@ def test_strmix_reference(outputdir, datatype, tmp_path):
         "-w",
         str_path,
         "--input",
-        "WD",
+        str(inputfile),
         "-o",
         "STRmix_Files",
         "--reference",
@@ -336,7 +345,7 @@ def test_D7(tmp_path):
     inputfile = data_file("test_D7.txt")
     exp_out = data_file("D7_microvariant_flagged.csv")
     obs_out = str(tmp_path / "WD/test/test_Flagged_Loci.csv")
-    arglist = ["config", "-w", str_path, "--input", "WD", "-o", "test"]
+    arglist = ["config", "-w", str_path, "--input", str(inputfile), "-o", "test"]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "test.csv"))
     shutil.copyfile(inputfile, os.path.join(str_path, "test.txt"))
@@ -392,7 +401,7 @@ def test_forward_strand_orientation(tmp_path):
         "-w",
         str_path,
         "--input",
-        "WD",
+        str(inputfile),
         "-o",
         "STRmix_Files",
         "--strand",
@@ -416,7 +425,7 @@ def test_lusplus_sequence_info(tmp_path):
         "-w",
         str_path,
         "--input",
-        "WD",
+        str(inputfile),
         "-o",
         "LUSPlus",
         "--strand",

diff --git a/lusSTR/tests/test_snps.py b/lusSTR/tests/test_snps.py
@@ -260,3 +260,27 @@ def test_uas_version5(tmp_path):
     all_arglist = ["snps", "all", "-w", str(tmp_path)]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(all_arglist))
     assert filecmp.cmp(exp_out, obs_out) is True
+
+
+def test_snp_logs(tmp_path):
+    inputdb = data_file("snps")
+    arglist = [
+        "config",
+        "-w",
+        str(tmp_path),
+        "-o",
+        "sr",
+        "--input",
+        str(inputdb),
+        "--snps",
+        "--analysis-software",
+        "straitrazor",
+    ]
+    lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
+    format_arglist = ["snps", "format", "-w", str(tmp_path)]
+    lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(format_arglist))
+    for dir in os.listdir(str(tmp_path / "logs/")):
+        assert os.path.exists(str(tmp_path / f"logs/{dir}/snp_config.yaml"))
+        assert os.path.exists(
+            str(tmp_path / f"logs/{dir}/input/Positive Control Sample Details Report 2315.xlsx")
+        )
diff --git a/lusSTR/tests/test_suite.py b/lusSTR/tests/test_suite.py
@@ -64,7 +64,7 @@ def test_convert_full_nocombine(
             "-o",
             infile,
             "--input",
-            "WD",
+            str(inputfile),
         ]
     else:
         arglist = [
@@ -78,7 +78,7 @@ def test_convert_full_nocombine(
             "-o",
             infile,
             "--input",
-            "WD",
+            str(inputfile),
             "--powerseq",
         ]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
@@ -110,7 +110,7 @@ def test_flanks(tmp_path):
         "--analysis-software",
         "straitrazor",
         "--input",
-        "WD",
+        str(inputfile),
     ]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "testflanks.csv"))
@@ -135,7 +135,7 @@ def test_convert_combine(input, exp_length, tmp_path):
         "--analysis-software",
         "straitrazor",
         "--input",
-        "WD",
+        str(inputfile),
     ]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile, os.path.join(str_path, "testflanks.csv"))
@@ -183,7 +183,7 @@ def test_powerseq_flanks(tmp_path):
         "--analysis-software",
         "straitrazor",
         "--input",
-        "WD",
+        str(inputfile),
         "--powerseq",
     ]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
@@ -199,7 +199,7 @@ def test_convert_uas_sexloci(tmp_path):
     inputfile_sex = data_file("testformat_uas_sexloci.csv")
     exp_sex_out = data_file("testformat_uas_sexloci.txt")
     obs_sex_out = str(tmp_path / "WD/testformatuas_sexloci.txt")
-    arglist = ["config", "-w", str_path, "-o", "testformatuas", "--sex", "--input", "WD"]
+    arglist = ["config", "-w", str_path, "-o", "testformatuas", "--sex", "--input", str(inputfile)]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     shutil.copyfile(inputfile_sex, os.path.join(str_path, "testformatuas_sexloci.csv"))
     shutil.copyfile(inputfile, os.path.join(str_path, "testformatuas.csv"))
@@ -242,7 +242,7 @@ def test_convert_sr_sexloci(input, testoutput, flank_output, kit, tmp_path):
             "testformatsr",
             "--sex",
             "--input",
-            "WD",
+            str(inputfile),
             "--analysis-software",
             "straitrazor",
         ]
@@ -255,7 +255,7 @@ def test_convert_sr_sexloci(input, testoutput, flank_output, kit, tmp_path):
             "testformatsr",
             "--sex",
             "--input",
-            "WD",
+            str(inputfile),
             "--analysis-software",
             "straitrazor",
             "--powerseq",
@@ -380,3 +380,17 @@ def test_deletions(tmp_path):
     snakemake_arglist = ["strs", "convert", "-w", str(tmp_path)]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(snakemake_arglist))
     assert filecmp.cmp(exp_output, obs_output) is True
+
+
+def test_log(tmp_path):
+    config = str(tmp_path / "config.yaml")
+    inputfile = data_file("UAS_bulk_input/Positive Control Sample Details Report 2315.xlsx")
+    arglist = ["config", "-w", str(tmp_path), "--input", str(inputfile)]
+    lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
+    snakemake_arglist = ["strs", "format", "-w", str(tmp_path)]
+    lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(snakemake_arglist))
+    for dir in os.listdir(str(tmp_path / "logs/")):
+        assert os.path.exists(str(tmp_path / f"logs/{dir}/config.yaml"))
+        assert os.path.exists(
+            str(tmp_path / f"logs/{dir}/input/Positive Control Sample Details Report 2315.xlsx")
+        )
diff --git a/lusSTR/workflows/snps.smk b/lusSTR/workflows/snps.smk
@@ -1,3 +1,4 @@
+from datetime import datetime
 import lusSTR
 
 
@@ -14,6 +15,18 @@ def format_filename(id, refs):
         return f"{id}_snp_reference"
 
 
+def create_log(log):
+    now = datetime.now()
+    dt = now.strftime("%m%d%Y_%H_%M_%S")
+    shell("mkdir -p logs/{dt}/input/")
+    shell("cp {log} logs/{dt}/strs.log")
+    if os.path.isdir(input_name):
+        shell("cp {input_name}/* logs/{dt}/input/")
+    else:
+        shell("cp '{input_name}' logs/{dt}/input/")
+    shell("cp snp_config.yaml logs/{dt}/")
+
+
 rule all:
     input:
         expand("{name}.txt", name=output_name),
@@ -49,3 +62,10 @@ rule convert:
         thresh=config["thresh"]
     script:
         lusSTR.wrapper("snps_convert")
+
+
+onsuccess:
+    create_log(log)
+
+onerror:
+    create_log(log)
diff --git a/lusSTR/workflows/strs.smk b/lusSTR/workflows/strs.smk
@@ -1,3 +1,4 @@
+from datetime import datetime
 import glob
 import lusSTR
 import openpyxl
@@ -72,6 +73,18 @@ def parse_sample_details(filename):
     return sampleID
 
 
+def create_log(log):
+    now = datetime.now()
+    dt = now.strftime("%m%d%Y_%H_%M_%S")
+    shell("mkdir -p logs/{dt}/input/")
+    shell("cp {log} logs/{dt}/strs.log")
+    if os.path.isdir(input_name):
+        shell("cp {input_name}/* logs/{dt}/input/")
+    else:
+        shell("cp '{input_name}' logs/{dt}/input/")
+    shell("cp config.yaml logs/{dt}/")
+
+
 def get_output():
     if custom:
         outname = expand("{name}_custom_range.txt", name=output_name)
@@ -115,7 +128,7 @@ rule convert:
         kit=config["kit"],
         custom=config["custom_ranges"]
     script:
-        lusSTR.wrapper("convert")
+        lusSTR.wrapper("convert") 
 
 
 rule filter:
@@ -139,4 +152,11 @@ rule filter:
         custom=config["custom_ranges"]
     script:
         lusSTR.wrapper("filter")
+
+
+onsuccess:
+    create_log(log)
+
+onerror:
+    create_log(log)