added test for deletions

lusSTR/tests/data/test_indels.csv

@@ -0,0 +1,4 @@
+Locus,Total_Reads,Sequence,SampleID,Project,Analysis
+PentaD,44,GAGCCATGATCACACCACTACACTCCAGCCTAGGTGACAGAGCAAGACACCATCTCAAGAAAGAAAAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAAACGAAGGGGAAAAAAAGAGAATCATAAACATAAATGTAAAATTTCTCAAAAAAATCGTTA,A01,test,test
+vWA,36,GATAGATGGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGATAGATCAATCCAAGTCACATACTGATTATTCTTATCATCCACTAGGGCTTTCACATCTCAGCCAAGTCAACTTGGATCCTCTAGACCTGTTTCTTCTTCTGGAA,A01,test,test
+D7S820,109,AGAATTGCACCACATATTGGTAATTAAATGTTTACTATAGACTATTTAGTGAGATAAAAAAAACTATCAATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCGTTAGTTCGTTCTAAACTATGACAAGTGTTCTATCATACCCTTTATATATATTAACCTTAAAATAACTC,A01,test,test

lusSTR/tests/data/test_indels.txt

@@ -0,0 +1,4 @@
+SampleID	Project	Analysis	Locus	UAS_Output_Sequence	Forward_Strand_Sequence	UAS_Output_Bracketed_Notation	Forward_Strand_Bracketed_Notation	CE_Allele	LUS	LUS_Plus	Reads
+A01	test	test	VWA	TCTATCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCCATCTA	TAGATGGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGATAGA	TCTA [TCTG]4 [TCTA]8 TCCA TCTA	TAGA TGGA [TAGA]8 [CAGA]4 TAGA	13	13_8	13_8_4_1	36
+A01	test	test	PENTA D	AAAAGAAAGAAAAGAAAAGAAAAGAAAAGA	AAAAGAAAGAAAAGAAAAGAAAAGAAAAGA	AAAAG [AAAGA]5	AAAAG [AAAGA]5	5	5_5	5_5	44
+A01	test	test	D7S820	GATAGATAGATAGATAGATAGATAGATAGATAGACAGATTGATAGTTT	AAACTATCAATCTGTCTATCTATCTATCTATCTATCTATCTATCTATC	[GATA]8 GACA GATT GATA GTTT	AAAC TATC AATC TGTC [TATC]8	8	8_8	8_8_1_0	109

lusSTR/tests/test_suite.py

@@ -357,3 +357,26 @@ def test_genemarker(tmp_path):
         print(exp_output)
         obs_output = str(tmp_path / f"genemarker_test{ext}")
         assert filecmp.cmp(exp_output, obs_output) is True
+
+
+def test_deletions(tmp_path):
+    input = data_file("test_indels.csv")
+    exp_output = data_file("test_indels.txt")
+    obs_output = str(tmp_path / "test_indels.txt")
+    arglist = [
+        "config",
+        "-w",
+        str(tmp_path),
+        "--out",
+        "test_indels",
+        "--input",
+        str(input),
+        "--analysis-software",
+        "genemarker",
+        "--powerseq",
+    ]
+    lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
+    shutil.copyfile(input, os.path.join(str(tmp_path), "test_indels.csv"))
+    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