Cleaned and finished tests

term_frag_sel/cli.py

@@ -18,6 +18,9 @@ def main(args: argparse.Namespace):
     Args:
         args (parser): list of arguments from CLI.
     """
+    if not isinstance(args, argparse.Namespace):
+        raise TypeError("Input should be argparse.Namespace")
+
     # Create or wipe output file
     with open(args.output, "w", encoding="utf-8") as _:
         pass

tests/test_cli.py

@@ -3,13 +3,29 @@ import pytest
 import pandas as pd
 # from Bio import SeqIO
 
-from term_frag_sel.cli import file_validation  # type: ignore
+from term_frag_sel.cli import file_validation, main  # type: ignore
 
 FASTA_FILE = "tests/test_files/test.fasta"
 CSV_FILE = "tests/test_files/test.csv"
+TAB_FILE = "tests/test_files/test_tab.csv"
+
+_, csv_counts = file_validation(FASTA_FILE, CSV_FILE, ",")
+_, tab_counts = file_validation(FASTA_FILE, TAB_FILE, "\t")
 
 def test_file():
     """Test file_validation function."""
     assert isinstance(file_validation(FASTA_FILE, CSV_FILE, ","), tuple[dict, pd.DataFrame])
+    assert isinstance(file_validation(FASTA_FILE, TAB_FILE, "\t"), tuple[dict, pd.DataFrame])
+    assert csv_counts.equals(tab_counts)
+
     with pytest.raises(FileNotFoundError):
-        file_validation("", "", ",")
+        file_validation(FASTA_FILE, "", ",")
+    with pytest.raises(FileNotFoundError):
+        file_validation("", CSV_FILE, ",")
+    with pytest.raises(ValueError):
+        file_validation(CSV_FILE, CSV_FILE, ",")
+
+def test_main():
+    """Test main() function."""
+    with pytest.raises(TypeError):
+        main("")

tests/test_files/test.csv

-,seqID,count
-0,1,120
+0,1,86
 1,2,60
-2,3,76
-3,4,141
-4,5,107
-5,6,59
-6,7,121
-7,8,72
-8,9,114
-9,10,126
-10,11,77
-11,12,130
-12,13,146
-13,14,69
-14,15,62
-15,16,93
-16,17,103
-17,18,150
-18,19,140
-19,20,56
-20,21,103
-21,22,115
-22,23,113
-23,24,53
-24,25,95
-25,26,112
-26,27,102
-27,28,53
-28,29,139
-29,30,143
-30,31,150
-31,32,126
-32,33,50
-33,34,94
-34,35,81
-35,36,116
-36,37,51
-37,38,110
-38,39,98
-39,40,60
-40,41,57
-41,42,73
-42,43,143
-43,44,116
-44,45,98
-45,46,139
-46,47,89
-47,48,63
-48,49,68
-49,50,84
+2,3,56
+3,4,129
+4,5,138
+5,6,89
+6,7,107
+7,8,52
+8,9,81
+9,10,83
+10,11,139
+11,12,66
+12,13,105
+13,14,59
+14,15,93
+15,16,134
+16,17,50
+17,18,64
+18,19,110
+19,20,119
+20,21,54
+21,22,105
+22,23,124
+23,24,109
+24,25,125
+25,26,98
+26,27,88
+27,28,55
+28,29,70
+29,30,147
+30,31,123
+31,32,66
+32,33,54
+33,34,60
+34,35,79
+35,36,121
+36,37,69
+37,38,63
+38,39,121
+39,40,149
+40,41,52
+41,42,100
+42,43,54
+43,44,81
+44,45,150
+45,46,116
+46,47,128
+47,48,73
+48,49,144
+49,50,89

tests/test_files/test_tab.csv

+0	1	86
+1	2	102
+2	3	81
+3	4	91
+4	5	121
+5	6	82
+6	7	103
+7	8	125
+8	9	135
+9	10	133
+10	11	110
+11	12	108
+12	13	89
+13	14	125
+14	15	76
+15	16	85
+16	17	130
+17	18	63
+18	19	137
+19	20	55
+20	21	148
+21	22	101
+22	23	145
+23	24	99
+24	25	50
+25	26	101
+26	27	134
+27	28	60
+28	29	107
+29	30	134
+30	31	76
+31	32	118
+32	33	99
+33	34	64
+34	35	97
+35	36	118
+36	37	131
+37	38	142
+38	39	119
+39	40	50
+40	41	90
+41	42	65
+42	43	140
+43	44	145
+44	45	84
+45	46	144
+46	47	103
+47	48	96
+48	49	50
+49	50	112