From 6993b862776f037d15802161ad97a3f764985441 Mon Sep 17 00:00:00 2001
From: "hugo.madgeleon" <hugo.madgeleon@stud.unibas.ch>
Date: Sun, 11 Dec 2022 21:02:52 +0100
Subject: [PATCH] Cleaned and finished tests
---
term_frag_sel/cli.py | 3 ++
tests/test_cli.py | 20 ++++++-
tests/test_files/test.csv | 99 +++++++++++++++++------------------
tests/test_files/test_tab.csv | 50 ++++++++++++++++++
4 files changed, 120 insertions(+), 52 deletions(-)
create mode 100644 tests/test_files/test_tab.csv
diff --git a/term_frag_sel/cli.py b/term_frag_sel/cli.py
index 843d17b..2ca6cf2 100644
--- a/term_frag_sel/cli.py
+++ b/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
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 7865c82..3b4b121 100644
--- a/tests/test_cli.py
+++ b/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("")
diff --git a/tests/test_files/test.csv b/tests/test_files/test.csv
index 011ccf1..82dfa39 100644
--- a/tests/test_files/test.csv
+++ b/tests/test_files/test.csv
@@ -1,51 +1,50 @@
-,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
diff --git a/tests/test_files/test_tab.csv b/tests/test_files/test_tab.csv
new file mode 100644
index 0000000..8b7c982
--- /dev/null
+++ b/tests/test_files/test_tab.csv
@@ -0,0 +1,50 @@
+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
--
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