From 0a2b1e6e498e06412044ba366b7f467fcf867005 Mon Sep 17 00:00:00 2001
From: Madan Mukundan <madan.mukundan@gmail.com>
Date: Mon, 20 Dec 2021 17:40:53 +0100
Subject: [PATCH] fix: removed GUI and fixed tests
---
src/plot_read_counts.py | 103 +--------------------------------
tests/test_plot_read_counts.py | 29 ++++++----
2 files changed, 19 insertions(+), 113 deletions(-)
diff --git a/src/plot_read_counts.py b/src/plot_read_counts.py
index 20af36a..fa489c1 100644
--- a/src/plot_read_counts.py
+++ b/src/plot_read_counts.py
@@ -1,9 +1,7 @@
"""Plots read counts of gene expression data."""
import logging
-import sys
from pathlib import Path
-from tkinter import Tk, ttk, filedialog, StringVar
from typing import Union
import pandas
@@ -15,7 +13,7 @@ import matplotlib.pyplot as plt
def plot_read_counts(
dir_path: Union[str, Path] = None,
gene_id: str = None
-) -> None:
+) -> bool:
"""Plots histogram of gene ID and read counts from .csv files.
This function reads .csv files from a directory formatted
@@ -118,101 +116,4 @@ def plot_read_counts(
plt.bar(range(len(gene_count_dict)), counts, tick_label=file_names)
plt.title('Counts for %s' % (gene_id))
plt.show()
-
-
-def prc_dialog() -> None:
- """Creates a GUI to select directory and enter gene."""
- # Create dialog window
- dialog = Tk()
- dialog.title("Plot Gene Read Counts")
- dialog.resizable(False, False)
- dialog.geometry("380x210+20+20")
- dialog.configure(background="black")
-
- # Create and attach welcome message to GUI
- wlcom_text = "Welcome to Plot Read Counts "
- wlcom_msg = ttk.Label(dialog,
- text=wlcom_text,
- font=("Helvetica", 12, "bold"),
- foreground="white",
- background="black",
- padding=5)
- wlcom_msg.grid(column=1, row=0, columnspan=2, pady=5)
-
- # Create and attach instruction message to GUI
- inst_msg = ttk.Label(dialog,
- text="Select a directory of .csv files and a gene ID to plot",
- font=("Helvetica", 12),
- foreground="white",
- background="black",
- padding=5)
- inst_msg.grid(column=1, row=1, columnspan=2, padx=10, pady=5)
-
- # Create and attach directory selection elements
- # Either globals are needed or all functions
- # need to be encapsulated
- global dir_str_var
- dir_str_var = StringVar()
- dir_lbl = ttk.Label(dialog,
- textvariable=dir_str_var,
- font=("Courier", 10, "bold"),
- background="black",
- foreground="green")
- dir_lbl.grid(column=1, row=4, padx=5, pady=1, sticky="e")
- dir_btn = ttk.Button(dialog, text="Select Directory",
- command=lambda: get_dir())
- dir_btn.grid(column=1, row=6, padx=5, pady=1)
-
- # Create and attach gene selection elements
- global gene_lbl
- gene_lbl = StringVar()
- gene_entry = ttk.Entry(dialog)
- gene_entry.grid(column=2, row=5, pady=1)
- gene_entry_lbl = ttk.Label(anchor="center",
- textvariable=gene_lbl,
- font=("Courier", 10, "bold"),
- background="black",
- foreground="green")
- gene_entry_lbl.grid(column=2, row=4, pady=1)
- gene_entry_btn = ttk.Button(dialog,
- text="Confirm Gene (Case Sensitive)",
- command=lambda: get_gene_id(gene_entry))
- gene_entry_btn.grid(column=2, row=6, padx=2, pady=2)
-
- # Create and attach confirm and close element
- kill_btn = ttk.Button(dialog, text="Exit and Plot",
- command=lambda: dialog.destroy())
- kill_btn.grid(column=1, row=8, columnspan=2, padx=5, pady=15)
-
- dialog.mainloop()
-
- if 'gui_path' in globals() and 'gui_gene_id' in globals():
- plot_read_counts(gui_path, gui_gene_id)
- else:
- sys.exit()
-
-
-def get_dir() -> Path:
- """Support function to retrieve dir from GUI."""
- global gui_path
- gui_path = Path(filedialog.askdirectory(
- title='Please select the directory containing \
- gene reads'))
- short_dir = ("%s/.../%s/" % (gui_path.drive, gui_path.name))
- dir_str_var.set(short_dir)
-
-
-def get_gene_id(gene_entry: StringVar) -> str:
- """Support function to retrieve gene ID from GUI."""
- global gui_gene_id
- gui_gene_id = gene_entry.get()
- gene_lbl.set(gene_entry.get())
-
-
-def main() -> None:
- """Main opens GUI for dir and gene ID selection."""
- prc_dialog()
-
-
-if __name__ == '__main__':
- main()
+ return True
diff --git a/tests/test_plot_read_counts.py b/tests/test_plot_read_counts.py
index add8572..293b450 100644
--- a/tests/test_plot_read_counts.py
+++ b/tests/test_plot_read_counts.py
@@ -1,10 +1,12 @@
-"Test for plot_read_counts module"
+"""Test for plot_read_counts module."""
import pytest
from pathlib import Path
from src.plot_read_counts import plot_read_counts
+
class TestPlotReadCounts ():
+ """Tests for plot_read_counts."""
@pytest.mark.parametrize(
"dir_path, gene_id, expected",
@@ -13,20 +15,23 @@ class TestPlotReadCounts ():
('Path.home()', 5, TypeError),
(None, None, ValueError),
('Path.home()', 'GENE1', AttributeError),
+ (Path(str(Path.parent())+"/tests/resources/"), 'GENE25', ValueError),
+
]
)
def test_invalid_input(self, dir_path, gene_id, expected):
+ """Tests invalid input."""
with pytest.raises(expected):
plot_read_counts(dir_path, gene_id)
- def validate_input():
-
- pass
-
- #plot_dir = PurePath('H:/My Drive/PhD/PLS/PLS scRNAseq Repo/scrna-seq-simulation/tests/resources')
- #plot_dir = 'H:/My Drive/PhD/PLS scRNAseq Repo/scrna-seq-simulation/'
- # plot_dir = PurePath(filedialog.askdirectory(title='Please select the directory containing \
- # gene reads'))
- # gene_of_interest = input('\nPlease type a gene ID to sample: ').upper()
- #gene_of_interest = 'GENE1'
-
\ No newline at end of file
+ @pytest.mark.parametrize(
+ "dir_path, gene_id, expected",
+ [
+ (Path(str(Path.parent())+"/tests/resources/"), 'GENE1', True),
+ (Path(str(Path.parent())+"/tests/resources/"), 'GENE1', True),
+ (Path(str(Path.parent())+"/tests/resources/"), 'GENE7', True),
+ ]
+ )
+ def validate_input(self, dir_path, gene_id):
+ """Tests valid input with return value boolean."""
+ assert plot_read_counts(dir_path, gene_id) is True
--
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