From 3accb9fd46b00161db98682267e859aa1152da19 Mon Sep 17 00:00:00 2001
From: Alex <alexandra.bekoy@gmail.com>
Date: Tue, 18 Jun 2024 19:40:28 +0300
Subject: [PATCH] Create GC calculator with a single sequence as input

---
 gc_calc.py | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 gc_calc.py

diff --git a/gc_calc.py b/gc_calc.py
new file mode 100644
index 0000000..800ecc3
--- /dev/null
+++ b/gc_calc.py
@@ -0,0 +1,47 @@
+# ===================================================== DEPENDENCIES =============================================================
+from Bio.Seq import Seq
+from Bio.SeqUtils import gc_fraction
+from matplotlib import pyplot as plt
+plt.style.use('ggplot')
+
+
+# ===================================================== FUNCTIONS =================================================================
+def calculate_gc(sequence):
+    print(gc_fraction(sequence))
+
+def calculate_window_gc(sequence, window, step):
+    gc_parts = []
+    window_count = 0
+    window_list = []
+    for i in range(0, len(sequence) - window +1, step):
+        gc_part = gc_fraction(sequence[i: i+window])
+        gc_parts.append(gc_part)
+        window_count +=1
+        window_list.append(f"Window {window_count}")
+    return window_list, gc_parts
+
+def create_window_plot():
+    x_axis, y_axis = calculate_window_gc(sequence, window_size, step_size)
+    plt.plot(x_axis, y_axis, color = "k", linestyle = "--", marker = "o")
+    plt.title("Sliding Window GC Content Calculation")
+    plt.xlabel("Sequence windows")
+    plt.ylabel("GC content")
+    plt.tight_layout()
+    plt.show()
+
+# ====================================================== LOGIC =====================================================================
+sequence = Seq(input('Please enter a DNA/RNA sequence. '))
+
+choice = input("Would you like to perform a sliding window GC content calculation? ")
+if choice.lower()[0] == 'n':
+    calculate_gc(sequence)
+else:
+    window_size = int(input("Please enter window size. "))
+    step_size = int(input("Please enter step size. "))
+    create_window_plot()
+
+
+
+
+
+