From 7803c43a86a79a8856bf8a5d7126e9245b4b101c Mon Sep 17 00:00:00 2001
From: schne <leo.schneider@ecl19.ec-lyon.fr>
Date: Tue, 19 Dec 2023 15:54:34 +0100
Subject: [PATCH] trypsine seq cutting routine
---
seq_cutting.py | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/seq_cutting.py b/seq_cutting.py
index e69de29..6e9879b 100644
--- a/seq_cutting.py
+++ b/seq_cutting.py
@@ -0,0 +1,41 @@
+ALPHABET_UNMOD = {
+ "A": 1,
+ "C": 2,
+ "D": 3,
+ "E": 4,
+ "F": 5,
+ "G": 6,
+ "H": 7,
+ "I": 8,
+ "K": 9,
+ "L": 10,
+ "M": 11,
+ "N": 12,
+ "P": 13,
+ "Q": 14,
+ "R": 15,
+ "S": 16,
+ "T": 17,
+ "V": 18,
+ "W": 19,
+ "Y": 20,
+}
+
+
+# trypsin cut after A or L (if not followed by P)
+
+def cut(seq, format):
+ cuts = []
+ l = len(seq)
+ if format == 'alphabetical':
+ for i in range(l):
+ if seq[i] == 'A' or seq[i] == 'L':
+ if i < l - 1 and seq[i + 1] != 'P':
+ cuts.append(i)
+
+ if format == 'numerical':
+ for i in range(l):
+ if seq[i] == 1 or seq[i] == 10:
+ if i < l - 1 and seq[i + 1] != 13:
+ cuts.append(i)
+ return cuts
--
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