From b4db52bf0b79d3224a8562639f3eff2132aad94e Mon Sep 17 00:00:00 2001
From: Nico Maillet <nicolas.maillet@pasteur.fr>
Date: Wed, 6 Dec 2023 12:49:05 +0100
Subject: [PATCH] CM-TP regex
---
8-Regex/tp8.py | 202 +++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 202 insertions(+)
create mode 100644 8-Regex/tp8.py
diff --git a/8-Regex/tp8.py b/8-Regex/tp8.py
new file mode 100644
index 0000000..05bf568
--- /dev/null
+++ b/8-Regex/tp8.py
@@ -0,0 +1,202 @@
+""" TP8 where we play with regex """
+# Import regex
+import re
+
+def read_file_old(file_in):
+ """ Read the file and return its content (array of tuples) """
+ content = []
+ # Open the file
+ with open(file_in) as file:
+ # The header of the current sequence
+ header = False
+ # For each line
+ for line in file:
+ # If the header is False, this is a new sequence
+ if not header:
+ # Backup the header
+ header = line.strip()
+ # Header is not False, we are in a sequence
+ else:
+ # Create a tuple (not modifiable) with the header and the sequence
+ tmp = (header, line.strip())
+ # Add it to the returned list
+ content.append(tmp)
+ # Put header to False
+ header = False
+ # Return the content of the file
+ return content
+
+def read_file(file_in):
+ """ Read the file and return its content (array of tuples) """
+ content = []
+ # Open the file
+ with open(file_in) as file:
+ # For each line
+ for line in file:
+ # Get the header
+ header = line.strip()
+ # Get the sequence
+ seq = file.readline().strip()
+ # Create a tuple (not modifiable) with the header and the sequence
+ tmp = (header, seq)
+ # Add it to the returned list
+ content.append(tmp)
+ # Return the content of the file
+ return content
+
+def main():
+ """ The main of TP8 that launch regex """
+ # The file to process
+ file_in = "sequences.fasta"
+ # Get its content
+ content = read_file(file_in)
+
+ # Get all occurrences of 'GTA'
+ res = []
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only
+ res += re.findall("GTA", i[1])
+ print("There is {} 'GTA' in the file".format(len(res)))
+
+
+ # Is there a sequence containing 'GTA(some characters)CT'?
+ # Not founded yet
+ founded = False
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only
+ if re.search("GTA.*CT", i[1]):
+ # We found one!
+ founded = True
+ # Stop the process
+ break
+ # Did we find it?
+ if founded:
+ print("\nThere is!")
+ else:
+ print("\nThere is not :(")
+
+
+ # Is there a sequence containing 'GTA(max 3 characters)CTAAT'?
+ # Not founded yet
+ founded = False
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only
+ if re.search("GTA.{0,3}CTAAT", i[1]):
+ # We found one!
+ founded = True
+ # Stop the process
+ break
+ # Did we find it?
+ if founded:
+ print("\nThere is!")
+ else:
+ print("\nThere is not :(")
+
+ # Is there a sequence containing 'GG T or C GG'?
+ # Not founded yet
+ founded = False
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only
+ if re.search("GG[TC]GG", i[1]):
+ # We found one!
+ founded = True
+ # Stop the process
+ break
+ # Did we find it?
+ if founded:
+ print("\nThere is!")
+ else:
+ print("\nThere is not :(")
+
+
+ # Is there a sequence finishing by 'ATATAT'?
+ # Not founded yet
+ founded = False
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only
+ if re.search("ATATAT$", i[1]):
+ # We found one!
+ founded = True
+ # Stop the process
+ break
+ # Did we find it?
+ if founded:
+ print("\nThere is!")
+ else:
+ print("\nThere is not :(")
+
+ # Is there a sequence starting or finishing by 'ATATAT'?
+ # Not founded yet
+ founded = False
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only
+ if re.search("^ATATAT|ATATAT$", i[1]):
+ # We found one!
+ founded = True
+ # Stop the process
+ break
+ # Did we find it?
+ if founded:
+ print("\nThere is!")
+ else:
+ print("\nThere is not :(")
+
+
+ # Get headers containing mmus or musm
+ res = []
+ # For each headers/sequences
+ for i in content:
+ # Regex on the header only, starting and ending by anything and containing something that is not A, C, G or T
+ if re.search("mmus|musm", i[0]):
+ res.append(i[0])
+ print("\nMus Musculus headers: {}".format(res))
+
+
+ # Count headers containing / or \
+ res = []
+ # For each headers/sequences
+ for i in content:
+ # Regex on the header only, you need to escape the escape... \\ is a literal \ IN THE REGEX, so you need to escape it. Python only.
+ if re.search("\\\\|\\/", i[0]):
+ res.append(i[0])
+ print("\nThere is {} headers containing (back)slash".format(len(res)))
+
+
+ # Find the sequence containing not only DNA
+ res = []
+ # For each headers/sequences
+ for i in content:
+ # Regex on the sequence only, starting and ending by anything and containing something that is not A, C, G or T
+ res += re.findall("^.*[^ACGT].*$", i[1])
+ print("\nBuggy sequence: {}".format(res))
+
+
+ # Get the part of headers containing an id composed of 3 letters, 1 digit, 1 alphanumeric character, 1 character and surrounded by spaces
+ res = []
+ # For each headers/sequences
+ for i in content:
+ # Regex on the header only
+ res += re.findall("\ [A-Za-z]{3}\d{1}\w{1}.{1}\ ", i[0])
+ print("\nSpecial header sequences: {}".format(res))
+
+
+ # Get the sequence where the header contains an email address.
+ res = ""
+ # For each headers/sequences
+ for i in content:
+ # Regex on the header only
+ if re.search("[^\W][a-zA-Z0-9_]+(\.[a-zA-Z0-9_]+)*\@[a-zA-Z0-9_]+(\.[a-zA-Z0-9_]+)*\.[a-zA-Z]{2,4}", i[0]):
+ res = i[1]
+ print("\nSequence with email on the header: {}".format(res))
+
+# Launch the main
+main()
+# Exit without error
+exit(0)
+# Always put one extra return line
--
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