From 222e3ee4473c45b94eaf07fff0e59a4dfa772420 Mon Sep 17 00:00:00 2001
From: Fizzizist <git@fizzizist.33mail.com>
Date: Tue, 18 Feb 2025 21:08:41 -0500
Subject: [PATCH] update ORF to python 3
---
python/ORF.py | 198 +++++++++++++++++++++++++++++++-------------------
1 file changed, 122 insertions(+), 76 deletions(-)
diff --git a/python/ORF.py b/python/ORF.py
index 3653328..a203782 100644
--- a/python/ORF.py
+++ b/python/ORF.py
@@ -1,102 +1,148 @@
#!/usr/bin/python
-#Solution to the ORF rosalind problem - 'Open Reading Frames'
-#Author: Peter Vlasveld
+# Solution to the ORF rosalind problem - 'Open Reading Frames'
+# Author: Peter Vlasveld
-#function to generate the orfs
+# function to generate the orfs
def orfGen(stri):
- #dictionary for translation
- translate = {
- "AAA":'K', "AAG":'K',
- "GAA":'E', "GAG":'E',
- "AAC":'N', "AAU":'N',
- "GAC":'D', "GAU":'D',
- "ACA":'T', "ACC":'T', "ACG":'T', "ACU":'T',
- "GCA":"A", "GCC":"A", "GCG":"A", "GCU":"A",
- "GGA":"G", "GGC":"G", "GGG":"G", "GGU":"G",
- "GUA":"V", "GUC":"V", "GUG":"V", "GUU":"V",
- "AUG":"M",
- "UAA":"*", "UAG":"*", "UGA":"*",
- "AUC":"I", "AUU":"I", "AUA":"I",
- "UAC":"Y", "UAU":"Y",
- "CAA":"Q", "CAG":"Q",
- "AGC":"S", "AGU":"S", "UCA":"S", "UCC":"S", "UCG":"S", "UCU":"S",
- "CAC":"H", "CAU":"H",
- "UGC":"C", "UGU":"C",
- "CCA":"P", "CCC":"P", "CCG":"P", "CCU":"P",
- "UGG":"W",
- "AGA":"R", "AGG":"R", "CGA":"R", "CGC":"R", "CGG":"R", "CGU":"R",
- "UUA":"L", "UUG":"L", "CUA":"L", "CUC":"L", "CUG":"L", "CUU":"L",
- "UUC":"F", "UUU":"F"
- }
-
- #list to contain protein sequences
- proteins = []
+ # dictionary for translation
+ translate = {
+ "AAA": "K",
+ "AAG": "K",
+ "GAA": "E",
+ "GAG": "E",
+ "AAC": "N",
+ "AAU": "N",
+ "GAC": "D",
+ "GAU": "D",
+ "ACA": "T",
+ "ACC": "T",
+ "ACG": "T",
+ "ACU": "T",
+ "GCA": "A",
+ "GCC": "A",
+ "GCG": "A",
+ "GCU": "A",
+ "GGA": "G",
+ "GGC": "G",
+ "GGG": "G",
+ "GGU": "G",
+ "GUA": "V",
+ "GUC": "V",
+ "GUG": "V",
+ "GUU": "V",
+ "AUG": "M",
+ "UAA": "*",
+ "UAG": "*",
+ "UGA": "*",
+ "AUC": "I",
+ "AUU": "I",
+ "AUA": "I",
+ "UAC": "Y",
+ "UAU": "Y",
+ "CAA": "Q",
+ "CAG": "Q",
+ "AGC": "S",
+ "AGU": "S",
+ "UCA": "S",
+ "UCC": "S",
+ "UCG": "S",
+ "UCU": "S",
+ "CAC": "H",
+ "CAU": "H",
+ "UGC": "C",
+ "UGU": "C",
+ "CCA": "P",
+ "CCC": "P",
+ "CCG": "P",
+ "CCU": "P",
+ "UGG": "W",
+ "AGA": "R",
+ "AGG": "R",
+ "CGA": "R",
+ "CGC": "R",
+ "CGG": "R",
+ "CGU": "R",
+ "UUA": "L",
+ "UUG": "L",
+ "CUA": "L",
+ "CUC": "L",
+ "CUG": "L",
+ "CUU": "L",
+ "UUC": "F",
+ "UUU": "F",
+ }
- #loop that runs through the sequences from each amino acid in the sequence
- for i in xrange(0, len(stri)-2):
- tempStr = ""
- tempBool = False
- j = i
- #find an orf and break when it is finished
- while j < len(stri)-2:
- if translate[stri[j:j+3]] == "*":
- tempBool = False
- if translate[stri[j:j+3]] == "M":
- tempBool = True
- if tempBool:
- tempStr += translate[stri[j:j+3]]
- else:
- break
- j += 3
- #add the orf to proteins only if it ends with a stop codon
- if tempStr != "" and tempBool == False:
- proteins.extend([tempStr])
- #return the protein list
- return proteins
+ # list to contain protein sequences
+ proteins = []
-#function to return the DNA compliment
+ # loop that runs through the sequences from each amino acid in the sequence
+ for i in range(0, len(stri) - 2):
+ tempStr = ""
+ tempBool = False
+ j = i
+ # find an orf and break when it is finished
+ while j < len(stri) - 2:
+ if translate[stri[j: j + 3]] == "*":
+ tempBool = False
+ if translate[stri[j: j + 3]] == "M":
+ tempBool = True
+ if tempBool:
+ tempStr += translate[stri[j: j + 3]]
+ else:
+ break
+ j += 3
+ # add the orf to proteins only if it ends with a stop codon
+ if tempStr != "" and tempBool is False:
+ proteins.extend([tempStr])
+ # return the protein list
+ return proteins
+
+
+# function to return the DNA compliment
def DNACompliment(stri):
- rev = stri[::-1]
- revList = list(rev)
- for i in xrange(0, len(revList)):
- if revList[i] == "A":
- revList[i] = "T"
- elif revList[i] == "T":
- revList[i] = "A"
- elif revList[i] == "G":
- revList[i] = "C"
- elif revList[i] == "C":
- revList[i] = "G"
- revCompStr = "".join(revList)
- return revCompStr
+ rev = stri[::-1]
+ revList = list(rev)
+ for i in range(0, len(revList)):
+ if revList[i] == "A":
+ revList[i] = "T"
+ elif revList[i] == "T":
+ revList[i] = "A"
+ elif revList[i] == "G":
+ revList[i] = "C"
+ elif revList[i] == "C":
+ revList[i] = "G"
+ revCompStr = "".join(revList)
+ return revCompStr
-#get file content
+
+# get file content
f = open("rosalind_orf.txt")
content = f.readlines()
f.close()
DNAStr = ""
-#construct full DNA sequence
-for i in xrange(1, len(content)):
- DNAStr += content[i]
+# construct full DNA sequence
+for i in range(1, len(content)):
+ DNAStr += content[i]
-#remove whitespace
+# remove whitespace
noWhiteDNA = "".join(DNAStr.split())
-#convert DNA to RNA
+# convert DNA to RNA
RNA = noWhiteDNA.replace("T", "U")
-#get DNA compliment and convert that to RNA as well
+# get DNA compliment and convert that to RNA as well
revCompRNA = DNACompliment(noWhiteDNA).replace("T", "U")
-#get orfs for both sequences
+# get orfs for both sequences
protList = orfGen(RNA)
protList.extend(orfGen(revCompRNA))
-#get rid of duplicates
+# get rid of duplicates
finalList = list(set(protList))
-#print the list
+# print the list
for i in finalList:
- print(i)
\ No newline at end of file
+ print(i)
+