rosalind-solutions/python/ORF.py

#!/usr/bin/python

# Solution to the ORF rosalind problem - 'Open Reading Frames'
# Author: Peter Vlasveld

# 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 = []

    # 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 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
f = open("rosalind_orf.txt")
content = f.readlines()
f.close()

DNAStr = ""
# construct full DNA sequence
for i in range(1, len(content)):
    DNAStr += content[i]

# remove whitespace
noWhiteDNA = "".join(DNAStr.split())

# convert DNA to RNA
RNA = noWhiteDNA.replace("T", "U")

# get DNA compliment and convert that to RNA as well
revCompRNA = DNACompliment(noWhiteDNA).replace("T", "U")

# get orfs for both sequences
protList = orfGen(RNA)
protList.extend(orfGen(revCompRNA))

# get rid of duplicates
finalList = list(set(protList))

# print the list
for i in finalList:
    print(i)