update ORF to python 3
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Fizzizist
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python/ORF.py
140
python/ORF.py
@ -1,65 +1,109 @@
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#!/usr/bin/python
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#Solution to the ORF rosalind problem - 'Open Reading Frames'
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#Author: Peter Vlasveld
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# Solution to the ORF rosalind problem - 'Open Reading Frames'
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# Author: Peter Vlasveld
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#function to generate the orfs
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# function to generate the orfs
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def orfGen(stri):
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#dictionary for translation
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# dictionary for translation
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translate = {
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"AAA":'K', "AAG":'K',
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"GAA":'E', "GAG":'E',
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"AAC":'N', "AAU":'N',
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"GAC":'D', "GAU":'D',
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"ACA":'T', "ACC":'T', "ACG":'T', "ACU":'T',
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"GCA":"A", "GCC":"A", "GCG":"A", "GCU":"A",
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"GGA":"G", "GGC":"G", "GGG":"G", "GGU":"G",
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"GUA":"V", "GUC":"V", "GUG":"V", "GUU":"V",
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"AUG":"M",
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"UAA":"*", "UAG":"*", "UGA":"*",
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"AUC":"I", "AUU":"I", "AUA":"I",
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"UAC":"Y", "UAU":"Y",
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"CAA":"Q", "CAG":"Q",
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"AGC":"S", "AGU":"S", "UCA":"S", "UCC":"S", "UCG":"S", "UCU":"S",
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"CAC":"H", "CAU":"H",
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"UGC":"C", "UGU":"C",
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"CCA":"P", "CCC":"P", "CCG":"P", "CCU":"P",
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"UGG":"W",
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"AGA":"R", "AGG":"R", "CGA":"R", "CGC":"R", "CGG":"R", "CGU":"R",
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"UUA":"L", "UUG":"L", "CUA":"L", "CUC":"L", "CUG":"L", "CUU":"L",
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"UUC":"F", "UUU":"F"
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"AAA": "K",
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"AAG": "K",
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"GAA": "E",
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"GAG": "E",
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"AAC": "N",
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"AAU": "N",
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"GAC": "D",
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"GAU": "D",
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"ACA": "T",
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"ACC": "T",
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"ACG": "T",
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"ACU": "T",
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"GCA": "A",
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"GCC": "A",
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"GCG": "A",
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"GCU": "A",
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"GGA": "G",
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"GGC": "G",
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"GGG": "G",
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"GGU": "G",
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"GUA": "V",
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"GUC": "V",
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"GUG": "V",
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"GUU": "V",
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"AUG": "M",
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"UAA": "*",
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"UAG": "*",
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"UGA": "*",
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"AUC": "I",
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"AUU": "I",
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"AUA": "I",
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"UAC": "Y",
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"UAU": "Y",
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"CAA": "Q",
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"CAG": "Q",
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"AGC": "S",
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"AGU": "S",
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"UCA": "S",
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"UCC": "S",
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"UCG": "S",
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"UCU": "S",
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"CAC": "H",
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"CAU": "H",
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"UGC": "C",
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"UGU": "C",
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"CCA": "P",
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"CCC": "P",
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"CCG": "P",
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"CCU": "P",
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"UGG": "W",
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"AGA": "R",
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"AGG": "R",
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"CGA": "R",
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"CGC": "R",
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"CGG": "R",
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"CGU": "R",
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"UUA": "L",
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"UUG": "L",
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"CUA": "L",
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"CUC": "L",
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"CUG": "L",
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"CUU": "L",
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"UUC": "F",
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"UUU": "F",
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}
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#list to contain protein sequences
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# list to contain protein sequences
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proteins = []
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#loop that runs through the sequences from each amino acid in the sequence
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for i in xrange(0, len(stri)-2):
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# loop that runs through the sequences from each amino acid in the sequence
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for i in range(0, len(stri) - 2):
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tempStr = ""
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tempBool = False
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j = i
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#find an orf and break when it is finished
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while j < len(stri)-2:
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if translate[stri[j:j+3]] == "*":
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# find an orf and break when it is finished
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while j < len(stri) - 2:
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if translate[stri[j: j + 3]] == "*":
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tempBool = False
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if translate[stri[j:j+3]] == "M":
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if translate[stri[j: j + 3]] == "M":
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tempBool = True
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if tempBool:
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tempStr += translate[stri[j:j+3]]
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tempStr += translate[stri[j: j + 3]]
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else:
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break
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j += 3
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#add the orf to proteins only if it ends with a stop codon
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if tempStr != "" and tempBool == False:
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# add the orf to proteins only if it ends with a stop codon
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if tempStr != "" and tempBool is False:
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proteins.extend([tempStr])
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#return the protein list
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# return the protein list
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return proteins
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#function to return the DNA compliment
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# function to return the DNA compliment
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def DNACompliment(stri):
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rev = stri[::-1]
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revList = list(rev)
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for i in xrange(0, len(revList)):
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for i in range(0, len(revList)):
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if revList[i] == "A":
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revList[i] = "T"
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elif revList[i] == "T":
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@ -71,32 +115,34 @@ def DNACompliment(stri):
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revCompStr = "".join(revList)
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return revCompStr
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#get file content
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# get file content
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f = open("rosalind_orf.txt")
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content = f.readlines()
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f.close()
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DNAStr = ""
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#construct full DNA sequence
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for i in xrange(1, len(content)):
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# construct full DNA sequence
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for i in range(1, len(content)):
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DNAStr += content[i]
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#remove whitespace
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# remove whitespace
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noWhiteDNA = "".join(DNAStr.split())
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#convert DNA to RNA
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# convert DNA to RNA
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RNA = noWhiteDNA.replace("T", "U")
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#get DNA compliment and convert that to RNA as well
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# get DNA compliment and convert that to RNA as well
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revCompRNA = DNACompliment(noWhiteDNA).replace("T", "U")
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#get orfs for both sequences
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# get orfs for both sequences
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protList = orfGen(RNA)
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protList.extend(orfGen(revCompRNA))
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#get rid of duplicates
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# get rid of duplicates
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finalList = list(set(protList))
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#print the list
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# print the list
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for i in finalList:
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print(i)
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