How to only run certain lines of text file through dictionary and keep everything else the same

If I understand correctly you can just keep two versions of the string, one with the meta data and one without (if you actually need the one without), while keeping the newline "n". Then loop through each line, and check if next character is "<" and if its is, just add the line without dictionary, if it is not, go through each character in the line.

Also, consider giving your variables better names 😉

This is not working with the examples you gave, but should guide you in the right direction:

# read through the dna string and replace each character with its rna counterpart
for line in dna.split("n"):
    if not line.startswith(">"):
        for char in line:
            rna += DNATORNADICT[char]
        rna += "n"
    else:
        rna += line
        rna += "n"

protein = ""

# read through the rna string and replace each codon with its protein counterpart
for line in rna.split("n"):
    if line.startswith(">"):
        protein += line + "n"
    else:
        for i in range(0, len(line), 3):
            codon = line[i:i+3]
            protein += rna2protein.get(codon) # not sure why you use .get here
        protein += "n"

print(protein)

I don’t have any domain specific knowledge about what you need to accomplish so let me know if I’m misunderstanding anything.

It looks like there is a line of metadata followed by the DNA sequence it relates to. If this is the case, I think it would be helpful to split these into separate entries that you can process sequentially.

Assuming that the > character only appears in front of the metadata lines and nowhere else in the file, you could use this as a delimiter to split the string:

my_sequences = []
with open('myfile.txt' , 'r') as file:
  # split along the metadata delimiter
  for entry in file.read().split('>')[1:]:
    # split the entry at the first newline character to separate the metadata and sequence
    [meta, seq] = (entry.split("n", 1))
    my_sequences.append({"meta":meta, "seq": seq})

with open('proteinSeq.txt', 'w') as proteinSeq:
  for entry in my_sequences:
    DNASequence = entry["seq"].replace("n", "")
    print('The original DNA sequence is', DNASequence)

    CompletmentDict = {'A':'T', 'T':'A', 'G':'C', 'C' : 'G'}
    final = ""

    for letter in DNASequence:    
        final += CompletmentDict[letter]
    
    print ("Your completement is: ", final)

    final2 = "" 
        
    DNATORNADICT = {'A':'U', 'T':'A', 'G':'C', 'C' : 'G'}

    for letters in final:
        final2 +=  DNATORNADICT[letters]

    print("Your Final DNA TO RNA TRANSCRIPTION IS: " + final2)

    rna2protein = {'UUU':'F', 'UUC':'F', 'UUA':'L', 'UUG':'L',
    'UCU':'S', 'UCC':'S', 'UCA':'S', 'UCG':'S',
    'UAU':'Y', 'UAC':'Y', 'UAA':'', 'UAG':'',
    'UGU':'C', 'UGC':'C', 'UGA':'', 'UGG':'W',
    'CUU':'L', 'CUC':'L', 'CUA':'L', 'CUG':'L',
    'CCU':'P', 'CCC':'P', 'CCA':'P', 'CCG':'P',
    'CAU':'H', 'CAC':'H', 'CAA':'Q', 'CAG':'Q',
    'CGU':'R', 'CGC':'R', 'CGA':'R', 'CGG':'R',
    'AUU':'I', 'AUC':'I', 'AUA':'I', 'AUG':'M',
    'ACU':'T', 'ACC':'T', 'ACA':'T', 'ACG':'T',
    'AAU':'N', 'AAC':'N', 'AAA':'K', 'AAG':'K',
    'AGU':'S', 'AGC':'S', 'AGA':'R', 'AGG':'R',
    'GUU':'V', 'GUC':'V', 'GUA':'V', 'GUG':'V',
    'GCU':'A', 'GCC':'A', 'GCA':'A', 'GCG':'A',
    'GAU':'D', 'GAC':'D', 'GAA':'E', 'GAG':'E',
    'GGU':'G', 'GGC':'G', 'GGA':'G', 'GGG':'G'}

    final3 = ""

    for p in range(0,len(final2),3):
        myKey = final2[p:p+3]
        final3 += rna2protein.get(myKey)
        
    print("Resulting protein is: ", final3)
    proteinSeq.write(f""">{entry["meta"]}n""")
    proteinSeq.write(f"{final3}n")
  proteinSeq.close()

You’ll end up with an array of dictionaries that you can loop over where each dictionary has a separate key value pair for the metadata and the following sequence.

I made some adjustement on your code :

import sys
file = open('2dna.fasta' , 'r')
proteinSeq = open('proteinSeq.txt', 'a')

metaData = []
DNAs = []

DNASequence = ''
for lines in file.readlines():
    if not (lines.startswith('>')):
        DNASequence = DNASequence +  lines 
    else:
        DNASequence = DNASequence.replace('n', '')
        DNAs.append(DNASequence)
        metaData.append(lines.split(" ")[0])
        DNASequence = ""

def showData(metaData,DNASequence):
    print('The original DNA sequence is', DNASequence)

    CompletmentDict = {'A':'T', 'T':'A', 'G':'C', 'C' : 'G'}
    final = ""

    for letter in DNASequence:    
        final += CompletmentDict[letter]
        
    print ("Your completement is: ", final)

    final2 = "" 
        
    DNATORNADICT = {'A':'U', 'T':'A', 'G':'C', 'C' : 'G'}

    for letters in final:
        final2 +=  DNATORNADICT[letters]

    print("Your Final DNA TO RNA TRANSCRIPTION IS: " + final2)

    rna2protein = {'UUU':'F', 'UUC':'F', 'UUA':'L', 'UUG':'L',
    'UCU':'S', 'UCC':'S', 'UCA':'S', 'UCG':'S',
    'UAU':'Y', 'UAC':'Y', 'UAA':'', 'UAG':'',
    'UGU':'C', 'UGC':'C', 'UGA':'', 'UGG':'W',
    'CUU':'L', 'CUC':'L', 'CUA':'L', 'CUG':'L',
    'CCU':'P', 'CCC':'P', 'CCA':'P', 'CCG':'P',
    'CAU':'H', 'CAC':'H', 'CAA':'Q', 'CAG':'Q',
    'CGU':'R', 'CGC':'R', 'CGA':'R', 'CGG':'R',
    'AUU':'I', 'AUC':'I', 'AUA':'I', 'AUG':'M',
    'ACU':'T', 'ACC':'T', 'ACA':'T', 'ACG':'T',
    'AAU':'N', 'AAC':'N', 'AAA':'K', 'AAG':'K',
    'AGU':'S', 'AGC':'S', 'AGA':'R', 'AGG':'R',
    'GUU':'V', 'GUC':'V', 'GUA':'V', 'GUG':'V',
    'GCU':'A', 'GCC':'A', 'GCA':'A', 'GCG':'A',
    'GAU':'D', 'GAC':'D', 'GAA':'E', 'GAG':'E',
    'GGU':'G', 'GGC':'G', 'GGA':'G', 'GGG':'G'}

    final3 = ""

    for p in range(0,len(final2),3):
        myKey = final2[p:p+3]
        final3 += rna2protein.get(myKey)
        
    print("Resulting protein is: ", final3)
    proteinSeq.write("n " + metaData + "n " + final3)

for i in range(len(DNAs)):
    showData(metaData[i],DNAs[i])

proteinSeq.close()