added converter file and amino acids file

amino_acids.py

@@ -0,0 +1,132 @@
+def codons_to_acids(list_of_codons):
+    newlist = []
+    for i in list_of_codons:
+        if i == "GUU":
+            newlist.append("Valine")
+        if i == "GUC":
+            newlist.append("Valine")
+        if i == "GUA":
+            newlist.append("Valine")
+        if i == "GUG":
+            newlist.append("Valine")
+        if i == "GCU":
+            newlist.append("Alanine")
+        if i == "GCC":
+            newlist.append("Alanine")
+        if i == "GCA":
+            newlist.append("Alanine")
+        if i == "GCG":
+            newlist.append("Alanine")
+        if i == "GAU":
+            newlist.append("Aspartic Acid")
+        if i == "GAC":
+            newlist.append("Aspartic Acid")
+        if i == "GAA":
+            newlist.append("Glutamic Acid")
+        if i == "GAG":
+            newlist.append("Glutamic Acid")
+        if i == "GGU":
+            newlist.append("Glycine")
+        if i == "GGC":
+            newlist.append("Glycine")
+        if i == "GGA":
+            newlist.append("Glycine")
+        if i == "GGG":
+            newlist.append("Glycine")
+        if i == "UUU":
+            newlist.append("Phenylalanine")
+        if i == "UUC":
+            newlist.append("Phenylalanine")
+        if i == "UUA":
+            newlist.append("Leucine")
+        if i == "UUG":
+            newlist.append("Leucine")
+        if i == "UCU":
+            newlist.append("Serine")
+        if i == "UCC":
+            newlist.append("Serine")
+        if i == "UCA":
+            newlist.append("Serine")
+        if i == "UCG":
+            newlist.append("Serine")
+        if i == "UAU":
+            newlist.append("Tyrosine")
+        if i == "UAC":
+            newlist.append("Tyrosine")
+        if i == "UAA":
+            newlist.append("STOP")
+        if i == "UAG":
+            newlist.append("STOP")
+        if i == "UGU":
+            newlist.append("Cysteine")
+        if i == "UGC":
+            newlist.append("Cysteine")
+        if i == "UGA":
+            newlist.append("STOP")
+        if i == "UGG":
+            newlist.append("Tryptophan")
+        if i == "CUU":
+            newlist.append("Leucine")
+        if i == "CUC":
+            newlist.append("Leucine")
+        if i == "CUA":
+            newlist.append("Leucine")
+        if i == "CUG":
+            newlist.append("Leucine")
+        if i == "CCU":
+            newlist.append("Proline")
+        if i == "CCC":
+            newlist.append("Proline")
+        if i == "CCA":
+            newlist.append("Proline")
+        if i == "CCG":
+            newlist.append("Proline")
+        if i == "CAU":
+            newlist.append("Histidine")
+        if i == "CAC":
+            newlist.append("Histidine")
+        if i == "CAA":
+            newlist.append("Glutamine")
+        if i == "CAG":
+            newlist.append("Glutamine")
+        if i == "CGU":
+            newlist.append("Arginine")
+        if i == "CGC":
+            newlist.append("Arginine")
+        if i == "CGA":
+            newlist.append("Arginine")
+        if i == "CGG":
+            newlist.append("Arginine")
+        if i == "AUU":
+            newlist.append("Isoleucine")
+        if i == "AUC":
+            newlist.append("Isoleucine")
+        if i == "AUA":
+            newlist.append("Isoleucine")
+        if i == "AUG":
+            newlist.append("Methionine")
+        if i == "ACU":
+            newlist.append("Threonine")
+        if i == "ACC":
+            newlist.append("Threonine")
+        if i == "ACA":
+            newlist.append("Threonine")
+        if i == "ACG":
+            newlist.append("Threonine")
+        if i == "AAU":
+            newlist.append("Asparagine")
+        if i == "AAC":
+            newlist.append("Asparagine")
+        if i == "AAA":
+            newlist.append("Lysine")
+        if i == "AAG":
+            newlist.append("Lysine")
+        if i == "AGU":
+            newlist.append("Serine")
+        if i == "AGC":
+            newlist.append("Serine")
+        if i == "AGA":
+            newlist.append("Arginine")
+        if i == "AGG":
+            newlist.append("Arginine")
+    return newlist

converter.py

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+#This program turns a strand of DNA into mRNA, which is then converted into amino acids using a codon chart
+#MIT License as usual
+#Ravi Shah 2020
+from amino_acids import codons_to_acids
+
+stop_index = "NaN"
+
+def find_stop(mrna):
+    if "UAA" in mrna:
+        print("UAA STOP codon found")
+        stop_index = mrna.index("UAA")
+    elif "UAG" in mrna:
+        print("UAG STOP codon found")
+        stop_index = mrna.index("UAG")
+    elif "UGA" in mrna:
+        print("UGA STOP codon found")
+        stop_index = mrna.index("UGA")
+    else:
+        print("No STOP codon found. Exiting...")
+        quit()
+    return stop_index
+
+def transcription(dna):
+    res = []
+    newlist = []
+    res[:] = dna
+
+    for i in res:
+        if i == "G":
+            newlist.append("C")
+        elif i == "C":
+            newlist.append("G")
+        elif i == "A":
+            newlist.append("U")
+        elif i == "T":
+            newlist.append("A")
+
+    mrna_strand = ''.join(newlist)
+    return mrna_strand
+
+def start_to_stop(mrna):
+    global stop_index
+    try:
+        start_index = mrna.index("AUG")
+        inter_rna = mrna[start_index:]
+        stop_index = find_stop(inter_rna)
+        final_rna = inter_rna[0:stop_index+3]
+        return(final_rna)
+    except:
+        print("Please enter a valid DNA strand")
+        quit()
+
+def translation(final_rna):
+    print("The mRNA strand is:", final_rna)
+    n = 3
+    res = [final_rna[i:i+n] for i in range(0, len(final_rna), n)]
+    print("The codons are:", res)
+    list_of_amino_acids = codons_to_acids(res)
+    print("There are", len(list_of_amino_acids), "amino acids translated from this mRNA strand.")
+    return list_of_amino_acids
+
+strand = input("Enter the DNA strand to be transcribed and translated: ")
+strand = strand.upper()
+messenger_rna = transcription(strand)
+thing = start_to_stop(messenger_rna)
+print("Here are the amino acids:")
+print(translation(thing))