Bio genome sequence

translation_transcription.py

@@ -0,0 +1,299 @@
+from operator import add
+from functools import reduce
+import re,textwrap,csv
+
+def translate_dna(sequence):
+
+    codontable = {
+    'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
+    'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
+    'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
+    'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
+    'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
+    'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
+    'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
+    'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
+    'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
+    'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
+    'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
+    'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
+    'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
+    'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
+    'TAC':'Y', 'TAT':'Y', 'TAA':'', 'TAG':'',
+    'TGC':'C', 'TGT':'C', 'TGA':'', 'TGG':'W',
+    }
+    proteinsequence = ''
+
+    for n in range(0,len(sequence),3):
+        if sequence[n:n+3] in codontable:
+            proteinsequence += codontable[sequence[n:n+3]]
+        else:   
+            proteinsequence += ''
+    return proteinsequence
+
+def atgc(sequence):
+    freq = [0,0,0,0]
+    for i in sequence:
+        if i == 'A':
+            freq[0]+=1
+        elif i == 'T':
+            freq[1]+=1
+        elif i == 'G':
+            freq[2]+=1
+        elif i == 'C':
+            freq[3]+=1
+        else:
+            continue
+    return freq
+
+def tm(freq):
+    return ( 2*(freq[0]+freq[1]) + 4*(freq[2]+freq[3]))
+
+seq_dict = {'A':'T','T':'A','G':'C','C':'G','*':'*','Z':'Z'}
+
+def primer(sequence,lmno):
+    l = []
+    flag = 0
+    cunt = 0
+    for j in range(18,30):
+        flag = 0
+        for i in range(0, len(sequence)):
+            sum = 0
+            if (j+i > len(sequence)):
+                break
+
+            seq = (sequence)[i:j+i]
+            user = atgc(seq)
+            t = tm(user)
+            if (t > 60 and t < 70):
+                sum +=1
+
+            ratio = (user[2]+user[3]) / (user[0] + user[1] + user[2] + user[3])
+            if (ratio >= .40 and ratio <= .60):
+                adity= 1
+            else:
+                adity= 0
+            sum += adity
+            if not (re.compile(r'([CG]{4,30})').match(seq)):
+                sum+=1
+            if not (re.compile(r'([A]{5,30})').match(seq) or re.compile(r'([T]{5,30})').match(seq) or re.compile(r'([G]{5,30})').match(seq) or re.compile(r'([C]{5,30})').match(seq)):
+                sum+=1
+            if (seq[-1] == 'A'):
+                sum+=1
+            elif (seq[-1] == 'C'):
+                sum+=1
+            if ((user[1]+user[0]) / (user[0] + user[1] + user[2] + user[3]) >= .50):
+                sum+=1
+            if not (seq[0:9] == ("".join([seq_dict[base] for base in reversed(seq[-10:-1])]))[::-1]):
+                sum+= 1
+            if (sum == 7):
+                l.append(seq)
+                cunt +=1
+
+            if (cunt == lmno+2):
+                flag = 1
+                break
+
+        if (flag):
+            break
+    flag = 0
+
+    k = l[lmno]
+    for j in range(18,30):
+        flag = 0
+        for i in range(0, len(sequence)):
+            sum = 0
+            seq = ("".join([seq_dict[base] for base in reversed(sequence)]))[i:j+i]
+            if (j+i > len(sequence)):
+                break
+            user = atgc(seq)
+            t = tm(user)
+            if (t > 60 and t < 70):
+                sum +=1
+
+            ratio = (user[2]+user[3]) / (user[0] + user[1] + user[2] + user[3])
+            if (ratio >= .40 and ratio <= .60):
+                adity= 1
+            else:
+                adity= 0
+            sum += adity
+            if not (re.compile(r'([CG]{4,30})').match(seq)):
+                sum+=1
+            if not (re.compile(r'([A]{5,30})').match(seq) or re.compile(r'([T]{5,30})').match(seq) or re.compile(r'([G]{5,30})').match(seq) or re.compile(r'([C]{5,30})').match(seq)):
+                sum+=1
+            if (seq[-1] == 'A'):
+                sum+=1
+            elif (seq[-1] == 'C'):
+                sum+=1
+            if ((user[1]+user[0]) / (user[0] + user[1] + user[2] + user[3]) >= .50):
+                sum+=1
+            if not (seq[0:9] == ("".join([seq_dict[base] for base in reversed(seq[-10:-1])]))[::-1]):
+                sum+= 1
+            jpg = tm(atgc(k))
+            if (sum >=5):
+                if (abs(jpg-t) < 5):
+                    string = "Forward Primer - " + str(k) + "\t" + "Tm(in deg C) - " + str(jpg) + "\n" + "Reverse Primer - " + str(seq) + "\t" + "Tm(in deg C) - " + str(tm(user)) + "\n"
+                    open4_file.write(string)
+                    flag = 1
+                    break
+        if (flag):
+            break
+    return 
+
+in_file1 = open("sequence.fasta","r")
+s1 = in_file1.read()
+in_file1.close()
+in_file2 = open("Introns.csv")
+s2 = list(csv.reader(in_file2))
+in_file2.close()
+s2.pop(0)
+s2 = reduce(add, s2, [])
+
+l2=['*']
+
+info = []
+
+l1 = s1.split(">")
+l1.pop(0)
+sequence = []
+for i in l1:
+    info.append((i.split("\n"))[0])
+    l3 = i.split("\n")
+    l3.pop(0)
+    sequence.append(''.join(l3))
+
+isequence = []
+temp=''
+for i in sequence:
+    l3 = []
+    temp = ''
+    if not (int(s2[0])-1 < 0):
+        temp = i[0:int(s2[0])-1]
+        for j in range(0, len(s2),2):
+            for l in range(int(s2[j]),int(s2[j+1])+1):
+                temp += '*'
+            if (j+2 < len(s2)):
+                temp += i[int(s2[j+1]):int(s2[j+2])-1]
+            if (j+2 >= len(s2)):
+                break
+        if (int(s2[-1]) < len(i)):
+            temp += i[int(s2[j-1]):-1]
+            temp += i[-1]
+        break
+isequence.append(temp)
+refrence_frame1 = []
+refrence_frame4 = []
+
+for i in range(0,3):
+    refrence_frame1.append(sequence[0][i:]) 
+    refrence_frame4.append(isequence[0][i:])
+
+for i in range(0,3):
+    refrence_frame1.append(("".join([seq_dict[base] for base in reversed(sequence[0])]))[i:])
+    refrence_frame4.append(("".join([seq_dict[base] for base in reversed(isequence[0])]))[i:])
+
+counter = 0
+
+open4_file = open("4.txt","w")
+for i in refrence_frame1:
+    primer(str(i),counter)
+    counter+=1
+
+refrence_frame2 = []
+for i in refrence_frame4:
+    stseq = ''
+    count = 0
+    for j in i:
+        count+=1
+        stseq += j 
+        if (count%3 == 0):
+            stseq += 'Z'
+    refrence_frame2.append(stseq)
+pmer = (("".join([seq_dict[base] for base in reversed(refrence_frame2[0])]))[::-1])
+pmer = pmer.replace("*","")
+pmer = pmer.replace("Z","")
+refrence_frame7 = []
+for i in refrence_frame1:
+    stseq = ''
+    count = 0
+    for j in i:
+        count+=1
+        stseq += j 
+        if (count%3 == 0):
+            stseq += 'Z'
+    refrence_frame7.append(stseq)
+counter = 0
+open1_file = open("1.txt","w")
+for i in refrence_frame7:
+    counter += 1
+    slr = "> Reading Frame " + str(counter) + "\n"
+    open1_file.write(slr)
+    open1_file.write(textwrap.fill(i.replace("Z",""),70))
+    slr= "\n\n"
+    open1_file.write(slr)
+
+
+counter = 0
+length = 0
+cunt  = 0
+fsquirt = ''
+
+pattern = re.compile(r'(ATG(?:[ATGC]{3})*?([ATGCZ*])*?(?:TAA|TAG|TGA))')
+for i in refrence_frame2:
+    a = i.replace("Z"," ")
+    a = a.replace("*","X")
+    for key1 in range(0,len(i),4):
+        if (i[key1:key1+3] == 'ATG'):
+            break;
+    for key2 in range(len(i)-1,-1,-1):
+        if (i[key2] != '*' and i[key2] != 'Z'):
+            break;
+    i = i[key1:key2+1]
+    a = i.replace("Z","")
+    a = a.replace("*","")
+    stseq = ''
+    count = 0
+    for mem in a:
+        count+=1
+        stseq += mem 
+        if (count%3 == 0):
+            stseq += 'Z'
+    a = stseq
+    a = list(pattern.findall(a))
+    counter += 1
+    lona = 0
+    for j in a:
+        j = list(j)
+        j.pop(-1)
+        j[0] = j[0].replace("Z","")
+        j[0] = j[0].replace("*","X")
+        if (length < len(j[0])):
+            cunt  = counter
+            fsquirt = j[0]
+            length = len(j[0])
+
+open2_file = open("2.txt","w")
+slr = "> Reading Frame " + str(cunt) + "\n"
+open2_file.write(slr)
+open2_file.write(textwrap.fill(refrence_frame7[cunt-1].replace("Z",""),70))
+open2_file.write("\n")
+
+open3_file = open("3.txt","w")
+slr= "> Protein Sequence\n"
+open3_file.write(slr)
+open3_file.write(textwrap.fill(translate_dna(fsquirt),70))
+open3_file.write("\n")
+
+open5_file = open("5.txt","w")
+slr= "> E.coli cloning sequence \n"
+open5_file.write(slr)
+open5_file.write(textwrap.fill(fsquirt,70))
+slr="\n\n> Pichia pastoris cloning sequence \n"
+open5_file.write(slr)
+open5_file.write(textwrap.fill(refrence_frame7[cunt-1].replace("Z",""),70))
+slr="\n\n> HEK293 cloning sequence \n"
+open5_file.write(slr)
+open5_file.write(textwrap.fill(refrence_frame7[cunt-1].replace("Z",""),70))
+slr="\n\n"
+open5_file.write(slr)
+