Update for MSc course

Author: kipkurui

Files/dna.fa

@@ -0,0 +1,66 @@
+def get_genes(infile,outfile):
+    """
+    Function to extract a list of genes and write to file
+    """
+    gene_list = []
+    with open(infile) as  gene:
+        tag = False
+        for line in gene:
+            if line.startswith('name'):
+                tag = True
+                pass
+            if tag:
+                items = line.split()
+                if len(items) > 0:
+                    gene_list.append(items[0])
+    gene_list = gene_list[1:-7]
+    with open(outfile, 'w') as outfile:
+        for i in gene_list:
+            outfile.write(i+'\n')
+            
+
+def dnatest(dnaseq):
+    testdna =[]
+    dna = dnaseq.upper()
+    for i in dna:
+        result = str(i) in ['T', 'A', 'G', 'C']
+        testdna.append(result)
+    if testdna.count(False) > 0:
+        return False
+    else:
+        return True
+
+    def dnaTest(x):
+    dnaset = set("AGCT")
+    y = set(x.upper()).union(dnaset) == dnaset
+    return y
+
+def percentGC(dna):
+    '''calculates the percentage GC content, given a DNA sequence'''
+    if dnacheck(dna):
+        dna_len= len(dna)
+        gs = dna.count('G')
+        cs = dna.count('C')
+        
+        return (gs+cs)/dna_len*100
+        
+        #print("The sequence input is not a valid DNA")
+
+def dnacheck(dna):
+    counter = 0
+    check = True
+    valid_dna = 'ACGT'
+    for i in dna.upper():
+        counter += 1
+        if i in valid_dna:
+            pass
+        else:
+            check = False
+            print("There is an invalid base '%s' at position %d"
+                  % (i,counter))
+    return check
+
+dna = 'ACZGTCYTTgZCABG'
+dnacheck(dna)
+dnaseq ='acgtaaqat'
+dnatest(dnaseq)