burton_doherty_submission

Exercise08_1.py

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+#Exercise 8, Python question 1
+#10/13/17, MMD
+import vcf
+import re
+#Open files to read and write
+vcffile = open("Cflorida.vcf","r")
+outfile = open("CfloridaCounts.txt","w")
+
+#assign regex to variable name, or compile to variable name
+
+lineNumber=0
+#loop over file
+for line in vcffile:#look at old code to see how you looped over a file
+    #strip end of line
+    line=line.strip()
+    if lineNumber==0: #how can you tell if this is the header line?
+        outfile.write(line+"\n")
+        #write unchanged header line to file
+    elif lineNumber==1: #how can you tell if this is the line with the column headings?
+        #standardize (replace) sample names with TX and FL regexes
+        re.sub(((CF|cf){1}.?{4}\.,(Cf.Sfa.),line) ###Having trouble gettig re.sub to work, syntax not working. Trying to replace CF and then any 4 characters leading to a period
+        re.sub(((CF|cf){1}.?{4}\.,(Cf.Gai.),line)
+        #write new version of line to file
+        outfile.write(line+"\n")
+    else: #now you're in the data
+        #replace full SNP info with allele counts only
+        #replace missing data with NA
+        #write new version of line to new file
+
+#Close files
+
+