tutorial 8 part 1

[amidlige]

No description provided.

[lyy005]

for line in vcffile:
line = line.strip()
# if the line starts with "##", skip
if line[0:1] == "##":
outfile.write(line + "\n")
#if the line starts with "#", replace names with fixed names
elif line[0] == "#":
# apply all substitutions
names = re.sub("[Cc]Ff?.[Aa]2?","Cf.Sfa",line)
names = re.sub("[Cc][Ff].(G2|GAI|gai)","Cf.Gai",names)
# write line
outfile.write(names + "\n")
else:
#grab allele
sub = re.sub("[01.]/[01.]:([0-9,.]+):[0-9.]+:[0-9.]+:[0-9,.]+",r"\1",line)
#if allele counts . replace with NA
sub = re.sub(".","NA",sub)
#write line to new file
outfile.write(sub + "\n")

-0.5 points