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tutorial 8 part 1 #7

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25 changes: 25 additions & 0 deletions exercise8.py
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Original file line number Diff line number Diff line change
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import os
import pandas
import numpy

vcffile = open("Cflorida.vcf","r")
outfile = open("CfloridaCounts.txt","w")


for line in vcffile:

line = line.rstrip()

var=re.match('[CFcf]\.[Aa]*?\.', line)
var.replace('var','Cf.Sfa')
outfile.write(var)
var2=re.match('[CFcf]\.[Gg][Aa]?[Ii]?\.', line)
var2.replace('var2','Cf.Sfa')
outfile.write(var2)

var3=re.match([0-9],[0-9],line)
outfile.write(var3)


@lyy005 lyy005 Nov 2, 2017 •
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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