burton_doherty_submission#8
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lyy005
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Nov 2, 2017
| 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? |
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Or you can use
if line[0:1] == "##":
lyy005
reviewed
Nov 2, 2017
| 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) |
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Quotation mark is missing.
names = re.sub("[Cc]Ff?.[Aa]2?","Cf.Sfa",line)
names = re.sub("[Cc][Ff].(G2|GAI|gai)","Cf.Gai",names)
lyy005
reviewed
Nov 2, 2017
| #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 |
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sub = re.sub("[01.]/[01.]:([0-9,.]+):[0-9.]+:[0-9.]+:[0-9,.]+",r"\1",line) # extract allele information
sub = re.sub(".","NA",sub) #if allele counts . replace with NA
lyy005
reviewed
Nov 2, 2017
| #write new version of line to new file | ||
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| #Close files | ||
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