Question

So I have file with about thousand line that look like this:

COADREAD    ZNF271  Missense_Mutation   TCGA-AA-3947    Q14591  A177T 
COADREAD    ZNF271  Missense_Mutation   TCGA-AA-A00N    Q14591  I26T  
COADREAD    ZNF271  Missense_Mutation   TCGA-AG-A002    Q14591  M418T

I have code that look for 5th column for the id and grab the number between two letter.

Is there a way that I can also grab whole token after id in 5th column (or column 6th token).

I want to grab that token so I can write it on to another file.

Here is what I have so far( This code will give me number, but is there way to get both number to calculate and whole string of that token to print on to the output file):
For example, if I call lookup[Q14591] it give me [‘177′,’26’,418] but I also want A177T I26T and M418T

lookup = defaultdict(list)
mydata = open('summaryfile.txt')
for line in csv.reader(mydata, delimiter='\t'):
    code = re.match('[a-z](\d+)[a-z]', line[-1], re.I)
    if code: 
        lookup[line[-2]].append(code.group(1))

Answer 1

When using regular expressions, group(0) should contain the whole matched string. So in your case:

code.group(0)

should contain the whole token. So if you modify your code to look like this:

lookup = defaultdict(list)
wholelookup = defaultdict(list)

mydata = open('summaryfile.txt')
for line in csv.reader(mydata, delimiter='\t'):
    code = re.match('[a-z](\d+)[a-z]', line[-1], re.I)
    if code: 
        lookup[line[-2]].append(code.group(1))
        wholelookup[line[-2]].append(code.group(0))

Then you can access whole tokens like this:

wholelookup['Q14591']

or the sub-tokens like this:

lookup['Q14591']