read and matching pattern with python

Question

I have read the content of a text file into pandas and needed some help matching the pattern.

Here is the pattern, where a can any number greater than zero and b can be zero or any number greater than zero:

father=a|0 || 0|a
mother=a|0 || 0|a
daughter1=b|0 || 0|b
daughter2=a|0 || 0|a
daughter3=b|0 || 0|b
son1=a|0 || 0|a
son2=b|0 || 0|b

Here is the function that reads the content of text file to pandas

import pandas as pd
def read():
    varian=pd.read_csv('file.txt',sep = "\t")

father=varian["FATHER"]
mother=varian["MOTHER"]
daughter1=varian["DAUGHTER1"]
daughter2=varian["DAUGHTER2"]
daughter3=varian["DAUGHTER3"]
son1=varian["SON1"]
son2=varian["SON2"]

The content of the file looks like this

HROM    POS REF ALT FATHER  MOTHER  DAUGHTER1   DAUGHTER2   DAUGHTER3   SON1    SON2    INFO    FREQUECY
1   1226852 G   C   1/0 0/0 1|0 1|0 1|0 1|0 0|0 AN=2184;AC=12   0.005494505
1   1847936 C   T   0/1 1/1 1|1 1|1 1|1 1|1 0|1 AC=1;AN=2184    0.000457875
1   2428427 C   G   0/1 0/0 0|0 0|0 0|0 0|0 1|0 AC=4;AN=2184    0.001831502
1   2515616 G   A   1/0 1/0 1/0 1|1 1|1 1/0 1/0 AC=1;AN=2184    0.000457875
1   3801895 T   C   1/0 1/0 0|0 1/0 1/0 0|0 1|1 AC=10;AN=2184   0.004578755

Answer 1

This is not a bioinformatics question, but a basic pandas question, so SO is a better place for this... But your odd looking VCF file can be parsed as follows without even using regex:

import pandas as pd

def splitter(cell, key):
    parts = cell.split('||')
    if key in parts[0]:
         p = parts[0].split('|')
    else:
         p = parts[1].split('|')
    sp = [x.strip() for x in p if key not in x]
    return float(sp[0])

def read():
    splitter_a = lambda v: v.split('||')[0].split('|')[1]) 
    varian=pd.read_csv('file.txt',sep = "\t")
    a_splitter = lambda c: splitter(c, 'a')
    b_splitter = lambda c: splitter(c, 'b')
    varian = varian.assign(father_a=varian.FATHER.apply(a_splitter)\
              .assign(father_a=varian.FATHER.apply(b_splitter)\
              .assign(mother_a=varian.MOTHER.apply(la_splitter)\

etc.

display(varian) or print(varian.columns) will show that you have new columns called father_a etc.

Answer 2

Its easy. You want to remove homozygotes and here is the solution for the FATHER class. Note the MOTHER class will comprise homozygotes in the answer because you are only searching for FATHER. To perform an intersection one approach is just to concatenate the mask.

import pandas as pd

genedict = {\
            'FATHER': ['1/0', '1/1', '0/0', '1/0', '0/1'], \
            'MOTHER': ['1/1', '1/1', '1/0', '1/0', '0/0']}

df = pd.DataFrame(genedict)    
mask = df.FATHER.str.contains(r'1[|/]0') + df.FATHER.str.contains(r'0[|/]1')
df[mask]

OUTPUT

  FATHER MOTHER
0    1/0    1/1
3    1/0    1/0
4    0/1    0/0

Note, this is not your original dataset, its a dictionary to demonstrate the principle and note all your other columns will carry across unless you want to 'drop' them. Finally, pandas has its own regex system, regardless the traditional r'' code is still needed