Dear Shrushti,

it is straightforward to deal with strained graphene. 

In the region you want to make strain, just set the function which modifies the site position (this mainly depends on the amount and type of the strain). Second, once you have shifted the site position you need to shift the hopping as illustrated in the file provided by Mr. Antonio.

here you find a simple script about how to shift the site position in the case of uniaxial strain (adjusted to you case)

def Triaxial_transform(pos, center, I):
    """ I is a parameter that lets us to control the intensity of the strain"""
    x, y = pos  
    cx, cy = center[0], center[1] # the center of the strain
    r=sqrt((x-cx)**2+(y-cy)**2)
    if r<sigma:
        ux = 2*I * x*y
        uy = I * (x**2 - y**2)
        return x + ux, y + uy
    else: 
        return x, y

Then use this position to set your hopping as illustrated in a previous discussion [Ref-1].

You have to be careful in case you are using a strain in the z axis since you will not be able to plot the current.  It is somehow tricky in this scenario.

[Ref-1] https://www.mail-archive.com/kwant-discuss@kwant-project.org/msg00574.html

I hop this will help

Best wishes