Supplementary Data

ALK wild type

BRAF wild type

ERBB2 wild type

KRAS wild type

NTRK1 wild type

PXN wild type

ROS1 wild type

EGFR L858R

EGFR T790M

EGFR G719A

EGFR S768I

EGFR P373L (VUS)

EGFR V441F (VUS)

EGFR c.2572C>T L858L

EGFR c.2574G>T L858L

EGFR c.2574G>A L858L

EGFR c.2574G>C L858L

MET 2888-5_2944del62

KIF5B-MET fusion: KIF5Bexon1-24_METexon14-21

KRAS G12C

KRAS G12D

KRAS G12V Python Script for single DNA walk: # -*- coding: utf-8 -*-

"""

Created on Tue Aug 8 10:59:55 2017

@author: hali

This code reads the DNA sequeunce in FASTA format and plot DNA walk

diagram.

For A, set path blue color and move west

For T, set path red color and move east

For C, set path green color and move south

For G, set path black color and move north

for each letter, move 10 turtle distance

"""

import turtle

import canvasvg

import re

from Bio import SeqIO

turtle.screensize(12000,8000)

wn = turtle.Screen() # create the screen to plot the DNA walk

turtle1 = turtle.Turtle()

turtle1.speed(0)

turtle1.hideturtle()

turtle1.color("black")

turtle1.pencolor("red")

count = 0

noATCG = 0

stepsize = 2

item = input('input fastq file name : ')

for record in SeqIO.parse(item, "fasta"):

while count < len(record):

#print(record[count])

if re.search(record[count],"ATCG"):

turtle1.pencolor("black")

if record[count]=="A":

#move A

turtle1.setheading(180)

turtle1.forward(stepsize)

elif record[count]=="T":

#move T

turtle1.setheading(0)

turtle1.forward(stepsize)

elif record[count]=="C":

#move C

turtle1.setheading(270)

turtle1.forward(stepsize)

elif record[count]=="G":

#move G

turtle1.setheading(90)

turtle1.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

else:

turtle1.pencolor("red")

if record[count]=="a":

#move A

turtle1.setheading(180)

turtle1.forward(stepsize)

elif record[count]=="t":

#move T

turtle1.setheading(0)

turtle1.forward(stepsize)

elif record[count]=="c":

#move C

turtle1.setheading(270)

turtle1.forward(stepsize)

elif record[count]=="g":

#move G

turtle1.setheading(90)

turtle1.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

count = count +1

print("unknow sequence count (such as N) = ",noATCG)

print("Done")

ts = turtle1.getscreen()

try:

canvasvg.saveall(item+".svg",ts.getcanvas())

except IOError:

print("save svg error")

try:

ts.getcanvas().postscript(file=item+".eps")

except IOError:

print("save eps error")

wn.mainloop() # Wait for user to close window

Python Script for multiple DNA walks in a single plot Diagram: # -*- coding: utf-8 -*-

"""

Created on Tue Aug 8 10:59:55 2017

@author: hali

This code reads the DNA sequeunce in FASTA format and plot DNA walk

diagram.

For A, set path blue color and move west

For T, set path red color and move east

For C, set path green color and move south

For G, set path black color and move north

for each letter, move 10 turtle distance

"""

import turtle

import canvasvg

from Bio import SeqIO

turtle.screensize(12000,8000)

wn = turtle.Screen() # create the screen to plot the DNA walk

turtle1 = turtle.Turtle()

turtle1.speed(0)

turtle1.hideturtle()

turtle1.color("black")

turtle1.pencolor("black")

turtle2 = turtle.Turtle()

turtle2.speed(0)

turtle2.hideturtle()

turtle2.color("black")

turtle2.pencolor("red")

turtle3 = turtle.Turtle()

turtle3.speed(0)

turtle3.hideturtle()

turtle3.color("black")

turtle3.pencolor("blue")

turtle4 = turtle.Turtle()

turtle4.speed(0)

turtle4.hideturtle()

turtle4.color("black")

turtle4.pencolor("brown")

turtle5 = turtle.Turtle()

turtle5.speed(0)

turtle5.hideturtle()

turtle5.color("black")

turtle5.pencolor("orange")

turtle6 = turtle.Turtle()

turtle6.speed(0)

turtle6.hideturtle()

turtle6.color("black")

turtle6.pencolor("green")

turtle7 = turtle.Turtle()

turtle7.speed(0)

turtle7.hideturtle()

turtle7.color("black")

turtle7.pencolor("magenta")

turtle8 = turtle.Turtle()

turtle8.speed(0)

turtle8.hideturtle()

turtle8.color("black")

turtle8.pencolor("cyan")

turtle9 = turtle.Turtle()

turtle9.speed(0)

turtle9.hideturtle()

turtle9.color("black")

turtle9.pencolor("grey")

count = 0

noATCG = 0

stepsize = 2

for record in SeqIO.parse("EGFR_NM_005228_4.fa", "fasta"):

len1=len(record)

for record2 in SeqIO.parse("ROS1_NM_002944_2.fa", "fasta"):

len2=len(record2)

for record3 in SeqIO.parse("NTRK1_NM_001012331_1.fa", "fasta"):

len3=len(record3)

for record4 in SeqIO.parse("PXN_NM_001243756.fa", "fasta"):

len4=len(record4)

for record5 in SeqIO.parse("NM_000245.fa", "fasta"): #MET

len5=len(record5)

for record6 in SeqIO.parse("KARS_NM_004985.fa", "fasta"):

len6=len(record6)

for record7 in SeqIO.parse("ERBB2_NM_001005862_2.fa", "fasta"):

len7=len(record7)

for record8 in SeqIO.parse("BRAF_NM_004333_5.fa", "fasta"):

len8=len(record8)

for record9 in SeqIO.parse("ALK_NM_004304.fa", "fasta"):

len9=len(record9)

while count < len1:

#print(record[count])

if record[count]=="A":

#move A

turtle1.setheading(180)

turtle1.forward(stepsize)

elif record[count]=="T":

#move T

turtle1.setheading(0)

turtle1.forward(stepsize)

elif record[count]=="C":

#move C

turtle1.setheading(270)

turtle1.forward(stepsize)

elif record[count]=="G":

#move G

turtle1.setheading(90)

turtle1.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count < len2:

if record2[count]=="A":

#move A

turtle2.setheading(180)

turtle2.forward(stepsize)

elif record2[count]=="T":

#move T

turtle2.setheading(0)

turtle2.forward(stepsize)

elif record2[count]=="C":

#move C

turtle2.setheading(270)

turtle2.forward(stepsize)

elif record2[count]=="G":

#move G

turtle2.setheading(90)

turtle2.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len3:

if record3[count]=="A":

#move A

turtle3.setheading(180)

turtle3.forward(stepsize)

elif record3[count]=="T":

#move T

turtle3.setheading(0)

turtle3.forward(stepsize)

elif record3[count]=="C":

#move C

turtle3.setheading(270)

turtle3.forward(stepsize)

elif record3[count]=="G":

#move G

turtle3.setheading(90)

turtle3.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len4:

if record4[count]=="A":

#move A

turtle4.setheading(180)

turtle4.forward(stepsize)

elif record4[count]=="T":

#move T

turtle4.setheading(0)

turtle4.forward(stepsize)

elif record4[count]=="C":

#move C

turtle4.setheading(270)

turtle4.forward(stepsize)

elif record4[count]=="G":

#move G

turtle4.setheading(90)

turtle4.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len5:

if record5[count]=="A":

#move A

turtle5.setheading(180)

turtle5.forward(stepsize)

elif record5[count]=="T":

#move T

turtle5.setheading(0)

turtle5.forward(stepsize)

elif record5[count]=="C":

#move C

turtle5.setheading(270)

turtle5.forward(stepsize)

elif record5[count]=="G":

#move G

turtle5.setheading(90)

turtle5.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len6:

if record6[count]=="A":

#move A

turtle6.setheading(180)

turtle6.forward(stepsize)

elif record6[count]=="T":

#move T

turtle6.setheading(0)

turtle6.forward(stepsize)

elif record6[count]=="C":

#move C

turtle6.setheading(270)

turtle6.forward(stepsize)

elif record6[count]=="G":

#move G

turtle6.setheading(90)

turtle6.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len7:

if record7[count]=="A":

#move A

turtle7.setheading(180)

turtle7.forward(stepsize)

elif record7[count]=="T":

#move T

turtle7.setheading(0)

turtle7.forward(stepsize)

elif record7[count]=="C":

#move C

turtle7.setheading(270)

turtle7.forward(stepsize)

elif record7[count]=="G":

#move G

turtle7.setheading(90)

turtle7.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len8:

if record8[count]=="A":

#move A

turtle8.setheading(180)

turtle8.forward(stepsize)

elif record8[count]=="T":

#move T

turtle8.setheading(0)

turtle8.forward(stepsize)

elif record8[count]=="C":

#move C

turtle8.setheading(270)

turtle8.forward(stepsize)

elif record8[count]=="G":

#move G

turtle8.setheading(90)

turtle8.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

if count <len9:

if record9[count]=="A":

#move A

turtle9.setheading(180)

turtle9.forward(stepsize)

elif record9[count]=="T":

#move T

turtle9.setheading(0)

turtle9.forward(stepsize)

elif record9[count]=="C":

#move C

turtle9.setheading(270)

turtle9.forward(stepsize)

elif record9[count]=="G":

#move G

turtle9.setheading(90)

turtle9.forward(stepsize)

else:

#do nothing

noATCG = noATCG+1

count = count +1

print("unknow sequence count (such as N) = ",noATCG)

print("Done")

ts = turtle1.getscreen()

try:

canvasvg.saveall("multiple_genes.svg",ts.getcanvas())

except IOError:

print("save svg error")

try:

ts.getcanvas().postscript(file="multiple_genes.eps")