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plotSARSCoV2eightSNPsCoverage.py
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plotSARSCoV2eightSNPsCoverage.py
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import os, sys, re, csv, statistics
import argparse, logging, warnings
from Bio import SeqIO
import numpy as np
from matplotlib import pyplot as plt
import matplotlib.colors as mcolors
## Script for plotting genome coverages and SNPs position coverages
## Outputs .png file of line plot
## Requires Biopython, Numpy, and Matplotlib
## Function: A closure for file extension checking
def ext_check(expected_ext, openner):
def extension(filename):
if not filename.endswith(expected_ext):
raise ValueError()
return openner(filename)
return extension
parser = argparse.ArgumentParser(description='Plots coverage from two .bed files line plots', usage="plotBedCoverage.py filepath/filename1.bed filepath/filename2.bed filepath/filename3.bed filepath/filename4.bed filepath/filename5.bed filepath/filename6.bed")
parser.add_argument('snpFile1', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile2', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile3', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile4', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile5', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile6', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile7', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile8', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile9', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile10', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile11', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile12', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile13', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile14', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile15', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('snpFile16', type=ext_check('.tab', argparse.FileType('r')))
parser.add_argument('--window', '-w', default='1', type=int)
args = parser.parse_args()
# echo input file name
print(args.snpFile1.name)
print(args.snpFile3.name)
print(args.snpFile5.name)
print(args.snpFile7.name)
print(args.snpFile9.name)
print(args.snpFile11.name)
print(args.snpFile13.name)
print(args.snpFile15.name)
myTitle1 = re.split(r'[\/]', args.snpFile1.name)
myTitle2 = re.split(r'[\/]', args.snpFile3.name)
myTitle3 = re.split(r'[\/]', args.snpFile5.name)
myTitle4 = re.split(r'[\/]', args.snpFile7.name)
myTitle5 = re.split(r'[\/]', args.snpFile9.name)
myTitle6 = re.split(r'[\/]', args.snpFile11.name)
myTitle7 = re.split(r'[\/]', args.snpFile13.name)
myTitle8 = re.split(r'[\/]', args.snpFile15.name)
#print(myTitle[len(myTitle) - 1])
shortTitle1 = re.split(r'[\.]', myTitle1[len(myTitle1) - 1])
shortTitle1t = shortTitle1[0].split(sep='_S')
shortTitle2 = re.split(r'[\.]', myTitle2[len(myTitle2) - 1])
shortTitle2t = shortTitle2[0].split(sep='_S')
shortTitle3 = re.split(r'[\.]', myTitle3[len(myTitle3) - 1])
shortTitle3t = shortTitle3[0].split(sep='_S')
shortTitle4 = re.split(r'[\.]', myTitle4[len(myTitle4) - 1])
shortTitle4t = shortTitle4[0].split(sep='_S')
shortTitle5 = re.split(r'[\.]', myTitle5[len(myTitle5) - 1])
shortTitle5t = shortTitle5[0].split(sep='_S')
shortTitle6 = re.split(r'[\.]', myTitle6[len(myTitle6) - 1])
shortTitle6t = shortTitle6[0].split(sep='_S')
shortTitle7 = re.split(r'[\.]', myTitle7[len(myTitle7) - 1])
shortTitle7t = shortTitle7[0].split(sep='_S')
shortTitle8 = re.split(r'[\.]', myTitle8[len(myTitle8) - 1])
shortTitle8t = shortTitle8[0].split(sep='_S')
csvRow = []
forwardLen = []
reverseLen = []
referenceName = ''
iter = 0
snpCoords1 = []
snpDepth1 = []
mySnps1 = open(args.snpFile1.name, "r")
for line in mySnps1:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords1.append(int(lineData[1]))
snpDepth1.append(int(lineData[5]))
iter = iter + 1
mySnps1.close()
iter = 0
snpCoords2 = []
snpDepth2 = []
mySnps2 = open(args.snpFile2.name, "r")
for line in mySnps2:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords2.append(int(lineData[1]))
snpDepth2.append(int(lineData[5]))
iter = iter + 1
mySnps2.close()
iter = 0
snpCoords3 = []
snpDepth3 = []
mySnps3 = open(args.snpFile3.name, "r")
for line in mySnps3:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords3.append(int(lineData[1]))
snpDepth3.append(int(lineData[5]))
iter = iter + 1
mySnps3.close()
iter = 0
snpCoords4 = []
snpDepth4 = []
mySnps4 = open(args.snpFile4.name, "r")
for line in mySnps4:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords4.append(int(lineData[1]))
snpDepth4.append(int(lineData[5]))
iter = iter + 1
mySnps4.close()
iter = 0
snpCoords5 = []
snpDepth5 = []
mySnps5 = open(args.snpFile5.name, "r")
for line in mySnps5:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords5.append(int(lineData[1]))
snpDepth5.append(int(lineData[5]))
iter = iter + 1
mySnps5.close()
iter = 0
snpCoords6 = []
snpDepth6 = []
mySnps6 = open(args.snpFile6.name, "r")
for line in mySnps6:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords6.append(int(lineData[1]))
snpDepth6.append(int(lineData[5]))
iter = iter + 1
mySnps6.close()
iter = 0
snpCoords7 = []
snpDepth7 = []
mySnps7 = open(args.snpFile7.name, "r")
for line in mySnps7:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords7.append(int(lineData[1]))
snpDepth7.append(int(lineData[5]))
iter = iter + 1
mySnps7.close()
iter = 0
snpCoords8 = []
snpDepth8 = []
mySnps8 = open(args.snpFile8.name, "r")
for line in mySnps8:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords8.append(int(lineData[1]))
snpDepth8.append(int(lineData[5]))
iter = iter + 1
mySnps8.close()
iter = 0
snpCoords9 = []
snpDepth9 = []
mySnps9 = open(args.snpFile9.name, "r")
for line in mySnps9:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords9.append(int(lineData[1]))
snpDepth9.append(int(lineData[5]))
iter = iter + 1
mySnps9.close()
iter = 0
snpCoords10 = []
snpDepth10 = []
mySnps10 = open(args.snpFile10.name, "r")
for line in mySnps10:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords10.append(int(lineData[1]))
snpDepth10.append(int(lineData[5]))
iter = iter + 1
mySnps10.close()
iter = 0
snpCoords11 = []
snpDepth11 = []
mySnps11 = open(args.snpFile11.name, "r")
for line in mySnps11:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords11.append(int(lineData[1]))
snpDepth11.append(int(lineData[5]))
iter = iter + 1
mySnps11.close()
iter = 0
snpCoords12 = []
snpDepth12 = []
mySnps12 = open(args.snpFile12.name, "r")
for line in mySnps12:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords12.append(int(lineData[1]))
snpDepth12.append(int(lineData[5]))
iter = iter + 1
mySnps12.close()
iter = 0
snpCoords13 = []
snpDepth13 = []
mySnps13 = open(args.snpFile13.name, "r")
for line in mySnps13:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords13.append(int(lineData[1]))
snpDepth13.append(int(lineData[5]))
iter = iter + 1
mySnps13.close()
iter = 0
snpCoords14 = []
snpDepth14 = []
mySnps14 = open(args.snpFile14.name, "r")
for line in mySnps14:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords14.append(int(lineData[1]))
snpDepth14.append(int(lineData[5]))
iter = iter + 1
mySnps14.close()
iter = 0
snpCoords15 = []
snpDepth15 = []
mySnps15 = open(args.snpFile15.name, "r")
for line in mySnps15:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords15.append(int(lineData[1]))
snpDepth15.append(int(lineData[5]))
iter = iter + 1
mySnps15.close()
iter = 0
snpCoords16 = []
snpDepth16 = []
mySnps16 = open(args.snpFile16.name, "r")
for line in mySnps16:
lineData = re.split(r'\s+', line)
if(iter > 1):
snpCoords16.append(int(lineData[1]))
snpDepth16.append(int(lineData[5]))
iter = iter + 1
mySnps16.close()
myXticks = []
iter = 0
# Generate X-axis labels
for count in range(0, max(snpCoords1)):
if(iter % 2000 == 0):
myXticks.append(int(count))
iter = iter + 1
#print(myXticks)
myYticks = []
topCoverage = snpDepth1
if(max(topCoverage) < max(snpDepth2)):
topCoverage = snpDepth2
if(max(topCoverage) < max(snpDepth3)):
topCoverage = snpDepth3
if(max(topCoverage) < max(snpDepth4)):
topCoverage = snpDepth4
if(max(topCoverage) < max(snpDepth5)):
topCoverage = snpDepth5
if(max(topCoverage) < max(snpDepth6)):
topCoverage = snpDepth6
if(max(topCoverage) < max(snpDepth7)):
topCoverage = snpDepth7
if(max(topCoverage) < max(snpDepth8)):
topCoverage = snpDepth8
if(max(topCoverage) < max(snpDepth9)):
topCoverage = snpDepth9
if(max(topCoverage) < max(snpDepth10)):
topCoverage = snpDepth10
if(max(topCoverage) < max(snpDepth11)):
topCoverage = snpDepth11
if(max(topCoverage) < max(snpDepth12)):
topCoverage = snpDepth12
if(max(topCoverage) < max(snpDepth13)):
topCoverage = snpDepth13
if(max(topCoverage) < max(snpDepth14)):
topCoverage = snpDepth14
if(max(topCoverage) < max(snpDepth15)):
topCoverage = snpDepth15
if(max(topCoverage) < max(snpDepth16)):
topCoverage = snpDepth16
print(max(topCoverage))
iter = 0
for count in range(0, int(max(topCoverage)) + 3000):
if(iter % 2000 == 0):
myYticks.append(int(count))
iter = iter + 1
iter = 0
tabColors = mcolors.TABLEAU_COLORS
colors=[tabColors['tab:blue'], tabColors['tab:orange'], tabColors['tab:cyan'], tabColors['tab:red'], tabColors['tab:green'], tabColors['tab:pink'], tabColors['tab:olive'], tabColors['tab:purple'] ]
##print(tabColors)
label1 = shortTitle1t[0] + " MiSeq"
label2 = shortTitle1t[0] + " iSeq"
label3 = shortTitle2t[0] + " MiSeq"
label4 = shortTitle2t[0] + " iSeq"
label5 = shortTitle3t[0] + " MiSeq"
label6 = shortTitle3t[0] + " iSeq"
label7 = shortTitle4t[0] + " MiSeq"
label8 = shortTitle4t[0] + " iSeq"
label9 = shortTitle5t[0] + " MiSeq"
label10 = shortTitle5t[0] + " iSeq"
label11 = shortTitle6t[0] + " MiSeq"
label12 = shortTitle6t[0] + " iSeq"
label13 = shortTitle7t[0] + " MiSeq"
label14 = shortTitle7t[0] + " iSeq"
label15 = shortTitle8t[0] + " MiSeq"
label16 = shortTitle8t[0] + " iSeq"
## A single plot in the subplots. Padding of 15% on bottom margin and 10% for the other three margins.
fig, axes = plt.subplots(nrows=1, ncols=1, sharex=True, sharey=True, figsize=(14,8.5), gridspec_kw=dict(left=0.1, right=0.9, bottom=0.15, top=0.9))
## Plot Genome Coverage as line plot
axes.scatter(snpCoords1, snpDepth1, label=label1, marker='.', c=colors[0], s=100)
axes.scatter(snpCoords2, snpDepth2, label=label2, marker='+', c=colors[0], s=85)
axes.scatter(snpCoords3, snpDepth3, label=label3, marker='.', c=colors[1], s=100)
axes.scatter(snpCoords4, snpDepth4, label=label4, marker='+', c=colors[1], s=85)
axes.scatter(snpCoords5, snpDepth5, label=label5, marker='.', c=colors[2], s=100)
axes.scatter(snpCoords6, snpDepth6, label=label6, marker='+', c=colors[2], s=85)
axes.scatter(snpCoords7, snpDepth7, label=label7, marker='.', c=colors[3], s=100)
axes.scatter(snpCoords8, snpDepth8, label=label8, marker='+', c=colors[3], s=85)
axes.scatter(snpCoords9, snpDepth9, label=label9, marker='.', c=colors[4], s=100)
axes.scatter(snpCoords10, snpDepth10, label=label10, marker='+', c=colors[4], s=85)
axes.scatter(snpCoords11, snpDepth11, label=label11, marker='.', c=colors[5], s=100)
axes.scatter(snpCoords12, snpDepth12, label=label12, marker='+', c=colors[5], s=85)
axes.scatter(snpCoords13, snpDepth13, label=label13, marker='.', c=colors[6], s=100)
axes.scatter(snpCoords14, snpDepth14, label=label14, marker='+', c=colors[6], s=85)
axes.scatter(snpCoords15, snpDepth15, label=label15, marker='.', c=colors[7], s=100)
axes.scatter(snpCoords16, snpDepth16, label=label16, marker='+', c=colors[7], s=85)
axes.legend()
axes.set_xticks(myXticks, myXticks, rotation='vertical', size=14)
axes.set_yticks(myYticks, myYticks, size=14)
#axes.set_title("SNPs of " + shortTitle1t[0] + ", " + shortTitle2t[0] + ", " + shortTitle3t[0] + ", " + shortTitle4t[0] + ", " + shortTitle5t[0] + ", and " + shortTitle6t[0], size=16)
axes.set_title("SNPs of MiSeq and iSeq SARS-CoV-2 Samples", size=28)
axes.set_xlabel('Reference Genome, MN908947, Coordinates', size=15)
axes.set_ylabel('Coverage (X) at Position', size=15)
#axes.margins(0.2)
fig.savefig('/scicomp/home-pure/ydn3/test_Python3.9.1/test_Biopython/rawSNP_w' + '_' + shortTitle1t[0] + '_' + shortTitle2t[0] + '_' + shortTitle3t[0] + '_' + shortTitle4t[0] + '_' + shortTitle5t[0] + '_' + shortTitle6t[0] + '_' + shortTitle7t[0] + '_and_' + shortTitle8t[0] + '_to_MN908947.png')