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Copy pathCurrito3.1_Images_PLASMID.py
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Currito3.1_Images_PLASMID.py
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from PIL import Image
from PIL import ImageFont
from PIL import ImageDraw
import sys, getopt
def main(argv):
InputImage1 = ""
InputImage2 = ""
InputImage3 = ""
PreStatisticsFile_1 = ""
PreStatisticsFile_2 = ""
PreStatisticsFile_3 = ""
OutputPathName = ""
TargetID = ""
SampleName = ""
try:
opts, args = getopt.getopt(argv,"i:j:k:a:b:c:o:s:w:",["InputImage1=","InputImage2=","InputImage3=","PreStatisticsFile_1=","PreStatisticsFile_2=","PreStatisticsFile_3=","OutputPathName=","TargetID=", "SampleName="])
except getopt.GetoptError:
print ('Images_.py -i <InputImage1> -j <nputImage2> -k <InputImage3> -a <PreStatisticsFile_1> -b <PreStatisticsFile_2> -c <PreStatisticsFile_3> -o <OutputPathName> -s <TargetID> -w <SampleName>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print ('Images_.py -i <InputImage1> -j <InputImage2> -k <InputImage3> -a <PreStatisticsFile_1> -b <PreStatisticsFile_2> -c <PreStatisticsFile_3> -o <OutputPathName> -s <TargetID> -w <SampleName>' )
sys.exit()
elif opt in ("-i", "-InputImage1"):
InputImage1 = arg
elif opt in ("-j", "-InputImage2"):
InputImage2 = arg
elif opt in ("-k", "-InputImage3"):
InputImage3 = arg
elif opt in ("-a", "-PreStatisticsFile_1"):
PreStatisticsFile_1 = arg
elif opt in ("-b", "-PreStatisticsFile_2"):
PreStatisticsFile_2 = arg
elif opt in ("-c", "-PreStatisticsFile_3"):
PreStatisticsFile_3 = arg
elif opt in ("-o", "-OutputPathName"):
OutputPathName = arg
elif opt in ("-s", "-TargetID"):
TargetID = arg
elif opt in ("-w", "-SampleName"):
SampleName = arg
print ('Input image 1 is : ', InputImage1)
print ('Input image 2 is : ', InputImage2)
print ('Input image 3 is : ', InputImage3)
print ('Input PreStatisticsFile_1 is : ',PreStatisticsFile_1)
print ('Input PreStatisticsFile_2 is : ',PreStatisticsFile_2)
print ('Input PreStatisticsFile_3 is : ',PreStatisticsFile_3)
print ('Output path is : ', OutputPathName)
print ('TargetID is : ', TargetID)
InputPrestatistics_1 = open(PreStatisticsFile_1)
InputPrestatistics_2 = open(PreStatisticsFile_2)
InputPrestatistics_3 = open(PreStatisticsFile_3)
subjectTitle_1 = ""
subjectTitle_2 = ""
subjectTitle_3 = ""
tempstring = "temp"
tempstring = InputPrestatistics_1.readline()
tempstring = InputPrestatistics_1.readline()
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
subjectTitle_1 = rowlist[2]
tempstring = "temp"
tempstring = InputPrestatistics_2.readline()
tempstring = InputPrestatistics_2.readline()
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
subjectTitle_2 = rowlist[2]
tempstring = "temp"
tempstring = InputPrestatistics_3.readline()
tempstring = InputPrestatistics_3.readline()
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
subjectTitle_3 = rowlist[2]
try:
Image1 = Image.open(InputImage1)
Image2 = Image.open(InputImage2)
Image3 = Image.open(InputImage3)
except:
print("Unable to load image")
print ("The original format, the size and the original mode of Image 1 are: ")
print(Image1.format, Image1.size, Image1.mode)
print ("The original format, the size and the original mode of Image 2 are: ")
print(Image2.format, Image2.size, Image2.mode)
print ("The original format, the size and the original mode of Image 3 are: ")
print(Image3.format, Image3.size, Image3.mode)
(width1, height1) = Image1.size
(width2, height2) = Image2.size
(width3, height3) = Image3.size
result_width = width1 + width2
result_height = max(height1, height2)
print(result_width)
print(result_height)
result = Image.new('RGB', (result_width, result_height))
result.paste(im=Image1, box=(0, 0))
result.paste(im=Image2, box=(width1, 0))
result2_height = result_height + height3
result2 = Image.new('RGB', (result_width, result2_height), color=(255,255,255,0))
result2.paste(im=result, box=(0,0))
result2.paste(im=Image3, box=(0, result_height))
draw = ImageDraw.Draw(result2)
font = ImageFont.truetype("arial.ttf", 40)
draw.text((1450, 1500),"SAMPLE ID:" + TargetID + " \n" + "SAMPLE NAME: " + SampleName,(0, 0, 0),font=font)
draw.text((1450, 1650),"a) Circular plot showing BLAST alignments of sample sequenced fragments against the",(0, 0, 0),font=font)
draw.text((1450, 1700)," first candidate reference plasmid.",(0, 0, 0),font=font)
draw.text((1450, 1750)," First candidate title:",(0, 0, 0),font=font)
draw.text((1450, 1800)," " + subjectTitle_1 + ".",(0, 0, 0),font=font)
draw.text((1450, 1900),"b) Circular plot showing BLAST alignments of sample sequenced fragments against the",(0, 0, 0),font=font)
draw.text((1450, 1950)," second candidate reference plasmid.",(0, 0, 0),font=font)
draw.text((1450, 2000)," Second candidate title:",(0, 0, 0),font=font)
draw.text((1450, 2050)," " + subjectTitle_2 + ".",(0, 0, 0),font=font)
draw.text((1450, 2150),"c) Circular plot showing BLAST alignments of sample sequenced fragments against the",(0, 0, 0),font=font)
draw.text((1450, 2200)," third candidate reference plasmid.",(0, 0, 0),font=font)
draw.text((1450, 2250)," Third candidate title:",(0, 0, 0),font=font)
draw.text((1450, 2300)," " + subjectTitle_3 + ".",(0, 0, 0),font=font)
draw.text((1450, 2400),"Explanation of circular plots:",(0, 0, 0),font=font)
draw.text((1450, 2450),"-Outer black circle represents the candidate reference plasmid with size",(0, 0, 0),font=font)
draw.text((1450, 2500)," indicated in basepairs (bp).",(0, 0, 0),font=font)
draw.text((1450, 2550),"-Middle blue circle shows aligned sequenced fragments obtained by complexity",(0, 0, 0),font=font)
draw.text((1450, 2600)," reduced genotyping.",(0, 0, 0),font=font)
draw.text((1450, 2650),"-Inner green / red circle shows the percentage identity of the alignments. ",(0, 0, 0),font=font)
draw.text((1450, 2700)," Values below 95% are red, values equal to or above 95% are green.",(0, 0, 0),font=font)
result2.save(OutputPathName)
result2.close()
result.close()
Image1.close()
Image2.close()
Image3.close()
InputPrestatistics_1.close()
InputPrestatistics_2.close()
InputPrestatistics_3.close()
if __name__ == "__main__":
main(sys.argv[1:])