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view SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.py @ 34:529e3e6a0954

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author m-zytnicki
date Tue, 30 Apr 2013 14:35:27 -0400
parents 94ab73e8a190
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#! /usr/bin/env python

import optparse, os, shutil
from optparse import OptionParser


def image(text, url):
	return "<center>%s</center><img src='%s'>" % (text, url)


def __main__():
	description = "Write all results in one HTML file."
	parser = OptionParser(description = description)
	parser.add_option("", "--input1Gff1", dest="input1Gff3_1", action="store", type="string", help="First gff3 result in the first analyse.(TRANS detection)")
	parser.add_option("", "--input1Gff2", dest="input1Gff3_2", action="store", type="string", help="Second gff3 result in the first analyse. (TRANS detection)")
	parser.add_option("", "--input1PNG1", dest="input1PNG1", action="store", type="string", help="PNG (getSize) result in the first analyse. (TRANS detection)")
	parser.add_option("", "--input1PNG2", dest="input1PNG2", action="store",type="string", help="PNG (plot) result in the first analyse. (TRANS detection)")	
	parser.add_option("", "--input2Gff1", dest="input2Gff3_1", action="store", type="string", help="First gff3 result in the second analyse. (ANTISENSE detection)")
	parser.add_option("", "--input2Gff2", dest="input2Gff3_2", action="store", type="string", help="Second gff3 result in the second analyse. (ANTISENSE detection)")
	parser.add_option("", "--input2PNG1", dest="input2PNG1", action="store", type="string", help="PNG (getSize) result in the second analyse. (ANTISENSE detection)")
	parser.add_option("", "--input2PNG2", dest="input2PNG2", action="store", type="string", help="PNG (plot) result in the second analyse. (ANTISENSE detection)")
	parser.add_option("", "--input3Gff1", dest="input3Gff3_1", action="store", type="string", help="First gff3 result in the third analyse. (CIS detection)")
	parser.add_option("", "--input3Gff2", dest="input3Gff3_2", action="store", type="string", help="Second gff3 result in the third analyse. (CIS detection)")
	parser.add_option("", "--input3PNG1", dest="input3PNG1", action="store", type="string", help="PNG (getSize) result in the third analyse. (CIS detection)")
	parser.add_option("", "--input3PNG2", dest="input3PNG2", action="store", type="string", help="PNG (plot) result in the third analyse. (CIS detection)")
	parser.add_option("", "--outHTML", dest="outHTML", action="store", type="string", help="An HTML output.")
	parser.add_option("", "--outImgDir", dest="imgDir", action="store", type="string", help="Copy all result images into imgDir, for Galaxy option.")
	(options, args) = parser.parse_args()


	if not os.path.exists(options.imgDir):
		os.makedirs(options.imgDir)

	shutil.copy(options.input1PNG1, options.imgDir)
	shutil.copy(options.input1PNG2, options.imgDir)
	shutil.copy(options.input2PNG1, options.imgDir)
	shutil.copy(options.input2PNG2, options.imgDir)
	shutil.copy(options.input3PNG1, options.imgDir)
	shutil.copy(options.input3PNG2, options.imgDir)
	

	outfile=open(options.outHTML, "w")
	#print >>outfile, "<html><head><title>The results for ncRNAs detections.</title></head><body>"
	print >>outfile, "<h1><center>The results for ncRNAs detections.</center></h1>"
	
	#write results for the first analysis
	print >>outfile, "<B><center><font color=red size=4>The results of intergenic sRNAs detection.(TRANS)</font></center></B>"
	print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>"
	input1Gff1 = open(options.input1Gff3_1, "r")
	lines = input1Gff1.readlines()
	input1Gff1.close()	  
	for line in lines:
		print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
	print >>outfile, "<p>"
	print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>"
	input1Gff2 = open(options.input1Gff3_2, "r")
	lines = input1Gff2.readlines()
	input1Gff2.close()	  
	for line in lines:
		print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
	print >>outfile, "<p>"
	img_input1PNG1 = os.path.basename(options.input1PNG1)
	image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input1PNG1)
	print >>outfile, "%s" % image1
	print >>outfile, "<p>"
	img_input1PNG2 = os.path.basename(options.input1PNG2)
	image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input1PNG2)
	print >>outfile, "%s" % image2
	print >>outfile, "<BR><p>"


	#write results for the second analysis
	print >>outfile, "<B><center><font color=red size=4>The results of asRNAs detection.(ANTISENSE)</font></center></B>"
	print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>"
	input2Gff1 = open(options.input2Gff3_1, "r")
	lines = input2Gff1.readlines()
	input2Gff1.close()	  
	for line in lines:
		print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
	print >>outfile, "<p>"
	print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>"
	input2Gff2 = open(options.input2Gff3_2, "r")
	lines = input2Gff2.readlines()
	input2Gff2.close()	  
	for line in lines:
		print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
	print >>outfile, "<p>"
	img_input2PNG1 = os.path.basename(options.input2PNG1)
	image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input2PNG1)
	print >>outfile, "%s" % image1
	print >>outfile, "<p>"
	img_input2PNG2 = os.path.basename(options.input2PNG2)
	image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input2PNG2)
	print >>outfile, "%s" % image2
	print >>outfile, "<BR><p>"
	
	
	#write results for the third analysis
	print >>outfile, "<B><center><font color=red size=4>The results of long 5'UTRs detection.(CIS)</font></center></B>"
	print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>"
	input3Gff1 = open(options.input3Gff3_1, "r")
	lines = input3Gff1.readlines()
	input3Gff1.close()	  
	for line in lines:
		print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
	print >>outfile, "<p>"
	print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>"
	input3Gff2 = open(options.input3Gff3_2, "r")
	lines = input3Gff2.readlines()
	input3Gff2.close()	  
	for line in lines:
		print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
	print >>outfile, "<p>"
	img_input3PNG1 = os.path.basename(options.input3PNG1)
	image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input3PNG1)
	print >>outfile, "%s" % image1
	print >>outfile, "<p>"
	img_input3PNG2 = os.path.basename(options.input3PNG2)
	image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input3PNG2)
	print >>outfile, "%s" % image2
	print >>outfile, "<BR><p>"	


if __name__=="__main__": __main__()