Mercurial > repos > yufei-luo > s_mart

comparison SMART/bacteriaRegulatoryRegion_Detection/writeResToHTML.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #! /usr/bin/env python
2
3 import optparse, os, shutil
4 from optparse import OptionParser
5
6
7 def image(text, url):
8 return "<center>%s</center><img src='%s'>" % (text, url)
9
10
11 def __main__():
12 description = "Write all results in one HTML file."
13 parser = OptionParser(description = description)
14 parser.add_option("", "--input1Gff1", dest="input1Gff3_1", action="store", type="string", help="First gff3 result in the first analyse.(TRANS detection)")
15 parser.add_option("", "--input1Gff2", dest="input1Gff3_2", action="store", type="string", help="Second gff3 result in the first analyse. (TRANS detection)")
16 parser.add_option("", "--input1PNG1", dest="input1PNG1", action="store", type="string", help="PNG (getSize) result in the first analyse. (TRANS detection)")
17 parser.add_option("", "--input1PNG2", dest="input1PNG2", action="store",type="string", help="PNG (plot) result in the first analyse. (TRANS detection)")
18 parser.add_option("", "--input2Gff1", dest="input2Gff3_1", action="store", type="string", help="First gff3 result in the second analyse. (ANTISENSE detection)")
19 parser.add_option("", "--input2Gff2", dest="input2Gff3_2", action="store", type="string", help="Second gff3 result in the second analyse. (ANTISENSE detection)")
20 parser.add_option("", "--input2PNG1", dest="input2PNG1", action="store", type="string", help="PNG (getSize) result in the second analyse. (ANTISENSE detection)")
21 parser.add_option("", "--input2PNG2", dest="input2PNG2", action="store", type="string", help="PNG (plot) result in the second analyse. (ANTISENSE detection)")
22 parser.add_option("", "--input3Gff1", dest="input3Gff3_1", action="store", type="string", help="First gff3 result in the third analyse. (CIS detection)")
23 parser.add_option("", "--input3Gff2", dest="input3Gff3_2", action="store", type="string", help="Second gff3 result in the third analyse. (CIS detection)")
24 parser.add_option("", "--input3PNG1", dest="input3PNG1", action="store", type="string", help="PNG (getSize) result in the third analyse. (CIS detection)")
25 parser.add_option("", "--input3PNG2", dest="input3PNG2", action="store", type="string", help="PNG (plot) result in the third analyse. (CIS detection)")
26 parser.add_option("", "--outHTML", dest="outHTML", action="store", type="string", help="An HTML output.")
27 parser.add_option("", "--outImgDir", dest="imgDir", action="store", type="string", help="Copy all result images into imgDir, for Galaxy option.")
28 (options, args) = parser.parse_args()
29
30
31 if not os.path.exists(options.imgDir):
32 os.makedirs(options.imgDir)
33
34 shutil.copy(options.input1PNG1, options.imgDir)
35 shutil.copy(options.input1PNG2, options.imgDir)
36 shutil.copy(options.input2PNG1, options.imgDir)
37 shutil.copy(options.input2PNG2, options.imgDir)
38 shutil.copy(options.input3PNG1, options.imgDir)
39 shutil.copy(options.input3PNG2, options.imgDir)
40
41
42 outfile=open(options.outHTML, "w")
43 #print >>outfile, "<html><head><title>The results for ncRNAs detections.</title></head><body>"
44 print >>outfile, "<h1><center>The results for ncRNAs detections.</center></h1>"
45
46 #write results for the first analysis
47 print >>outfile, "<B><center><font color=red size=4>The results of intergenic sRNAs detection.(TRANS)</font></center></B>"
48 print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>"
49 input1Gff1 = open(options.input1Gff3_1, "r")
50 lines = input1Gff1.readlines()
51 input1Gff1.close()
52 for line in lines:
53 print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
54 print >>outfile, "<p>"
55 print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>"
56 input1Gff2 = open(options.input1Gff3_2, "r")
57 lines = input1Gff2.readlines()
58 input1Gff2.close()
59 for line in lines:
60 print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
61 print >>outfile, "<p>"
62 img_input1PNG1 = os.path.basename(options.input1PNG1)
63 image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input1PNG1)
64 print >>outfile, "%s" % image1
65 print >>outfile, "<p>"
66 img_input1PNG2 = os.path.basename(options.input1PNG2)
67 image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input1PNG2)
68 print >>outfile, "%s" % image2
69 print >>outfile, "<BR><p>"
70
71
72 #write results for the second analysis
73 print >>outfile, "<B><center><font color=red size=4>The results of asRNAs detection.(ANTISENSE)</font></center></B>"
74 print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>"
75 input2Gff1 = open(options.input2Gff3_1, "r")
76 lines = input2Gff1.readlines()
77 input2Gff1.close()
78 for line in lines:
79 print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
80 print >>outfile, "<p>"
81 print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>"
82 input2Gff2 = open(options.input2Gff3_2, "r")
83 lines = input2Gff2.readlines()
84 input2Gff2.close()
85 for line in lines:
86 print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
87 print >>outfile, "<p>"
88 img_input2PNG1 = os.path.basename(options.input2PNG1)
89 image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input2PNG1)
90 print >>outfile, "%s" % image1
91 print >>outfile, "<p>"
92 img_input2PNG2 = os.path.basename(options.input2PNG2)
93 image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input2PNG2)
94 print >>outfile, "%s" % image2
95 print >>outfile, "<BR><p>"
96
97
98 #write results for the third analysis
99 print >>outfile, "<B><center><font color=red size=4>The results of long 5'UTRs detection.(CIS)</font></center></B>"
100 print >>outfile, "<center><strong>The results of comparison to already known ncRNA to validate some candidates.</strong></center><p>"
101 input3Gff1 = open(options.input3Gff3_1, "r")
102 lines = input3Gff1.readlines()
103 input3Gff1.close()
104 for line in lines:
105 print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
106 print >>outfile, "<p>"
107 print >>outfile, "<center><strong>The results of comparison to already known ncRNA to see which ncRNAs are not detected.</strong></center><p>"
108 input3Gff2 = open(options.input3Gff3_2, "r")
109 lines = input3Gff2.readlines()
110 input3Gff2.close()
111 for line in lines:
112 print >>outfile, "<font size=2><span style=line-height:3px>%s</span></font><p>" % line
113 print >>outfile, "<p>"
114 img_input3PNG1 = os.path.basename(options.input3PNG1)
115 image1=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input3PNG1)
116 print >>outfile, "%s" % image1
117 print >>outfile, "<p>"
118 img_input3PNG2 = os.path.basename(options.input3PNG2)
119 image2=image("<strong>Resulting image : get the candidates sizes distribution.</strong>", img_input3PNG2)
120 print >>outfile, "%s" % image2
121 print >>outfile, "<BR><p>"
122
123
124 if __name__=="__main__": __main__()