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