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17
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1 import sys
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2
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3 # Read a file and return it as a list
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4 def read(path, flag):
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5 if flag == 0:
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6 with open(path) as fp:
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7 file=fp.readlines()
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8 fp.close()
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9 return file
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10
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11 if flag == 1:
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12 with open(path) as fp:
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13 file = fp.read().splitlines()
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14 fp.close()
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15 return file
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16
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17
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18 #################################################################################################
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19 def pdf_before_DE(analysis):
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20
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21 # Import FPDF class
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22 from fpdf import FPDF, fpdf
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23
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24 # Import glob module to find all the files matching a pattern
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25 import glob
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26
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27 # Image extensions
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28 if analysis=="2":
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29 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_non.png","spider_red.png","spider_non_red.png","c_logo.png","t_logo.png","c_bar.png","t_bar.png")
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30 else:
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31 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_tem.png","spider_red.png","spider_non_red.png")
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32 # This list will hold the images file names
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33 images = []
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34
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35 # Build the image list by merging the glob results (a list of files)
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36 # for each extension. We are taking images from current folder.
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37 for extension in image_extensions:
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38 images.extend(glob.glob(extension))
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39 #sys.exit(images)
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40 # Create instance of FPDF class
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41 pdf = FPDF('P', 'in', 'A4')
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42 # Add new page. Without this you cannot create the document.
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43 pdf.add_page()
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44 # Set font to Arial, 'B'old, 16 pts
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45 pdf.set_font('Arial', 'B', 20.0)
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46
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47 # Page header
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48 pdf.cell(pdf.w-0.5, 0.5, 'IsomiR Profile Report',align='C')
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49 pdf.ln(0.7)
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50 pdf.set_font('Arial','', 16.0)
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51 pdf.cell(pdf.w-0.5, 0.5, 'sRNA Length Distribution',align='C')
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52
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53 # Smaller font for image captions
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54 pdf.set_font('Arial', '', 11.0)
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55
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56 # Image caption
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57 pdf.ln(0.5)
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58
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59 yh=FPDF.get_y(pdf)
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60 pdf.image(images[0],x=0.3,w=4, h=3)
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61 pdf.image(images[1],x=4,y=yh, w=4, h=3)
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62 pdf.ln(0.3)
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63
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64 # Image caption
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65 pdf.cell(0.2)
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66 pdf.cell(3.0, 0.0, " Mapped and unmapped reads to custom precussor arm reference DB (5p and 3p arms) in Control (left)")
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67 pdf.ln(0.2)
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68 pdf.cell(0.2)
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69 pdf.cell(3.0, 0.0, " and Treated (right) groups")
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70
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71
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72 pdf.ln(0.5)
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73 h1=FPDF.get_y(pdf)
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74 pdf.image(images[2],x=1, w=6.5, h=5)
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75 h2=FPDF.get_y(pdf)
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76 FPDF.set_y(pdf,h1+0.2)
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77 pdf.set_font('Arial','', 14.0)
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78 pdf.cell(pdf.w-0.5, 0.5, 'Template and non-template IsomiRs',align='C')
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79 pdf.set_font('Arial', '', 11.0)
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80 FPDF.set_y(pdf,h2)
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81 FPDF.set_y(pdf,9.5)
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82 # Image caption
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83 pdf.cell(0.2)
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84 if analysis=="2":
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85 pdf.cell(3.0, 0.0, " Template, non-template, miRNA reference and unmapped sequences as percentage of total sRNA")
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86 else:
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87 pdf.cell(3.0, 0.0, " Template, miRNA reference and unmapped sequences as percentage of total sRNA")
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88 pdf.ln(0.2)
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89 pdf.cell(0.2)
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90 pdf.cell(3.0, 0.0, " reads in Control (left) and treated (right) groups")
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91
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92
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93
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94 pdf.add_page()
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95 pdf.set_font('Arial', 'B', 16.0)
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96 pdf.cell(pdf.w-0.5, 0.5, "Reference form and isomiR among total miRNA reads",align='C')
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97 pdf.ln(0.7)
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98 pdf.set_font('Arial', 'B', 12.0)
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99 pdf.cell(pdf.w-0.5, 0.5, "Template isomiR profile (redundant)",align='C')
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100 pdf.ln(0.5)
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101 pdf.image(images[3],x=1.5, w=5.5, h=4)
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102 pdf.ln(0.6)
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103 pdf.cell(pdf.w-0.5, 0.0, "Template isomiR profile (non-redundant)",align='C')
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104 pdf.set_font('Arial', '', 12.0)
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105 pdf.ln(0.2)
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106 pdf.image(images[4],x=1.5, w=5.5, h=4)
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107 pdf.ln(0.3)
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108 pdf.set_font('Arial', '', 11.0)
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109 pdf.cell(0.2)
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110 pdf.cell(3.0, 0.0, " * IsomiRs potentialy initiated from multiple loci")
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111
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112
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113 if analysis=="2":
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114 pdf.add_page('L')
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115
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116 pdf.set_font('Arial', 'B', 16.0)
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117 pdf.cell(pdf.w-0.5, 0.5, "Non-template IsomiRs",align='C')
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118 pdf.ln(0.5)
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119 pdf.set_font('Arial', 'B', 12.0)
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120 pdf.cell(pdf.w-0.5, 0.5, "3' Additions of reference of isomiR sequence",align='C')
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121 pdf.ln(0.7)
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122
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123 yh=FPDF.get_y(pdf)
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124 pdf.image(images[5],x=1.5,w=3.65, h=2.65)
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125 pdf.image(images[7],x=6.5,y=yh, w=3.65, h=2.65)
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126 pdf.ln(0.5)
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127 yh=FPDF.get_y(pdf)
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128 pdf.image(images[6],x=1.5,w=3.65, h=2.65)
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129 pdf.image(images[8],x=6.5,y=yh, w=3.65, h=2.65)
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130
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131 pdf.close()
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132 pdf.output('report1.pdf','F')
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133
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134
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135
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136
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137 #############################################################################################################################################################3
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138
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139 def pdf_after_DE(analysis,top):
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140
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141 # Import FPDF class
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142 from fpdf import FPDF
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143
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144 # Import glob module to find all the files matching a pattern
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145 import glob
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146
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147 # Image extensions
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148 if analysis=="2":
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149 image_extensions = ("tem.png","a2.png","non.png")
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150 else:
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151 image_extensions = ("tem.png","a2.png")
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152
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153 # This list will hold the images file names
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154 images = []
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155
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156 # Build the image list by merging the glob results (a list of files)
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157 # for each extension. We are taking images from current folder.
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158 for extension in image_extensions:
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159 images.extend(glob.glob(extension))
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160 #sys.exit(images)
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161 # Create instance of FPDF class
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162 pdf = FPDF('P', 'in', 'letter')
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163 # Add new page. Without this you cannot create the document.
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164 pdf.add_page()
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165 # Set font to Arial, 'B'old, 16 pts
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166 pdf.set_font('Arial', 'B', 16.0)
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167
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168 # Page header
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169 pdf.cell(pdf.w-0.5, 0.5, 'Differential expression of miRNAs and Isoforms',align='C')
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170 #pdf.ln(0.25)
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171
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172 pdf.ln(0.7)
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173 pdf.set_font('Arial','B', 12.0)
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174 if "tem.png" in images:
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175 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed miRNA and template isoforms',align='C')
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176 # Smaller font for image captions
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177 pdf.set_font('Arial', '', 10.0)
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178 # Image caption
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179 pdf.ln(0.4)
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180 pdf.image(images[images.index("tem.png")],x=0.8, w=7, h=8)
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181 pdf.ln(0.3)
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182 pdf.set_font('Arial','B', 12.0)
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183 else:
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184 print("WARNING: There aren't miRNAs which fullfiled these criteria" )
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185
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186 if "non.png" in images and analysis=="2":
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187 if "tem.png" in images: pdf.add_page()
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188 pdf.ln(0.7)
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189 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed non-template isomiRs',align='C')
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190 pdf.ln(0.4)
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191 pdf.image(images[images.index("non.png")],x=0.5, w=7.5, h=6.5)
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192 else:
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193 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" )
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194
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195
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196 if "a2.png" in images:
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197 if len(images)>=2: pdf.add_page()
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198 pdf.ln(0.5)
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199 pdf.cell(pdf.w-0.5, 0.5, 'Top '+top+' most differentially expressed miRNAs and isomiRs grouped by arm',align='C')
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200 pdf.ln(0.4)
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201 pdf.image(images[images.index("a2.png")],x=0.8, w=7, h=8)
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202 pdf.ln(0.3)
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203 else:
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204 print("WARNING: There aren't non-template miRNAs which fullfiled these criteria" )
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205
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206
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207 pdf.output('report2.pdf', 'F')
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208
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209
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210
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