Mercurial > repos > cpt > cpt_fasta_charges

annotate fasta_charges.py @ 3:a39d312f95c7 draft default tip

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planemo upload commit 83c1184008f5967a8265194a4b3496042827cda1
author cpt
date Fri, 20 Sep 2024 05:36:05 +0000
parents 054f96a0d0fb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
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1 #!/usr/bin/env python
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2 import argparse
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3 from Bio import SeqIO
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4 import logging
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5
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6 logging.basicConfig(level=logging.INFO)
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7 log = logging.getLogger(name="charges")
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8
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9 HTML_HEADER = "<html><head><title>Charges Report</title></head><body>"
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10 HTML_FOOTER = "</body></html>"
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11
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12 SVG_HEADER = '<svg width="%i" height="%i" xmlns="http://www.w3.org/2000/svg">\n' # % (calcWidth, calcHeight)
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13 SVG_FOOTER = "</svg>"
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14
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15 FULL_AA = [
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16 "H",
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17 "S",
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18 "Q",
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19 "T",
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20 "N",
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21 "C",
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22 "Y",
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23 "A",
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24 "V",
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25 "I",
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26 "L",
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27 "M",
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28 "P",
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29 "F",
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30 "W",
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31 "G",
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32 "E",
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33 "R",
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34 "D",
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35 "K",
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36 ]
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37
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38
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39 def charges_html(svg, fasta, aa, fgColor, bgColor, width=120):
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40 colour_scheme = zip([x.upper() for x in aa], bgColor, fgColor)
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41 copy_colour_scheme = zip([x.upper() for x in aa], bgColor, fgColor)
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42
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43 # CSS and header styling
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44 css = """<style type="text/css">
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45 .list li { list-style: none; margin:10px }
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46 .info { float:left; width:20px }
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47 pre { font-size:1.3em }
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48 """
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49 info = '<h1>Charges</h1><h3>Legend</h3><ul class="list">'
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50 for group in colour_scheme:
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51 css += ".%s{ background: %s; color: %s}\n" % group
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52 info += '<li><span class="%s" style="padding:5px">%s</span></li>\n' % (
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53 group[0],
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54 group[0],
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55 )
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56 css += "</style>"
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57 info += "</ul>"
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58
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59 # Pre-calculate, so we can use for testing 'in'
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60 match_list = [group[0] for group in copy_colour_scheme]
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61
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62 page = ""
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63 # Parse sequences from fasta file
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64 for record in SeqIO.parse(fasta, "fasta"):
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65 page += "<pre><h3>&gt;%s %s</h3>\n" % (record.id, record.description)
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66 seq = list(str(record.seq).upper())
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67
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68 idx = 0
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69 for i in range(0, len(seq), width):
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70 line_charges = []
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71 line_residues = seq[i : i + width]
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72 line_numbers = []
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73
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74 for char in range(len(line_residues)):
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75 if line_residues[char] in "KRkr":
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76 line_charges.append("+")
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77 elif line_residues[char] in "DEde":
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78 line_charges.append("-")
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79 else:
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80 line_charges.append(" ")
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81
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82 # Could be swapped out for math with i+char...
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83 idx += 1
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84 if idx % 10 == 0:
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85 line_numbers.append("%10s" % idx)
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86
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87 # Replace with <span>
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88 for m in match_list:
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89 if line_residues[char].upper() in m:
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90 line_residues[char] = '<span class="%s">%s</span>' % (
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91 m,
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92 line_residues[char],
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93 )
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94
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95 page += "".join(line_charges) + "\n"
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96 page += "".join(line_residues) + "\n"
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97 page += "".join(line_numbers) + "\n"
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98 page += "\n"
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99 page += "</pre>"
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100 return HTML_HEADER + css + info + page + HTML_FOOTER
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101
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102
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103 def charges_svg(svg, fasta, aa, fgColor, bgColor, width=120):
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104 colour_scheme = zip([x.upper() for x in aa], bgColor, fgColor)
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105
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106 svgWidth = 1100
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107
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108 # CSS and header styling
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109 classList = []
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110 classes = '<style type="text/css">\n<![CDATA[\n'
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111
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112 defClass = ""
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113 for x in FULL_AA:
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114 addAA = True
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115 for y in aa:
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116 if x in y:
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117 addAA = False
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118 if addAA:
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119 defClass += x
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120
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121 defBox = "#ffffff"
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122 defText = "#000000"
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123
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124 for group in colour_scheme:
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125 classList.append(group[0])
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126 classes += "text.text_%s{fill: %s;}\n" % (group[0], group[2])
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127 classes += "rect.rect_%s{fill: %s; stroke: %s;}\n" % (
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128 group[0],
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129 group[1],
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130 group[1],
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131 )
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132 # info += '<li><span class="%s" style="padding:5px">%s</span></li>\n' % (group[0], group[0])
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133 if defClass != "":
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134 classes += "text.text_%s{fill: %s;}\n" % (defClass, defText)
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135 classes += "rect.rect_%s{fill: %s; stroke: %s;}\n" % (defClass, defBox, defBox)
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136 classList.append(defClass)
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137 classes += "text.info_text{white-space: pre;}\n"
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138 classes += "rect.rEven{fill: #fdfdfd; stroke: #fbfbfb;}\n"
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139 classes += "rect.rOdd{fill: #f2f2fc; stroke: #fbfbfb;}\n"
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140 classes += "]]></style>\n"
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141 body = ""
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142 groups = ""
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143 # Pre-calculate, so we can use for testing 'in'
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144
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145 match_list = aa
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146 prevIndex = -1
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147 boxLen = 0
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148 page = ""
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149 title = ""
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150
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151 yInd = 60
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152 yInc = 15
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153 seqIndent = 35
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154 idIndent = 20
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155 letterLen = 8.4375
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156 recNum = -1
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157
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158 title += (
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159 '<text x="'
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160 + str(idIndent * 0.5)
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161 + '" y="'
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162 + str(yInd)
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163 + '" style="font-weight:bold; font-size:40px">Charges</text>\n'
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164 )
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165 yInd += 2 * yInc
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166 title += (
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167 '<text x="'
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168 + str(idIndent)
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169 + '" y="'
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170 + str(yInd)
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171 + '" style="font-size:18px">Legend:</text>\n'
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172 )
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173 yInd += 2 * yInc
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174
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175 for i in range(len(classList)):
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176 title += (
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177 '<rect x="'
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178 + str(seqIndent)
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179 + '" y="'
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180 + str(yInd - yInc + 2)
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181 + '" width="'
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182 + str(len(classList[i]) * letterLen)
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183 + '" height="'
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184 + str(yInc)
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185 + '" class="rect_%s"/>\n' % classList[i]
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186 )
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187 title += (
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188 '<text x="'
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189 + str(seqIndent)
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190 + '" y="'
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parents:
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191 + str(yInd)
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parents:
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192 + '" class="text_%s" font-family="monospace" font-size="14">%s</text>\n'
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193 % (classList[i], classList[i])
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194 )
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195 yInd += yInc + 3
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196 yInd += yInc * 1.5
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197
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198 # Parse sequences from fasta file
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199 for record in SeqIO.parse(fasta, "fasta"):
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parents:
diff changeset
200
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201 recNum += 1
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parents:
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202 seqHeader = (
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parents:
diff changeset
203 '<g><text x="'
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parents:
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204 + str(idIndent)
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parents:
diff changeset
205 + '" y="'
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parents:
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206 + str(yInd)
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parents:
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207 + '" style="font-weight:bold">&gt;%s %s</text>\n'
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parents:
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208 % (record.id, record.description)
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parents:
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209 )
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210 body += seqHeader
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parents:
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211 seq = list(str(record.seq).upper())
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parents:
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212 yTop = yInd - yInc - 3
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parents:
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213 yInd += yInc
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parents:
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214 idx = 0
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parents:
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215 for i in range(0, len(seq), width):
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parents:
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216 line_charges = []
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parents:
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217 line_residues = seq[i : i + width]
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parents:
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218 line_numbers = []
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parents:
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219
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220 boxList = []
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221 groupList = []
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parents:
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222 seqList = []
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223 prevIndex = -1
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224 boxLen = 0
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225 for char in range(len(line_residues)):
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226
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227 thisInd = 0
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228 for x in match_list:
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parents:
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229
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230 if line_residues[char] in x:
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parents:
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231 break
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232 thisInd += 1
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233
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234 if thisInd == len(match_list):
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parents:
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235 thisInd = -1
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236
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237 if char != 0 and thisInd != prevIndex:
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238 boxList.append(boxLen)
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parents:
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239 seqList.append((line_residues[char - boxLen : char]))
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parents:
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240 groupList.append(prevIndex)
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241 boxLen = 0
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242 prevIndex = thisInd
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243 boxLen += 1
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244
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245 if line_residues[char] in "KRkr":
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246 line_charges.append("+")
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247 elif line_residues[char] in "DEde":
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248 line_charges.append("-")
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249 else:
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250 line_charges.append(" ")
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251
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252 # Could be swapped out for math with i+char...
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253 idx += 1
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254 if idx % 10 == 0:
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255 line_numbers.append("%10s" % idx)
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256
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257 # Replace with <span>
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258 # for m in match_list:
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259 # if line_residues[char].upper() in m:
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260 # line_residues[char] = '<span class="%s">%s</span>' % (m, line_residues[char])
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261
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262 seqList.append((line_residues[-boxLen:]))
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263 boxList.append(boxLen)
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264 groupList.append(prevIndex)
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265 # Write line charges
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266 line = "".join(line_charges)
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267 body += (
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268 '<text x="'
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269 + str(seqIndent)
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270 + '" y="'
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271 + str(yInd)
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272 + '" class="info_text" font-family="monospace" font-size="14">%s</text>\n'
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273 % line
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274 )
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275 yInd += yInc
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276 # Write sequence
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277 sumSeq = 0
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278 for i in range(len(seqList)):
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279 res = ""
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280 for sub in seqList[i]:
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281 res += sub
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282 body += (
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283 '<rect x="'
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284 + str(0.5 + seqIndent + (letterLen * sumSeq))
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285 + '" y="'
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286 + str(yInd - yInc + 2)
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287 + '" width="'
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288 + str(boxList[i] * letterLen)
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289 + '" height="'
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290 + str(yInc)
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291 + '" class="rect_%s"/>\n' % classList[groupList[i]]
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292 )
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293 body += (
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294 '<text x="'
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295 + str(seqIndent + (letterLen * sumSeq))
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296 + '" y="'
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297 + str(yInd)
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298 + '" class="text_%s" font-family="monospace" font-size="14">%s</text>\n'
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299 % (classList[groupList[i]], res)
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300 )
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301 sumSeq += len(seqList[i])
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302 yInd += yInc
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303 # Write numbers
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304 line = "".join(line_numbers) + "\n"
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305 body += (
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306 '<text x="'
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307 + str(seqIndent)
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308 + '" y="'
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309 + str(yInd)
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310 + '" class="info_text" font-size="14" font-family="monospace">%s</text>\n'
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311 % line
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312 )
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313 yInd += yInc
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314
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315 body += "</g>\n"
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316 yInd += yInc
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317 if recNum % 2 == 0:
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318 groups += (
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319 '<rect x="0" y="'
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320 + str(yTop)
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321 + '" width="'
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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322 + str(svgWidth + 1)
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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323 + '" height="'
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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324 + str(yInd - yTop)
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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325 + '" class="rEven"/>\n'
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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326 )
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327 else:
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328 groups += (
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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329 '<rect x="0" y="'
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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330 + str(yTop)
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
331 + '" width="'
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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332 + str(svgWidth + 1)
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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333 + '" height="'
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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334 + str(yInd - yTop)
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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335 + '" class="rOdd"/>\n'
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diff changeset
336 )
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337 svgHeight = yInd
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338
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339 return (
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340 (SVG_HEADER % (svgWidth, svgHeight))
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341 + title
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342 + classes
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343 + groups
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344 + body
054f96a0d0fb planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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345 + SVG_FOOTER
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346 )
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347
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348
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349 if __name__ == "__main__":
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350 parser = argparse.ArgumentParser(description="Top related genomes")
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351 parser.add_argument("--svg", action="store_true")
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352 parser.add_argument("fasta", type=argparse.FileType("r"), help="Fasta protein file")
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353 parser.add_argument("--width", type=int, help="Plot width", default=120)
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354 parser.add_argument("--aa", nargs="+")
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355 parser.add_argument("--fgColor", nargs="+")
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356 parser.add_argument("--bgColor", nargs="+")
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357
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358 args = parser.parse_args()
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359 if args.svg:
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360 print(charges_svg(**vars(args)))
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361 else:
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362 print(charges_html(**vars(args)))