annotate linear_genome_plot.py @ 4:318248986ee7 draft

planemo upload commit 4c7a6921e41a04d27f3ac202732bb5fb86801904-dirty
author cpt
date Fri, 28 Jun 2024 04:16:12 +0000
parents e923c686ead9
children
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1
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1 #!/usr/bin/env python
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2 from Bio import SeqIO
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3 from dna_features_viewer import BiopythonTranslator, GraphicRecord
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4 from matplotlib import rc_context
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5 import matplotlib
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6 import matplotlib.pyplot as plt
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7 from itertools import cycle
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8 import re
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9 import sys
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10 import argparse
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11
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12
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13 class CPTTranslator(BiopythonTranslator):
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14 """
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15 This is a customized translator from the dna_features_viewer module to fit Galaxy
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16 """
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17
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18 global custom_feature_colors
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19 global box_status
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20 global label_fields
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21 global custom_name_colors
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22 global ignored_features_types
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23 global ignored_gene_labels
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24 global ignored_feature_labels
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25
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26 def compute_feature_color(self, feature):
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27 if feature.type == "CDS":
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28 if "product" in feature.qualifiers:
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29 color_specific = any(
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30 re.search(
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31 ("(\\b" + str(item) + "\\b)"), feature.qualifiers["product"][0]
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32 )
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33 for item in custom_name_colors.keys()
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34 ) or any(
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35 re.search((item), feature.qualifiers["product"][0])
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36 for item in custom_name_colors.keys()
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37 )
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38 if color_specific:
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39 try:
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40 return custom_name_colors[feature.qualifiers["product"][0]]
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41 except KeyError:
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42 for item in custom_name_colors.keys():
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43 if item in feature.qualifiers["product"][0]:
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44 custom_name_colors[
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45 feature.qualifiers["product"][0]
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46 ] = custom_name_colors[item]
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47 return custom_name_colors[
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48 feature.qualifiers["product"][0]
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49 ]
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50 # print(feature.qualifiers["product"][0])
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51 else:
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52 try:
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53 return custom_feature_colors[feature.type]
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54 except KeyError:
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55 return BiopythonTranslator.compute_feature_color(self, feature)
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56 else:
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57 if feature.type not in ignored_features_types:
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58 try:
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59 return custom_feature_colors[feature.type]
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60 except KeyError:
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61 return BiopythonTranslator.compute_feature_color(self, feature)
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62
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63 def compute_feature_label(self, feature): # remove the chop_blocks
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64 self.label_fields = label_fields
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65 if feature.type == "CDS":
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66 if "product" in feature.qualifiers:
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67 if ignored_gene_labels: # product name drop
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68 verify_chops = any(
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69 re.search(
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70 ("(\\b" + str(item) + "\\b)"),
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71 feature.qualifiers["product"][0],
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72 )
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73 for item in ignored_gene_labels
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74 ) or any(
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75 re.search((item), feature.qualifiers["product"][0])
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76 for item in ignored_gene_labels
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77 )
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78 if verify_chops:
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79 return None
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80 else:
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81 return BiopythonTranslator.compute_feature_label(self, feature)
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82 else:
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83 return BiopythonTranslator.compute_feature_label(self, feature)
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84 elif feature.type in ignored_feature_labels:
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85 return None
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86 else:
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87 return BiopythonTranslator.compute_feature_label(self, feature)
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88
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89 def compute_filtered_features(self, features):
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90 return [
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91 feature
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92 for feature in features
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93 if feature.type not in ignored_features_types
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94 ]
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95
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96 def compute_feature_legend_text(self, feature):
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97 return feature.type
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98
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99 def compute_feature_box_color(self, feature):
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100 if feature.type == "CDS":
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101 return "white"
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102
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103 def compute_feature_label_link_color(self, feature):
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104 return "black"
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105
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106 def compute_feature_box_linewidth(self, feature):
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107 if box_status:
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108 return 0.5
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109 else:
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110 return 0
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111
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112
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113 def parse_gbk(file):
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114 """simple function to parse out the feature information AND products"""
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115
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116 record = SeqIO.read(file, "genbank")
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117 count = 0
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118 feature_types = {}
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119 product_names = []
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120 for feat in record.features:
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121 if feat.type not in feature_types:
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122 feature_types[feat.type] = 1
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123 else:
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124 feature_types[feat.type] += 1
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125 if "product" in feat.qualifiers:
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126 product_names.append(feat.qualifiers["product"][0])
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127
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128 return feature_types, product_names, record
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129
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130
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131 if __name__ == "__main__":
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132 parser = argparse.ArgumentParser(description="Linear Genome Plot")
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133 # Input and Parameters
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134 parser.add_argument(
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135 "input_file", type=argparse.FileType("r"), help="genbank or gff3 file"
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136 )
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137 parser.add_argument("--plot_width", type=int, default=20)
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138 # parser.add_argument("--plot_height",type=int,default=4)
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139 parser.add_argument(
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140 "--title", type=str, default="genome plot"
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141 ) # NEED TO ADD TO XML
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142 parser.add_argument(
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143 "--common_features_excluded", default="", help="common features to be excluded"
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144 )
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145 parser.add_argument(
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146 "--features_excluded",
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147 default="",
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148 help="features to be excluded from plot, separate by commas",
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149 )
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150 parser.add_argument(
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151 "--common_ignore_feature_labels",
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152 default="",
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153 help="common feature labels to be excluded",
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154 )
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155 parser.add_argument(
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156 "--ignored_feature_labels",
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157 default="",
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158 help="ignore labeling of specific features",
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159 )
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160 parser.add_argument(
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161 "--common_ignore_product_labels",
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162 default="",
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163 help="common product names to not label",
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164 )
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165 parser.add_argument(
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166 "--ignore_labeling",
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167 default="",
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168 help="labeling for specific products to ignore, separate by commas",
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169 )
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170 parser.add_argument(
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171 "--feature_label_order",
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172 default="locus_tag",
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173 help="label order, where the first choice is the first feature listed to pull name labels from",
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174 ) # NEED TO ADD TO XML
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175 parser.add_argument(
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176 "--label_box",
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177 action="store_true",
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178 help="Use to have label box around feature labels",
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179 )
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180 parser.add_argument(
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181 "--label_algo",
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182 action="store_true",
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183 help="use dna features spacing algo for label placement (in or above feature)",
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184 )
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185 # parser.add_argument("--level_offset",type=int,default=0,help="All features and annotations will be pushed up by the input amount. Useful for when plotting several sets of features successively on the same axis.") # Will exclude for now
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186 # parser.add_argument("--custom_region",action="store_true",help="cropped region for plot")
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187 parser.add_argument("--sz", type=int, help="beginning location for crop")
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188 parser.add_argument("--ez", type=int, help="end location for crop")
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189 parser.add_argument("--st", type=int, help="start site of translation")
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190 parser.add_argument("--et", type=int, help="end site of translation")
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191 parser.add_argument(
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192 "--translation_on", action="store_true", help="plot the translation sub-axis"
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193 )
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194 parser.add_argument(
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195 "--feature_id",
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196 nargs="*",
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197 action="append",
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198 help="feature label to have custom color",
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199 ) # NEED TO ADD TO XML
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200 parser.add_argument(
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201 "--feature_id_color",
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202 nargs="*",
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203 action="append",
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204 help="feature's accompanying color",
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205 )
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206 parser.add_argument(
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207 "--gene_id",
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208 nargs="*",
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209 action="append",
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210 help="gene/cds label to have custom color",
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211 )
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212 parser.add_argument(
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213 "--gene_id_color",
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214 nargs="*",
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215 action="append",
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216 help="gene/cds's accompanying color",
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217 )
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218 parser.add_argument("--multiline", action="store_true", help="Plot multiline plot")
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219 parser.add_argument(
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220 "--nucl_per_line", type=int, help="nucleotides per line of multiline"
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221 )
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222 # Output
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223 parser.add_argument(
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224 "--file_stats",
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225 type=argparse.FileType("w"),
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226 default="out_stats.txt",
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227 help="output stat file",
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228 )
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229 # parser.add_argument("--tmp_img",dest="tmp_img",type=argparse.FileType("wb"),default="out_tmp.svg")
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230 parser.add_argument(
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231 "--out_img",
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232 dest="out_img",
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233 type=argparse.FileType("wb"),
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234 default="out_img.svg",
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235 help="svg genome plot",
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236 )
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237 args = parser.parse_args()
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238
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239 ## Part I ; Parse and send output of features count and the list of product names
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240 feature_counts, products, genome = parse_gbk(args.input_file)
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241 with args.file_stats as f:
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242 f.writelines("---::: FILE BREAKDOWN :::---\n\n")
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243 f.writelines("------::: Feature Count :::------\n")
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244 for feature, count in feature_counts.items():
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245 f.writelines(f"Feature: {feature} ::::: Count: {count}\n")
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246 f.writelines("------::: Product Names :::------\n")
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247 if products != []:
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248 for product in products:
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249 f.writelines(f"Product Name: {product}\n")
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250 else:
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251 f.writelines("No Annotated Product Names Found")
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252
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253 ## Part II ; Prep Global Variables
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254 ## Make K:V pairs for Feature Colors
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255 if args.label_box:
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256 box_status = True
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257 else:
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258 box_status = False
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259
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260 if args.feature_id:
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261 feature_ids = [f for listed_obj in args.feature_id for f in listed_obj]
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262 feature_ids_colors = [
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263 f for listed_obj in args.feature_id_color for f in listed_obj
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264 ]
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265 custom_feature_colors = dict(zip(feature_ids, feature_ids_colors))
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266 else:
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267 custom_feature_colors = {}
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268
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269 ## Make K:V pairs for Name Colors (as above)
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270 if args.gene_id:
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271 gene_ids = [g for listed_obj in args.gene_id for g in listed_obj]
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272 gene_ids_colors = [g for listed_obj in args.gene_id_color for g in listed_obj]
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273 custom_name_colors = dict(zip(gene_ids, gene_ids_colors))
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274 else:
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275 custom_name_colors = {}
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276
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277 ## Ignored Features
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278 # ignored_features_types = str.split(args.features_excluded,",")
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279 if args.common_features_excluded:
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280 ignored_features_types = str.split(args.common_features_excluded, ",")
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281 if args.features_excluded:
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282 ignored_features_types += str.split(args.features_excluded, ",")
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283 elif args.features_excluded:
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284 ignored_features_types = str.split(args.features_excluded, ",")
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285 else:
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286 ignored_features_types = False
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287
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288 print(ignored_features_types)
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289
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290 ## product labels
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291 if args.common_ignore_product_labels:
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292 ignored_gene_labels = str.split(args.common_ignore_product_labels, ",")
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293 if args.ignore_labeling:
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294 ignored_gene_labels += str.split(args.ignore_labeling, ",")
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295 elif args.ignore_labeling:
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296 ignored_gene_labels = str.split(args.ignore_labeling, ",")
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297 else:
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298 ignored_gene_labels = False
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299
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300 print(ignored_gene_labels)
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301
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302 if args.feature_label_order != [""]:
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303 label_fields = str.split(args.feature_label_order, ",")
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304
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305 # if ignored_gene_labels == ['']:
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306 # ignored_gene_labels = False
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307
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308 ## Ignored Labeling
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309 if args.common_ignore_feature_labels:
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310 ignored_feature_labels = str.split(args.common_ignore_feature_labels, ",")
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311 if args.ignored_feature_labels:
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312 ignored_feature_labels += str.split(args.ignored_feature_labels, ",")
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313 elif args.ignored_feature_labels:
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314 ignored_feature_labels = str.split(args.ignored_feature_labels, ",")
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315 else:
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316 ignored_feature_labels = False
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317
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318 print(ignored_feature_labels)
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319 ## Print Statements for Debugging
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320 # print(custom_feature_colors)
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321 # print(custom_name_colors)
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322 # print(ignored_features_types)
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323 # print(ignored_gene_labels)
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324 # print(label_fields)
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325
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326 ## Part III ; PLOT
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327 # Housekeeping
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328 rc_context(
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329 {
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330 "font.family": ["monospace"],
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331 }
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332 ) # courier-like
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333 matplotlib.use("Agg") # I think this has to be used...
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334
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335 if args.label_algo:
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336 lab_algo = True
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337 else:
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338 lab_algo = False
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339
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340 translator = CPTTranslator()
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341 graphic_record = translator.translate_record(genome)
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342
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343 with open("tmp.svg", "wb") as img:
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344 img.truncate(0)
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345 img.close()
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346
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347 if (
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348 args.sz and not args.multiline
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349 ): # if user is wanting to look at a subset region of the genome
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350 zoom_start, zoom_end = args.sz, args.ez
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351 cropped = graphic_record.crop((zoom_start, zoom_end))
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352 ax, _ = cropped.plot(
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353 figure_width=args.plot_width, annotate_inline=lab_algo, figure_height=None
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354 )
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355 if args.translation_on:
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356 crop_seq = (args.st - 1, args.et)
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357 cropped.plot_translation(
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358 ax,
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359 location=crop_seq,
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360 fontdict={"size": 8, "weight": "bold"},
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361 y_offset=1,
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362 )
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363 ax.set_title(args.title)
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364 # Galaxy specific shenanigans
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365 tmp_fig = "./tmp.svg"
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366 plt.savefig(tmp_fig)
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367 plt.close()
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368 elif args.multiline:
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369 if args.sz:
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370 zoom_start, zoom_end = args.sz, args.ez
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371 else:
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372 zoom_start, zoom_end = 1, graphic_record.sequence_length
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373 cropped = graphic_record.crop((zoom_start, zoom_end))
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374 ax, _ = cropped.plot_on_multiple_lines(
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375 figure_width=args.plot_width,
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376 annotate_inline=lab_algo,
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377 figure_height=None,
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378 nucl_per_line=args.nucl_per_line,
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379 plot_sequence=False,
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380 )
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381 # ax.set_title(args.title)
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382 tmp_fig = "./tmp.svg"
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383 plt.savefig(tmp_fig)
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384 plt.close()
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385 else:
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386 ax, _ = graphic_record.plot(
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387 figure_width=args.plot_width, annotate_inline=lab_algo
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388 )
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389 ax.set_title(args.title)
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390 tmp_fig = "./tmp.svg"
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391 # Galaxy specific shenanigans
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392 plt.savefig(tmp_fig)
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393 plt.close()
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394 with open("tmp.svg", "rb") as img:
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395 for line in img:
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396 args.out_img.write(line)