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1 <tool name="plotlyblast" id="plotlyblast" version="3.0">
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2 <!--Source in git at: https://github.com/fubar2/galaxy-->
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3 <!--Created by toolfactory@galaxy.org at 25/07/2023 14:13:15 using the Galaxy Tool Factory.-->
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4 <description>Plotly plot generator</description>
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5 <requirements>
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6 <requirement type="package" version="1.5.3">pandas</requirement>
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7 <requirement type="package" version="5.9.0">plotly</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal"/>
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11 </stdio>
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12 <version_command><![CDATA[echo "3.0"]]></version_command>
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13 <command><![CDATA[python
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14 $runme
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15 --input_tab
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16 $input_tab
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17 --htmlout
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18 $htmlout
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19 --xcol
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20 "$xcol"
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21 --ycol
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22 "$ycol"
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23 --colourcol
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24 "$colourcol"
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25 --hovercol
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26 "$hovercol"
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27 --title
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28 "$title"
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29 --header
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30 "$header"]]></command>
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31 <configfiles>
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32 <configfile name="runme"><![CDATA[#raw
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33
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34 import argparse
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35 import sys
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36 import math
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37 import plotly.express as px
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38 import pandas as pd
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39 # Ross Lazarus July 2023
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40 # based on various plotly tutorials
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41 # Expects a blastn search result passed in as the first command line parameter.
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42 parser = argparse.ArgumentParser()
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43 a = parser.add_argument
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44 a('--input_tab',default='')
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45 a('--header',default='qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles')
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46 a('--htmlout',default="test_run.html")
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47 a('--xcol',default='gaps')
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48 a('--ycol',default='qseq')
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49 a('--colourcol',default='qaccver')
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50 a('--hovercol',default='qseq')
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51 a('--title',default='test blast plot of mismatch by bitscore coloured by qaccver ')
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52 args = parser.parse_args()
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53 df = pd.read_csv(args.input_tab, sep='\t')
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54 NCOLS = df.columns.size
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55 MAXLEN = 40 # tricky way to truncate long axis tickmarks
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56 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
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57 if len(args.header.strip()) > 0:
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58 newcols = args.header.split(',')
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59 if len(newcols) == NCOLS:
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60 df.columns = newcols
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61 else:
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62 sys.stderr.write('#### Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns - using col1,...coln' % (args.header, len(newcols), NCOLS))
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63 df.columns = defaultcols
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64 else:
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65 df.columns = defaultcols
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66 df['evalue'] = [-math.log(x) for x in df['evalue']] # convert so large values reflect statistical surprise
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67 if len(args.colourcol.strip()) == 0:
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68 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
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69 else:
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70 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
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71 if args.title:
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72 ftitle=dict(text=args.title, font=dict(size=50))
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73 fig.update_layout(title=ftitle)
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74 for scatter in fig.data:
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75 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
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76 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
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77 fig.write_html(args.htmlout)
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78
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79 #end raw]]></configfile>
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80 </configfiles>
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81 <inputs>
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82 <param name="input_tab" type="data" optional="false" label="Tabular input file to plot" help="" format="tabular" multiple="false"/>
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83 <param name="xcol" type="text" value="mismatch" label="x axis for plat" help=""/>
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84 <param name="ycol" type="text" value="bitscore" label="y axis for plot" help=""/>
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85 <param name="colourcol" type="text" value="qaccver" label="column containing a groupable variable for colour. Default none." help="Adds a legend so choose wisely "/>
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86 <param name="hovercol" type="text" value="qseq" label="columname for hover string" help=""/>
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87 <param name="title" type="text" value="Test title default" label="Title for the plot" help=""/>
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88 <param name="header" type="text" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" label="Use this comma delimited list of column header names for this tabular file__sq__s columns" help="Default for Galaxy blast outputs with 25 columns."/>
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89 </inputs>
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90 <outputs>
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91 <data name="htmlout" format="html" label="htmlout" hidden="false"/>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/>
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96 <param name="input_tab" value="input_tab_sample"/>
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97 <param name="xcol" value="mismatch"/>
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98 <param name="ycol" value="bitscore"/>
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99 <param name="colourcol" value="qaccver"/>
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100 <param name="hovercol" value="qseq"/>
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101 <param name="title" value="Test title default"/>
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102 <param name="header" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles"/>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106
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107 This is a specialised version of a generic tabular file plotter tool plotlytabular
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108
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109
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110
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111 .. class:: warningmark
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112
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113
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114
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115 Long strings in x and y tickmarks WILL BE TRUNCATED if they are too long - ".." is added to indicate truncation - otherwise some plots are squished.
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116
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117 The evalues WILL BE CONVERTED as -log10(evalue) so they are scaled in a way that doesn't confuse plotly.express with the tiny values.
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118
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119
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120
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121 ----
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122
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123
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124
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125 The main reason to run this tool is to have an interactive hover text specified so it appears when hovering over each data point to supply useful information.
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126
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127
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128
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129 Assumes you want a hover display for an interactive plot to be informative
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130
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131
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132
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133 Column names are auto-generated as col1,...coln unless a comma separated list of column names is supplied as the header parameter.
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134
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135
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136
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137 For example, using a Galaxy blastn output with 25 columns, the following comma delimited string supplied as the "header" parameter will match the names of each column.
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138
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139 qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles
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140
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141
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142
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143 When a header is supplied, the xcol and other column names must match one of those supplied column names.
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144
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145 So for example, xcol = "qaccver" for the blastn header example rather than xcol = "col1" when no header is supplied.
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146
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147
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148
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149 Relies on Plotly python code released under the MIT licence: https://github.com/plotly/plotly.py/blob/master/LICENSE.txt
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150
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151
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152
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153 ------
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154
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155
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156 Script::
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157
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158 import argparse
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159 import sys
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160 import math
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161 import plotly.express as px
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162 import pandas as pd
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163 # Ross Lazarus July 2023
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164 # based on various plotly tutorials
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165 # Expects a blastn search result passed in as the first command line parameter.
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166 parser = argparse.ArgumentParser()
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167 a = parser.add_argument
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168 a('--input_tab',default='')
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169 a('--header',default='qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles')
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170 a('--htmlout',default="test_run.html")
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171 a('--xcol',default='gaps')
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172 a('--ycol',default='qseq')
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173 a('--colourcol',default='qaccver')
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174 a('--hovercol',default='qseq')
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175 a('--title',default='test blast plot of mismatch by bitscore coloured by qaccver ')
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176 args = parser.parse_args()
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177 df = pd.read_csv(args.input_tab, sep='\t')
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178 NCOLS = df.columns.size
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179 MAXLEN = 40 # tricky way to truncate long axis tickmarks
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180 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
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181 if len(args.header.strip()) > 0:
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182 newcols = args.header.split(',')
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183 if len(newcols) == NCOLS:
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184 df.columns = newcols
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185 else:
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186 sys.stderr.write('#### Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns - using col1,...coln' % (args.header, len(newcols), NCOLS))
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187 df.columns = defaultcols
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188 else:
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189 df.columns = defaultcols
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190 df['evalue'] = [-math.log(x) for x in df['evalue']] # convert so large values reflect statistical surprise
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191 if len(args.colourcol.strip()) == 0:
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192 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
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193 else:
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194 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
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195 if args.title:
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196 ftitle=dict(text=args.title, font=dict(size=50), automargin=True)
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197 fig.update_layout(title=ftitle)
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198 for scatter in fig.data:
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199 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
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200 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
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201 fig.write_html(args.htmlout)
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202 fig.show()
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203
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204 ]]></help>
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205 <citations>
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206 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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207 </citations>
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208 </tool>
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209
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