Mercurial > repos > azomics > clustergrammer_flow

annotate clustergrammerIPG.py @ 1:c90127c2a1ae draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
author azomics
date Sun, 27 Jun 2021 22:13:16 +0000
parents fee56ee2f7ac
children
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fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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1 #!/usr/bin/env python
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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2
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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3 ######################################################################
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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4 # Copyright (c) 2016 Northrop Grumman.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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5 # All rights reserved.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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6 ######################################################################
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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7
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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8 # version 1.1 -- August 2017
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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9 # added checks for consistency between input files
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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10 # and upper limit on nb of cluster to look at
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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11 # version 1.2 -- June 2018
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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12 # added clustergrammer clustering parameters and normalization options
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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13
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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15 from __future__ import print_function
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
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c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
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diff changeset
17 import os
0
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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18 import sys
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
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c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
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20 from clustergrammer import Network
0
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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22 from jinja2 import Environment, FileSystemLoader
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
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23
0
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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24 import pandas as pd
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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25
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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26
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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27 def is_integer(s):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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28 try:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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29 int(s)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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30 return True
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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31 except ValueError:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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32 return False
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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33
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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34
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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35 def get_indices(input_text):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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36 output_list = []
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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37 default_value = ['i.e.:1,2,5', 'i.e.:3,6,7']
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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38 if input_text in default_value:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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39 sys.exit(2)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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40 else:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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41 tmp_col = input_text.split(",")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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42 if len(tmp_col) == 1:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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43 if not tmp_col[0].strip():
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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44 sys.exit(2)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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45 elif not is_integer(tmp_col[0].strip()):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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46 sys.exit(3)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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47 else:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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48 output_list.append(int(tmp_col[0].strip()) - 1)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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49 else:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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50 for c in range(0, len(tmp_col)):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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51 if not is_integer(tmp_col[c].strip()):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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52 sys.exit(3)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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53 else:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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54 output_list.append(int(tmp_col[c].strip()) - 1)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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55 return(output_list)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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56
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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57
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
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58 def prepare_heatmap(matrix_input, html_file, html_dir, tools_dir,
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
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59 categories, distance, linkage):
0
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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60 # prepare directory and html
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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61 os.mkdir(html_dir)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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62
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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63 env = Environment(loader=FileSystemLoader(tools_dir + "/templates"))
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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64 template = env.get_template("clustergrammer.template")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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65 overview = template.render()
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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66 with open(html_file, "w") as outf:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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67 outf.write(overview)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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68
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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69 json_output = html_dir + "/mult_view.json"
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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70
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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71 net = Network()
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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72 net.load_file(matrix_input)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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73 if (categories['row']):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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74 net.add_cats('row', categories['row'])
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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75 if (categories['col']):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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76 net.add_cats('col', categories['col'])
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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77 net.cluster(dist_type=distance, linkage_type=linkage)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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78 net.write_json_to_file('viz', json_output)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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79
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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80
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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81 if __name__ == "__main__":
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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82
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
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83 args = sys.argv
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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diff changeset
84 categories = {
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
85 'row': [],
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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86 'col': []
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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87 }
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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88 norm = {}
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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diff changeset
89
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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90 if (len(args) > 7):
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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91 df = pd.read_table(args[1])
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
92 names = {
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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diff changeset
93 'row': df.iloc[:, 0],
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
94 'col': df.columns[1:]
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
95 }
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
96
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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97 tmp_string = "-=-".join(args[8:])
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
parents: 0
diff changeset
98 print(tmp_string + "\n")
0
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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99 # get categories
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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100 cats = tmp_string.split("-=-new_cat-=-")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
101 for cat in cats:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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diff changeset
102 tmp_cat = cat.split("-=-")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
103 group = {
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
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104 "title": tmp_cat[1],
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
105 "cats": {}
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
106 }
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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107 stg_groups = "--".join(tmp_cat[2:])
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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108 groups = stg_groups.split("--new_label--")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
109 cat_indices = []
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
110 for g in groups:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
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111 print(g + "\n")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
112 elem = g.split("--")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
113 index_list = get_indices(elem[1])
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
114 index_names = []
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
115 for i in index_list:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
116 if i in cat_indices:
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
117 sys.exit(4)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
118 index_names.append(str(names[tmp_cat[0]][i]))
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
119 cat_indices = cat_indices + index_list
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
120 print(index_names, elem[0], sep="\t")
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
121 group["cats"][elem[0]] = index_names
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
122 categories[tmp_cat[0]].append(group)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
123 print(categories)
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
124
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
parents: 0
diff changeset
125 prepare_heatmap(args[1], args[2], args[3],
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
parents: 0
diff changeset
126 args[4], categories, args[5], args[6])