Mercurial > repos > jay > pdaug_peptide_ngrams
annotate PDAUG_Sequence_Network/PDAUG_Sequence_Network.py @ 3:b2a7b957cd52 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit edb37634e419f75dd66292e712de51278746d883"
author  jay 

date  Wed, 30 Dec 2020 03:06:50 +0000 
parents  7557b48b2872 
children 
rev  line source 

0
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 import Levenshtein 
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import matplotlib.pyplot as plt 
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import networkx as nx 
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4 import os 
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5 
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6 
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7 def SeqSimilarityNetwork(InFile, OutFile): 
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8 
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9 f = open(InFile) 
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10 lines = f.readlines() 
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11 
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12 record = [] 
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13 seq = [] 
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14 
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15 G = nx.Graph() 
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16 
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17 for line in lines: 
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18 
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19 if ">" in line: 
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20 record.append(line.strip('\n')) 
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 else: 
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22 seq.append(line.strip('\n')) 
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23 
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24 for x, i in enumerate(seq): 
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25 for X, I in enumerate(seq): 
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26 L = Levenshtein.ratio(i, I ) 
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27 if L >= 0.4: 
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28 G.add_edge(record[x], record[X], weight=float(Levenshtein.ratio(i, I ))) 
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29 
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30 elarge = [(u, v) for (u, v, d) in G.edges(data=True) if d['weight'] >= 0.4] 
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31 
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32 pos = nx.spring_layout(G) 
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33 nx.draw_networkx_nodes(G, pos, node_size=10) 
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34 nx.draw_networkx_edges(G, pos, edgelist=elarge,width=1) 
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35 plt.axis('off') 
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36 
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37 plt.savefig(OutFile) 
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38 
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39 
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40 
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41 if __name__=="__main__": 
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42 
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43 import argparse 
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44 
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45 parser = argparse.ArgumentParser() 
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46 
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47 parser.add_argument("I", "InFile", required=True, default=None, help="Path to target tsv file") 
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48 parser.add_argument("O","OutFile", required=False, help="HTML out file", default="out.png") 
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49 args = parser.parse_args() 
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50 
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51 SeqSimilarityNetwork(args.InFile, args.OutFile) 
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52 
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53 