Mercurial > repos > jay > pdaug_tsvtofasta
view PDAUG_Sequence_Network/PDAUG_Sequence_Network.py @ 10:39fc376c99a8 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
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date | Sun, 09 Jan 2022 03:39:01 +0000 |
parents | c3f0b3a6339e |
children |
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import Levenshtein import matplotlib.pyplot as plt import networkx as nx import os def SeqSimilarityNetwork(InFile, OutFile): f = open(InFile) lines = f.readlines() record = [] seq = [] G = nx.Graph() for line in lines: if ">" in line: record.append(line.strip('\n')) else: seq.append(line.strip('\n')) for x, i in enumerate(seq): for X, I in enumerate(seq): L = Levenshtein.ratio(i, I ) if L >= 0.4: G.add_edge(record[x], record[X], weight=float(Levenshtein.ratio(i, I ))) elarge = [(u, v) for (u, v, d) in G.edges(data=True) if d['weight'] >= 0.4] pos = nx.spring_layout(G) nx.draw_networkx_nodes(G, pos, node_size=10) nx.draw_networkx_edges(G, pos, edgelist=elarge,width=1) plt.axis('off') plt.savefig(OutFile) if __name__=="__main__": import argparse parser = argparse.ArgumentParser() parser.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") parser.add_argument("-O","--OutFile", required=False, help="HTML out file", default="out.png") args = parser.parse_args() SeqSimilarityNetwork(args.InFile, args.OutFile)