Mercurial > repos > jay > pdaug_peptide_length_distribution

annotate PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py @ 4:e62e03a4d81e draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author jay
date Tue, 12 Jan 2021 19:02:11 +0000
parents 3f9bdcf83244
children
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1 import matplotlib
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2 matplotlib.use('Agg')
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3 import os
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4 import sys
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5 sys.path.insert(0, os.path.abspath('..'))
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6 from quantiprot.utils.io import load_fasta_file
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7 from quantiprot.utils.feature import Feature, FeatureSet
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8 from quantiprot.utils.sequence import compact
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9 from quantiprot.metrics.aaindex import get_aa2charge, get_aa2hydropathy
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10 from quantiprot.metrics.basic import average, average_absolute
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11 from matplotlib import pyplot as plt
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15 def Run_Uverskey(Fasta1, Fasta2, OutFile):
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18 amyload_seq = load_fasta_file(Fasta1)
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19 disprot_seq = load_fasta_file(Fasta2)
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21 net_abs_charge = Feature(get_aa2charge(default=0)).then(average_absolute)
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22 mean_hydropathy = Feature(get_aa2hydropathy(default=0)).then(average)
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24 uversky_fs = FeatureSet("uversky")
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25 uversky_fs.add(mean_hydropathy, name="mean_hydropathy")
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26 uversky_fs.add(net_abs_charge, name="net_abs_charge")
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28 amyload_uversky_seq = uversky_fs(amyload_seq)
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29 disprot_uversky_seq = uversky_fs(disprot_seq)
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32 amyload_data_x = amyload_uversky_seq.columns(feature="mean_hydropathy")[0]
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33 amyload_data_y = amyload_uversky_seq.columns(feature="net_abs_charge")[0]
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34 plt.plot(amyload_data_x, amyload_data_y,'.', label="Amyload")
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36 disprot_data = compact(disprot_uversky_seq).columns()
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37 plt.plot(disprot_data[0], disprot_data[1],'.', label="Disprot")
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39 plt.plot([-0.78, 0.835], [0.0, 0.5],'k')
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40 plt.xlabel("mean hydrophobicity")
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41 plt.ylabel("net abs charge")
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42 plt.legend()
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44 plt.savefig(OutFile)
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48 if __name__=="__main__":
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50 import argparse
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52 parser = argparse.ArgumentParser()
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53 parser.add_argument("-f1", "--Fasta1", required=True, default=None, help="pep file")
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54 parser.add_argument("-f2", "--Fasta2", required=True, default=None, help="out put file name for str Descriptors")
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55 parser.add_argument("--OutFile", required=False, help="HTML out file", default="out.png")
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59 args = parser.parse_args()
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61 Run_Uverskey(args.Fasta1, args.Fasta2, args.OutFile)