Mercurial > repos > jay > padaug_peptide_sequence_analysis
comparison PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py @ 0:5d01ab729b2b draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:43:12 +0000 |
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-1:000000000000 | 0:5d01ab729b2b |
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1 import matplotlib | |
2 matplotlib.use('Agg') | |
3 import os | |
4 import sys | |
5 sys.path.insert(0, os.path.abspath('..')) | |
6 from quantiprot.utils.io import load_fasta_file | |
7 from quantiprot.utils.feature import Feature, FeatureSet | |
8 from quantiprot.utils.sequence import compact | |
9 from quantiprot.metrics.aaindex import get_aa2charge, get_aa2hydropathy | |
10 from quantiprot.metrics.basic import average, average_absolute | |
11 from matplotlib import pyplot as plt | |
12 | |
13 | |
14 | |
15 def Run_Uverskey(Fasta1, Fasta2, OutFile): | |
16 | |
17 | |
18 amyload_seq = load_fasta_file(Fasta1) | |
19 disprot_seq = load_fasta_file(Fasta2) | |
20 | |
21 net_abs_charge = Feature(get_aa2charge(default=0)).then(average_absolute) | |
22 mean_hydropathy = Feature(get_aa2hydropathy(default=0)).then(average) | |
23 | |
24 uversky_fs = FeatureSet("uversky") | |
25 uversky_fs.add(mean_hydropathy, name="mean_hydropathy") | |
26 uversky_fs.add(net_abs_charge, name="net_abs_charge") | |
27 | |
28 amyload_uversky_seq = uversky_fs(amyload_seq) | |
29 disprot_uversky_seq = uversky_fs(disprot_seq) | |
30 | |
31 | |
32 amyload_data_x = amyload_uversky_seq.columns(feature="mean_hydropathy")[0] | |
33 amyload_data_y = amyload_uversky_seq.columns(feature="net_abs_charge")[0] | |
34 plt.plot(amyload_data_x, amyload_data_y,'.', label="Amyload") | |
35 | |
36 disprot_data = compact(disprot_uversky_seq).columns() | |
37 plt.plot(disprot_data[0], disprot_data[1],'.', label="Disprot") | |
38 | |
39 plt.plot([-0.78, 0.835], [0.0, 0.5],'k') | |
40 plt.xlabel("mean hydrophobicity") | |
41 plt.ylabel("net abs charge") | |
42 plt.legend() | |
43 | |
44 plt.savefig(OutFile) | |
45 | |
46 | |
47 | |
48 if __name__=="__main__": | |
49 | |
50 import argparse | |
51 | |
52 parser = argparse.ArgumentParser() | |
53 parser.add_argument("-f1", "--Fasta1", required=True, default=None, help="pep file") | |
54 parser.add_argument("-f2", "--Fasta2", required=True, default=None, help="out put file name for str Descriptors") | |
55 parser.add_argument("--OutFile", required=False, help="HTML out file", default="out.png") | |
56 | |
57 | |
58 | |
59 args = parser.parse_args() | |
60 | |
61 Run_Uverskey(args.Fasta1, args.Fasta2, args.OutFile) |