Mercurial > repos > jay > pdaug_peptide_length_distribution
comparison PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py @ 0:3f9bdcf83244 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
| author | jay |
|---|---|
| date | Wed, 28 Oct 2020 02:02:04 +0000 |
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| children |
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| -1:000000000000 | 0:3f9bdcf83244 |
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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) |