annotate PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py @ 4:f46f1d9b3899 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"

import matplotlib
matplotlib.use('Agg')
import os
import sys
sys.path.insert(0, os.path.abspath('..'))
from quantiprot.utils.io import load_fasta_file
from quantiprot.utils.feature import Feature, FeatureSet
from quantiprot.utils.sequence import compact
from quantiprot.metrics.aaindex import get_aa2charge, get_aa2hydropathy
from quantiprot.metrics.basic import average, average_absolute
from matplotlib import pyplot as plt



def Run_Uverskey(Fasta1, Fasta2, OutFile):


    amyload_seq = load_fasta_file(Fasta1)
    disprot_seq = load_fasta_file(Fasta2)

    net_abs_charge = Feature(get_aa2charge(default=0)).then(average_absolute)
    mean_hydropathy = Feature(get_aa2hydropathy(default=0)).then(average)

    uversky_fs = FeatureSet("uversky")
    uversky_fs.add(mean_hydropathy, name="mean_hydropathy")
    uversky_fs.add(net_abs_charge, name="net_abs_charge")

    amyload_uversky_seq = uversky_fs(amyload_seq)
    disprot_uversky_seq = uversky_fs(disprot_seq)


    amyload_data_x = amyload_uversky_seq.columns(feature="mean_hydropathy")[0]
    amyload_data_y = amyload_uversky_seq.columns(feature="net_abs_charge")[0]
    plt.plot(amyload_data_x, amyload_data_y,'.', label="Amyload")

    disprot_data = compact(disprot_uversky_seq).columns()
    plt.plot(disprot_data[0], disprot_data[1],'.', label="Disprot")

    plt.plot([-0.78, 0.835], [0.0, 0.5],'k')
    plt.xlabel("mean hydrophobicity")
    plt.ylabel("net abs charge")
    plt.legend()

    plt.savefig(OutFile)



if __name__=="__main__":
    
    import argparse
    
    parser = argparse.ArgumentParser()
    parser.add_argument("-f1", "--Fasta1", required=True, default=None, help="pep file")                 
    parser.add_argument("-f2", "--Fasta2", required=True, default=None, help="out put file name for str Descriptors")   
    parser.add_argument("--OutFile",  required=False,  help="HTML out file",  default="out.png")


                                       
    args = parser.parse_args()
    
    Run_Uverskey(args.Fasta1, args.Fasta2, args.OutFile)