diff PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py @ 0:5d01ab729b2b draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py	Wed Oct 28 01:43:12 2020 +0000
@@ -0,0 +1,61 @@
+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)