diff PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py @ 0:7557b48b2872 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,117 @@
+from modlamp.descriptors import *
+import os
+import pandas as pd
+ 
+def Descriptor_calcultor(DesType, inputfile, ph, amide,OutFile ):
+
+    list_pep_name = []
+    f = open(inputfile)
+    lines = f.readlines()
+    
+    for line in lines:
+        if ">" in line:
+            pass
+        else:
+            list_pep_name.append(line.strip('\n'))
+
+    desc = GlobalDescriptor(list_pep_name)
+
+    if DesType == "Length":
+        desc.length()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "Weight":
+
+        desc.calculate_MW()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "Charge":
+        desc.calculate_charge(ph=int(ph), amide=amide)
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "ChargeDensity":
+        desc.charge_density(ph=int(ph), amide=amide)
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "IsoelectricPoint":
+        desc.isoelectric_point(amide=amide)
+        df = desc.descriptor
+        dfN = desc.featurenames
+ 
+    elif DesType == "InstabilityIndex":
+        desc.instability_index()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "Aromaticity":
+        desc.aromaticity()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "AliphaticIndex":
+        desc.aliphatic_index()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "BomanIndex":
+        desc.boman_index()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "HydrophobicRatio":
+        desc.hydrophobic_ratio()
+        df = desc.descriptor
+        dfN = desc.featurenames
+
+    elif DesType == "All":
+        desc.calculate_all(ph=int(ph), amide=amide)
+        df = desc.descriptor
+        dfN = desc.featurenames
+    else:
+        pass
+
+    df = desc.descriptor
+    dfN = desc.featurenames
+    dfOut = pd.DataFrame(df,columns=dfN)
+
+    dfOut.to_csv(OutFile, index=False, sep='\t')
+
+if __name__=="__main__":
+
+    import argparse
+    
+    parser = argparse.ArgumentParser()
+    
+    parser.add_argument("-t", "--DesType",
+                        required=True,
+                        default=None,
+                        help="Descriptors Type")
+                        
+    parser.add_argument("-i", "--InFile",
+                        required=True,
+                        default=None,
+                        help="Peptide File")   
+
+    parser.add_argument("-p", "--Ph",
+                        required=False,
+                        default=7.0,
+                        help="Ph 0-14") 
+
+    parser.add_argument("-a", "--Amide",
+                        required=False,
+                        default="True",
+                        help="True or False")   
+
+    parser.add_argument("-O", "--OutFile",
+                        required=False,
+                        default="out.tsv",
+                        help="True or False") 
+
+                          
+    args = parser.parse_args()
+
+    Descriptor_calcultor(args.DesType, args.InFile, args.Ph, args.Amide, args.OutFile)