diff PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.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_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,125 @@
+import glob
+import pandas as pd 
+import sys
+import os
+import argparse
+
+from modlamp.wetlab import CD
+
+parser = argparse.ArgumentParser(description='Deployment tool')
+subparsers = parser.add_subparsers()
+
+calc_ellipticity = subparsers.add_parser('calc_ellipticity')
+calc_ellipticity.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence")
+calc_ellipticity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
+calc_ellipticity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
+calc_ellipticity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
+calc_ellipticity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
+calc_ellipticity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
+calc_ellipticity.add_argument("-O","--OutPut", required=False, default="OutFile.tsv", help="Mutated output fasta")
+
+PlotData = subparsers.add_parser('PlotData')
+
+PlotData.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
+PlotData.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence")
+PlotData.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
+PlotData.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
+PlotData.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
+PlotData.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
+
+Dichroweb = subparsers.add_parser("Dichroweb")
+Dichroweb.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
+Dichroweb.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence")
+Dichroweb.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
+Dichroweb.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
+Dichroweb.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
+Dichroweb.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
+
+helicity = subparsers.add_parser('helicity')
+
+helicity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
+helicity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
+helicity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
+helicity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
+helicity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
+helicity.add_argument("-t","--temperature", required=False, default=24.0, help="")
+helicity.add_argument("-k","--k", required=True, default=2.4, help="")
+helicity.add_argument("-I","--Induction", required=False, default=True, help="")
+helicity.add_argument("-O","--OutPut", required=False, default="result.tsv", help="")
+
+
+args = parser.parse_args()
+
+if sys.argv[1] == "calc_ellipticity":
+
+    if args.Type == "calc_molar_ellipticity":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_molar_ellipticity()
+        df = cd.molar_ellipticity
+        df = pd.DataFrame(df[0])
+        df.to_csv(args.OutPut, index=None, sep="\t")
+
+    elif args.Type == "calc_meanres_ellipticity":
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_meanres_ellipticity()
+        df = cd.meanres_ellipticity
+        df = pd.DataFrame(df[0])
+        df.to_csv(args.OutPut, index=None, sep="\t")
+    else:
+        pass
+
+if sys.argv[1] == "PlotData":
+
+    os.system('ls temp')
+
+    if args.Type == "mean residue ellipticity":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_meanres_ellipticity()
+        cd.plot(data="mean residue ellipticity", combine='solvent')
+
+    elif args.Type == "molar ellipticity":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_molar_ellipticity()
+        cd.plot(data="molar ellipticity", combine='solvent')
+
+    elif args.Type == "circular dichroism":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_molar_ellipticity()
+        cd.plot(data="circular dichroism", combine='solvent')
+
+    else:
+        pass
+
+if sys.argv[1] == "Dichroweb":
+
+    if args.Type == "mean residue ellipticity":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_meanres_ellipticity()
+        cd.dichroweb(data="mean residue ellipticity")
+
+    elif args.Type == "molar ellipticity":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_molar_ellipticity()
+        cd.dichroweb(data='molar ellipticity')
+
+    elif args.Type == "circular dichroism":
+
+        cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
+        cd.calc_molar_ellipticity()
+        cd.dichroweb(data='circular dichroism')
+
+
+if sys.argv[1] == "helicity":
+    cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))    
+    cd.calc_meanres_ellipticity()
+    cd.helicity(temperature=float(args.temperature), k=float(args.k), induction=args.Induction, filename=args.OutPut )
+
+
+
+