Mercurial > repos > jay > pdaug_word_vector_descriptor
diff PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py @ 0:a3a1d9bea1ad draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:29:04 +0000 |
parents | |
children | 8de738fa6552 |
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--- /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 02:29:04 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 ) + + + +