Mercurial > repos > jay > pdaug_basic_plots
comparison PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py @ 0:7d247e27ff11 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:52:18 +0000 |
parents | |
children | 4c3242563796 |
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-1:000000000000 | 0:7d247e27ff11 |
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1 import glob | |
2 import pandas as pd | |
3 import sys | |
4 import os | |
5 import argparse | |
6 | |
7 from modlamp.wetlab import CD | |
8 | |
9 parser = argparse.ArgumentParser(description='Deployment tool') | |
10 subparsers = parser.add_subparsers() | |
11 | |
12 calc_ellipticity = subparsers.add_parser('calc_ellipticity') | |
13 calc_ellipticity.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence") | |
14 calc_ellipticity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") | |
15 calc_ellipticity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") | |
16 calc_ellipticity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") | |
17 calc_ellipticity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") | |
18 calc_ellipticity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") | |
19 calc_ellipticity.add_argument("-O","--OutPut", required=False, default="OutFile.tsv", help="Mutated output fasta") | |
20 | |
21 PlotData = subparsers.add_parser('PlotData') | |
22 | |
23 PlotData.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") | |
24 PlotData.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence") | |
25 PlotData.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") | |
26 PlotData.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") | |
27 PlotData.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") | |
28 PlotData.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") | |
29 | |
30 Dichroweb = subparsers.add_parser("Dichroweb") | |
31 Dichroweb.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") | |
32 Dichroweb.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence") | |
33 Dichroweb.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") | |
34 Dichroweb.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") | |
35 Dichroweb.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") | |
36 Dichroweb.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") | |
37 | |
38 helicity = subparsers.add_parser('helicity') | |
39 | |
40 helicity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") | |
41 helicity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") | |
42 helicity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") | |
43 helicity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") | |
44 helicity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") | |
45 helicity.add_argument("-t","--temperature", required=False, default=24.0, help="") | |
46 helicity.add_argument("-k","--k", required=True, default=2.4, help="") | |
47 helicity.add_argument("-I","--Induction", required=False, default=True, help="") | |
48 helicity.add_argument("-O","--OutPut", required=False, default="result.tsv", help="") | |
49 | |
50 | |
51 args = parser.parse_args() | |
52 | |
53 if sys.argv[1] == "calc_ellipticity": | |
54 | |
55 if args.Type == "calc_molar_ellipticity": | |
56 | |
57 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
58 cd.calc_molar_ellipticity() | |
59 df = cd.molar_ellipticity | |
60 df = pd.DataFrame(df[0]) | |
61 df.to_csv(args.OutPut, index=None, sep="\t") | |
62 | |
63 elif args.Type == "calc_meanres_ellipticity": | |
64 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
65 cd.calc_meanres_ellipticity() | |
66 df = cd.meanres_ellipticity | |
67 df = pd.DataFrame(df[0]) | |
68 df.to_csv(args.OutPut, index=None, sep="\t") | |
69 else: | |
70 pass | |
71 | |
72 if sys.argv[1] == "PlotData": | |
73 | |
74 os.system('ls temp') | |
75 | |
76 if args.Type == "mean residue ellipticity": | |
77 | |
78 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
79 cd.calc_meanres_ellipticity() | |
80 cd.plot(data="mean residue ellipticity", combine='solvent') | |
81 | |
82 elif args.Type == "molar ellipticity": | |
83 | |
84 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
85 cd.calc_molar_ellipticity() | |
86 cd.plot(data="molar ellipticity", combine='solvent') | |
87 | |
88 elif args.Type == "circular dichroism": | |
89 | |
90 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
91 cd.calc_molar_ellipticity() | |
92 cd.plot(data="circular dichroism", combine='solvent') | |
93 | |
94 else: | |
95 pass | |
96 | |
97 if sys.argv[1] == "Dichroweb": | |
98 | |
99 if args.Type == "mean residue ellipticity": | |
100 | |
101 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
102 cd.calc_meanres_ellipticity() | |
103 cd.dichroweb(data="mean residue ellipticity") | |
104 | |
105 elif args.Type == "molar ellipticity": | |
106 | |
107 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
108 cd.calc_molar_ellipticity() | |
109 cd.dichroweb(data='molar ellipticity') | |
110 | |
111 elif args.Type == "circular dichroism": | |
112 | |
113 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
114 cd.calc_molar_ellipticity() | |
115 cd.dichroweb(data='circular dichroism') | |
116 | |
117 | |
118 if sys.argv[1] == "helicity": | |
119 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) | |
120 cd.calc_meanres_ellipticity() | |
121 cd.helicity(temperature=float(args.temperature), k=float(args.k), induction=args.Induction, filename=args.OutPut ) | |
122 | |
123 | |
124 | |
125 |