Mercurial > repos > jay > pdaug_peptide_core_functions

annotate PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py @ 0:e743e76b8991 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:07:30 +0000
parents
children 48eedcb9bfa7
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e743e76b8991 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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diff changeset
1 import glob
e743e76b8991 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import pandas as pd
e743e76b8991 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import sys
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4 import os
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5 import argparse
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7 from modlamp.wetlab import CD
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9 parser = argparse.ArgumentParser(description='Deployment tool')
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10 subparsers = parser.add_subparsers()
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12 calc_ellipticity = subparsers.add_parser('calc_ellipticity')
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13 calc_ellipticity.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence")
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14 calc_ellipticity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
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15 calc_ellipticity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
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16 calc_ellipticity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
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17 calc_ellipticity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
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18 calc_ellipticity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
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19 calc_ellipticity.add_argument("-O","--OutPut", required=False, default="OutFile.tsv", help="Mutated output fasta")
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21 PlotData = subparsers.add_parser('PlotData')
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23 PlotData.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
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24 PlotData.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence")
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25 PlotData.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
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26 PlotData.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
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27 PlotData.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
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28 PlotData.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
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29
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30 Dichroweb = subparsers.add_parser("Dichroweb")
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31 Dichroweb.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
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32 Dichroweb.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence")
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33 Dichroweb.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
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34 Dichroweb.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
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35 Dichroweb.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
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36 Dichroweb.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
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37
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38 helicity = subparsers.add_parser('helicity')
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39
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40 helicity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence")
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41 helicity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence")
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42 helicity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence")
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43 helicity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta")
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44 helicity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta")
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45 helicity.add_argument("-t","--temperature", required=False, default=24.0, help="")
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46 helicity.add_argument("-k","--k", required=True, default=2.4, help="")
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47 helicity.add_argument("-I","--Induction", required=False, default=True, help="")
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48 helicity.add_argument("-O","--OutPut", required=False, default="result.tsv", help="")
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49
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51 args = parser.parse_args()
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52
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53 if sys.argv[1] == "calc_ellipticity":
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54
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55 if args.Type == "calc_molar_ellipticity":
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56
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57 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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58 cd.calc_molar_ellipticity()
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59 df = cd.molar_ellipticity
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60 df = pd.DataFrame(df[0])
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61 df.to_csv(args.OutPut, index=None, sep="\t")
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62
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63 elif args.Type == "calc_meanres_ellipticity":
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64 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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65 cd.calc_meanres_ellipticity()
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66 df = cd.meanres_ellipticity
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67 df = pd.DataFrame(df[0])
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68 df.to_csv(args.OutPut, index=None, sep="\t")
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69 else:
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70 pass
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72 if sys.argv[1] == "PlotData":
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74 os.system('ls temp')
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75
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76 if args.Type == "mean residue ellipticity":
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77
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78 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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79 cd.calc_meanres_ellipticity()
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80 cd.plot(data="mean residue ellipticity", combine='solvent')
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81
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82 elif args.Type == "molar ellipticity":
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83
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84 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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85 cd.calc_molar_ellipticity()
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86 cd.plot(data="molar ellipticity", combine='solvent')
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87
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88 elif args.Type == "circular dichroism":
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89
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90 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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91 cd.calc_molar_ellipticity()
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92 cd.plot(data="circular dichroism", combine='solvent')
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93
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94 else:
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95 pass
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96
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97 if sys.argv[1] == "Dichroweb":
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98
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99 if args.Type == "mean residue ellipticity":
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100
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101 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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102 cd.calc_meanres_ellipticity()
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103 cd.dichroweb(data="mean residue ellipticity")
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104
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105 elif args.Type == "molar ellipticity":
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106
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107 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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108 cd.calc_molar_ellipticity()
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109 cd.dichroweb(data='molar ellipticity')
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110
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111 elif args.Type == "circular dichroism":
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112
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113 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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114 cd.calc_molar_ellipticity()
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115 cd.dichroweb(data='circular dichroism')
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116
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117
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118 if sys.argv[1] == "helicity":
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119 cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen))
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120 cd.calc_meanres_ellipticity()
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121 cd.helicity(temperature=float(args.temperature), k=float(args.k), induction=args.Induction, filename=args.OutPut )
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122
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123
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124
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125