Mercurial > repos > jay > pdaug_peptide_sequence_analysis

annotate PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py @ 0:e59674e3a391 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
author jay
date Fri, 20 Nov 2020 19:47:44 +0000
parents
children
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1 from modlamp.plot import helical_wheel
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2 from modlamp.plot import plot_pde
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3 from modlamp.plot import plot_violin
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4 from modlamp.plot import plot_aa_distr
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5 import pandas as pd
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6 import argparse
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7 import sys, os
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11 parser = argparse.ArgumentParser(description='Deployment tool')
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12 subparsers = parser.add_subparsers()
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14 HelWhl = subparsers.add_parser('HelWhl')
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16 HelWhl.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
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17 HelWhl.add_argument("-C","--colorcoding", required=False, default='rainbow', help="available: , charge, polar, simple, amphipathic, none")
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18 HelWhl.add_argument("-L","--lineweights", required=False, default=True, help="(boolean) defines whether connection lines decrease in thickness along the sequence")
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19 HelWhl.add_argument("-F","--filename", required=False, default="out.png", help="")
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20 HelWhl.add_argument("-s","--seq", required=False, default=False, help="")
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21 HelWhl.add_argument("-M","--movment", required=False, default=False, help="")
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22 HelWhl.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
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25 PltPde = subparsers.add_parser('PltPde')
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26 PltPde.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
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27 PltPde.add_argument("-l", "--ClmList", required=True, default=None, help="")
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28 PltPde.add_argument("-F","--filename", required=False, default="out.png", help="filename where to safe the plot. default = None > show the plot")
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29 PltPde.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
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31 PltVio = subparsers.add_parser('PltVio')
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32 PltVio.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
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33 PltVio.add_argument("-l", "--ClmList", required=True, default=None, help="Column list")
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34 PltVio.add_argument("-C","--colors", required=False, default=None, help='Data to be plotted')
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35 PltVio.add_argument("-B","--bp", required=False, default=False, help="Print a box blot inside violin")
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36 PltVio.add_argument("-T","--title", required=False, default=None, help="Title of the plot.")
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37 PltVio.add_argument("-a","--axlabels", required=False, default=None, help="list containing the axis labels for the plot")
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38 PltVio.add_argument("-M","--y_max", required=False, default=1, help='y-axis maximum.')
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39 PltVio.add_argument("-m","--y_min", required=False, default=0, help="y-axis minimum.")
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40 PltVio.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
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43 PltAaDis = subparsers.add_parser('PltAaDis')
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44 PltAaDis.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
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45 PltAaDis.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
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47 args = parser.parse_args()
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49
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50 if sys.argv[1] == 'HelWhl':
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51
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52 f = open(args.InFile)
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53 lines = f.readlines()
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54 sequence = lines[1].strip('\n')
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55
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56 if args.movment == 'true':
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57 mvt = True
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58 else:
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59 mvt = False
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61 if args.seq == 'true':
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62 sq = True
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63 else:
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64 sq = False
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65
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66 if args.lineweights == 'true':
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67 lw = True
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68 else:
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69 lw = False
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71 helical_wheel(sequence, colorcoding=args.colorcoding, lineweights=args.lineweights, filename=args.OutFile, seq=args.seq, moment=mvt)
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74 elif sys.argv[1] == 'PltPde':
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76 df = pd.read_csv(args.InFile, sep="\t")
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78 data = df[args.ClmList.split(',')].as_matrix().T
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80 plot_pde(data, filename=args.OutFile)
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81
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82 elif sys.argv[1] == 'PltVio':
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83
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84 df = pd.read_csv(args.InFile, sep="\t")
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86 data = df[args.ClmList.split(',')].as_matrix().T
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87
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88 c = ['#0B486B']*len(args.ClmList.split(','))
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89
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90 plot_violin(data, colors=c, bp=True, filename=args.OutFile)
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91
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92
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93 elif sys.argv[1] == 'PltAaDis':
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94
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95 f = open(args.InFile)
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96 lines = f.readlines()
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97
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98 sequences = []
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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100 for line in lines:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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101 if '>' in line:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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102 pass
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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103 else:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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104 sequences.append(line.strip('\n'))
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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105
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106 plot_aa_distr(sequences, color='#0B486B', filename=args.OutFile)
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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107
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108
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109
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110
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111
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112
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