Mercurial > repos > jay > pdaug_peptide_ngrams

annotate PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py @ 5:d7e684975db3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author jay
date Thu, 28 Jan 2021 04:05:16 +0000
parents 7557b48b2872
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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diff changeset
1 import pandas as pd
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 from pydpi.pypro import PyPro
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import os
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5
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6 def BinaryDescriptor(seq):
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 BinaryCode = {
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9
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 'A':"1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0",
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11 'C':"0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0",
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12 'D':"0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0",
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13 'E':"0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0",
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14 'F':"0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0",
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15 'G':"0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0",
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16 'H':"0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0",
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17 'I':"0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0",
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18 'K':"0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0",
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19 'L':"0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0",
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20 'M':"0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0",
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21 'N':"0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0",
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22 'P':"0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0",
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23 'Q':"0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0",
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24 'R':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0",
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25 'S':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0",
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26 'T':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0",
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27 'V':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0",
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28 'W':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0",
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29 'Y':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1",
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30 }
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31
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32 lines = []
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33 Df = []
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34
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35
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36 for s in seq:
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37 des = []
7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 for n in s:
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39 des.append(BinaryCode[n.upper()])
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40 lines.append(','.join(des).split(','))
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41
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42 df = pd.DataFrame(lines)
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43
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44 return df
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45
5
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46 def Decriptor_generator(infile, lamda, weight, maxlag, destype, out_file):
0
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47
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48 list_pep_name = []
5
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49 f = open(infile)
0
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50 lines = f.readlines()
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51
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52 for line in lines:
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53 if ">" in line:
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54 pass
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55 else:
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56 list_pep_name.append(line.strip('\n'))
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57
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58 out_df = pd.DataFrame()
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59
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60 for seq in list_pep_name:
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61
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62 protein = PyPro()
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63 protein.ReadProteinSequence(seq)
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64
5
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65
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66 if destype == "GetAAComp":
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67 DS = protein.GetAAComp()
0
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68 df = pd.DataFrame(DS, index=[0])
5
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69 elif destype == "GetDPComp":
0
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70 DS = protein.GetDPComp()
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71 df = pd.DataFrame(DS, index=[0])
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72 elif destype == "GetTPComp":
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73 DS = protein.GetTPComp()
0
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74 df = pd.DataFrame(DS, index=[0])
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75 elif destype == "GetMoreauBrotoAuto":
0
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76 DS = protein.GetMoreauBrotoAuto()
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77 df = pd.DataFrame(DS, index=[0])
5
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78 elif destype =="GetMoranAuto":
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79 DS = protein.GetMoranAuto()
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80 df = pd.DataFrame(DS, index=[0])
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81 elif destype =="GetGearyAuto":
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82 DS = protein.GetGearyAuto()
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83 df = pd.DataFrame(DS, index=[0])
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84 elif destype == "GetCTD":
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85 DS = protein.GetCTD()
0
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86 df = pd.DataFrame(DS, index=[0])
5
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87 elif destype == "GetPAAC":
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88 DS = protein.GetPAAC(lamda=int(lamda), weight=float(weight))
0
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89 df = pd.DataFrame(DS, index=[0])
5
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90 elif destype == "GetAPAAC":
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91 DS = protein.GetAPAAC(lamda=int(lamda), weight=float(weight))
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92 df = pd.DataFrame(DS, index=[0])
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93 elif destype =="GetSOCN":
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94 DS = protein.GetSOCN(maxlag=int(maxlag))
0
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95 df = pd.DataFrame(DS, index=[0])
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96 elif destype =="GetQSO":
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97 DS = protein.GetQSO(maxlag=int(maxlag), weight=float(weight))
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98 df = pd.DataFrame(DS, index=[0])
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99 elif destype == "GetTriad":
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100 DS = protein.GetTriad()
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101 df = pd.DataFrame(DS, index=[0])
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102 elif destype == "All":
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103 DS1 = protein.GetAAComp()
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104 DS2 = protein.GetDPComp()
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105 DS3 = protein.GetTPComp()
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106 DS4 = protein.GetMoreauBrotoAuto()
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107 DS5 = protein.GetMoranAuto()
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108 DS6 = protein.GetGearyAuto()
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109 DS7 = protein.GetCTD()
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110 DS8 = protein.GetPAAC(lamda=int(lamda), weight=float(weight))
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111 DS9 = protein.GetAPAAC(lamda=int(lamda), weight=float(weight))
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112 DS10 = protein.GetSOCN(maxlag=int(maxlag))
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113 DS11 = protein.GetQSO(maxlag=int(maxlag), weight=float(weight))
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114 DS12 = protein.GetTriad()
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115
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116 DS = {}
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117
5
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118 for D in (DS1,DS2,DS3,DS4,DS5,DS6,DS7,DS8,DS9,DS10,DS11,DS12):
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119 print(D)
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120 DS.update(D)
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121 df = pd.DataFrame(DS, index=[0])
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122
5
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123 if destype == 'BinaryDescriptor':
0
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124 out_df = BinaryDescriptor(list_pep_name)
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125 else:
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126 out_df = pd.concat([out_df, df], axis=0)
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127
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128
5
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129 out_df.to_csv(out_file, index=False, sep='\t')
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130
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131
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132 if __name__=="__main__":
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133
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134
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135 import argparse
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136
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137 parser = argparse.ArgumentParser()
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138
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139 parser.add_argument("-I", "--InFile",
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140 required=True,
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141 default=None,
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142 help="pep file")
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143
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144 parser.add_argument("-l", "--Lamda",
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145 required=False,
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146 default=50,
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147 help="pep file")
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148
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149 parser.add_argument("-w", "--Weight",
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150 required=False,
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151 default=0.5,
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152 help="pep file")
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153
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154 parser.add_argument("-m", "--MaxLag",
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155 required=False,
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156 default=10,
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157 help="pep file")
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158
0
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159 parser.add_argument("-t", "--DesType",
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160 required=True,
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161 default=None,
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162 help="out put file name for str Descriptors")
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163
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164 parser.add_argument("-O", "--Out_file",
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165 required=False,
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166 default="Out.tsv",
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167 help="Path to target tsv file")
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168
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169 args = parser.parse_args()
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170 Decriptor_generator(args.InFile, args.Lamda, args.Weight, args.MaxLag, args.DesType, args.Out_file)
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171
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172