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1 """
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2 This program is intended to create the output table for the disruptin finder workflow
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3 """
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4 from Bio import SeqIO
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5 from Bio.SeqUtils.ProtParam import ProteinAnalysis
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6 from Bio.SeqUtils import ProtParamData
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7 import csv
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8 import argparse
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9 import sys
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10
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11
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12 def disruptin_table(garnier_file, fasta_file):
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13 # Iterable variables
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14 position = 1
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15 net_charge = 0
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16 charge_res = 0
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17 record_number = 0
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18
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19 # loop structures
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20 names = []
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21 sec_struct = []
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22
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23 # reading the lines from the garnier csv file
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24 # with open(garnier_file,'r') as csvfile:
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25 # garnierreader = csv.reader(csvfile)
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26 for row in garnier_file:
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27 if row[0] == 'Sequence: ':
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28 names += [row[1]]
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29 elif row[0] in 'HETC':
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30 row = row.split('\t')
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31 sec_struct += [''.join(row)]
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32
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33 record = []
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34 p = []
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35 r = []
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36 c = []
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37 h = []
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38 s = []
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39
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40 # Parse the .fasta file and get the sequence
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41 for rec in SeqIO.parse(fasta_file, "fasta"):
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42 sequence = str(rec.seq)
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43
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44 # Set up the information vectors: for position #, residue, hydrophobic/charge/polar/nonpolar, and secondary
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45 # structure
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46 record += [rec.id]
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47 position_vec = []
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48 residue_vec = []
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49 charge_sym_vec = []
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50 sec_struct_vec = []
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51
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52 for aa in sequence:
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53 position_vec += [str(position)]
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54 residue_vec += [str(aa)]
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55 sec_struct_vec += [str(sec_struct[record_number][position - 1])]
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56
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57 # For R and K residues a positive charge is given
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58 if aa in "RK":
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59 symbol = "+"
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60 # For D and E residues a negative charge is given
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61 elif aa in "DE":
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62 symbol = "-"
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63 elif aa in "AVMILPWFG":
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64 symbol = "N"
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65 elif aa in "HSYTCQN":
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66 symbol = "P"
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67 charge_sym_vec += symbol
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68 position += 1
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69
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70 # Calculating hyrophobicity based on Kyte and Doolittle scale. Using binning value of 9. Since the binning
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71 # is 9, the first 4 residues and last 4 residues as set blank so as to center the values to their
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72 # approximate position on the sequence.
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73 prot_ana_seq = ProteinAnalysis(sequence)
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74 hydro = [0] * 4 + prot_ana_seq.protein_scale(ProtParamData.kd, 9) + [0] * 4
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75
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76 record_number += 1
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77 position = 1
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78
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79 p += [position_vec]
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80 r += [residue_vec]
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81 c += [charge_sym_vec]
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82 h += [hydro]
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83 s += [sec_struct_vec]
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84
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85 # returns values for name of the sequence
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86 return record, p, r, c, h, s
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87
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88
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89 if __name__ == "__main__":
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90 # Grab all of the filters from our plugin loader
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91 parser = argparse.ArgumentParser(description="Disruptin Table Output")
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92 parser.add_argument(
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93 "garnier_file", type=argparse.FileType("r"), help="csv file from garnier reader"
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94 )
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95 parser.add_argument(
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96 "fasta_file",
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97 type=argparse.FileType("r"),
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98 help="fasta file of disruptin candidates",
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99 )
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100 args = parser.parse_args()
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101
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102 # Set up output location
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103 # f = open(sys.stdout, 'w', newline='')
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104 # writer1 = csv.writer(f)
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105
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106 iden, position, residue, charge, hydro, struct = disruptin_table(**vars(args))
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107
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108 for i in range(len(iden)):
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109 # writer1.writerow(['Protein ID']+[iden[i]])
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110 # writer1.writerow(['Position'] + [format(x, 's') for x in position[i]])
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111 # writer1.writerow(['Residue'] + [format(x, 's') for x in residue[i]])
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112 # writer1.writerow(['Charge'] + [format(x, 's') for x in charge[i]])
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113 # writer1.writerow(['Hydrophobicity'] + [format(x, '.3f') for x in hydro[i]])
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114 # writer1.writerow(['Secondary Structure'] + [format(x, 's') for x in struct[i]])
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115 # writer1.writerow([''])
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116
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117 print(str(iden[i]))
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118 print("Position \t " + "\t".join(position[i]))
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119 print("Residue \t" + "\t".join(residue[i]))
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120 print("Charge \t" + "\t".join(charge[i]))
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121 print("Hydrophobicity \t" + "\t".join(format(x, ".3f") for x in hydro[i]))
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122 print("Secondary Structure \t" + "\t".join(struct[i]))
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