Mercurial > repos > galaxy-australia > alphafold2

annotate validate_fasta.py @ 0:67c179acafdd draft default tip

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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
author galaxy-australia
date Thu, 03 Mar 2022 02:54:20 +0000
parents
children
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67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
galaxy-australia
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1 """Validate input FASTA sequence."""
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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2
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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3 import re
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
galaxy-australia
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4 import argparse
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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5 from typing import List, TextIO
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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6
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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7
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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8 class Fasta:
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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9 def __init__(self, header_str: str, seq_str: str):
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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10 self.header = header_str
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11 self.aa_seq = seq_str
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12
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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13
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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14 class FastaLoader:
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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15 def __init__(self, fasta_path: str):
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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16 """Initialize from FASTA file."""
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17 self.fastas = []
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18 self.load(fasta_path)
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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19 print("Loaded FASTA sequences:")
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20 for f in self.fastas:
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21 print(f.header)
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22 print(f.aa_seq)
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23
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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24 def load(self, fasta_path: str):
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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25 """Load bare or FASTA formatted sequence."""
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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26 with open(fasta_path, 'r') as f:
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27 self.content = f.read()
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28
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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29 if "__cn__" in self.content:
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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30 # Pasted content with escaped characters
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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31 self.newline = '__cn__'
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32 self.caret = '__gt__'
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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33 else:
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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34 # Uploaded file with normal content
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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35 self.newline = '\n'
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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36 self.caret = '>'
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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37
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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38 self.lines = self.content.split(self.newline)
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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39 header, sequence = self.interpret_first_line()
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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40
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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41 i = 0
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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42 while i < len(self.lines):
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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43 line = self.lines[i]
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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44 if line.startswith(self.caret):
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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45 self.update_fastas(header, sequence)
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46 header = '>' + self.strip_header(line)
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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47 sequence = ''
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48 else:
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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49 sequence += line.strip('\n ')
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50 i += 1
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51
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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52 # after reading whole file, header & sequence buffers might be full
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53 self.update_fastas(header, sequence)
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54
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55 def interpret_first_line(self):
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56 line = self.lines[0]
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57 if line.startswith(self.caret):
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58 header = '>' + self.strip_header(line)
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59 return header, ''
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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60 else:
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61 return '', line
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62
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63 def strip_header(self, line):
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64 """Strip characters escaped with underscores from pasted text."""
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65 return re.sub(r'\_\_.{2}\_\_', '', line).strip('>')
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66
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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67 def update_fastas(self, header: str, sequence: str):
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68 # if we have a sequence
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69 if sequence:
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70 # create generic header if not exists
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71 if not header:
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72 fasta_count = len(self.fastas)
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73 header = f'>sequence_{fasta_count}'
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74
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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75 # Create new Fasta
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76 self.fastas.append(Fasta(header, sequence))
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77
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78
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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79 class FastaValidator:
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80 def __init__(self, fasta_list: List[Fasta]):
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81 self.fasta_list = fasta_list
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82 self.min_length = 30
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83 self.max_length = 2000
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84 self.iupac_characters = {
67c179acafdd "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
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85 'A', 'B', 'C', 'D', 'E', 'F', 'G',
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86 'H', 'I', 'K', 'L', 'M', 'N', 'P',
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87 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
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88 'Y', 'Z', '-'
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89 }
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90
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91 def validate(self):
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92 """performs fasta validation"""
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93 self.validate_num_seqs()
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94 self.validate_length()
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95 self.validate_alphabet()
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96 # not checking for 'X' nucleotides at the moment.
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97 # alphafold can throw an error if it doesn't like it.
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98 #self.validate_x()
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99
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100 def validate_num_seqs(self) -> None:
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101 if len(self.fasta_list) > 1:
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102 raise Exception(f'Error encountered validating fasta: More than 1 sequence detected ({len(self.fasta_list)}). Please use single fasta sequence as input')
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103 elif len(self.fasta_list) == 0:
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104 raise Exception(f'Error encountered validating fasta: input file has no fasta sequences')
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105
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106 def validate_length(self):
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107 """Confirms whether sequence length is valid. """
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108 fasta = self.fasta_list[0]
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109 if len(fasta.aa_seq) < self.min_length:
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110 raise Exception(f'Error encountered validating fasta: Sequence too short ({len(fasta.aa_seq)}aa). Must be > 30aa')
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111 if len(fasta.aa_seq) > self.max_length:
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112 raise Exception(f'Error encountered validating fasta: Sequence too long ({len(fasta.aa_seq)}aa). Must be < 2000aa')
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113
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114 def validate_alphabet(self):
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115 """
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116 Confirms whether the sequence conforms to IUPAC codes.
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117 If not, reports the offending character and its position.
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118 """
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119 fasta = self.fasta_list[0]
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120 for i, char in enumerate(fasta.aa_seq.upper()):
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121 if char not in self.iupac_characters:
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122 raise Exception(f'Error encountered validating fasta: Invalid amino acid found at pos {i}: "{char}"')
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123
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124 def validate_x(self):
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125 """checks if any bases are X. TODO check whether alphafold accepts X bases. """
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126 fasta = self.fasta_list[0]
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127 for i, char in enumerate(fasta.aa_seq.upper()):
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128 if char == 'X':
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129 raise Exception(f'Error encountered validating fasta: Unsupported aa code "X" found at pos {i}')
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130
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131
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132 class FastaWriter:
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133 def __init__(self) -> None:
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134 self.outfile = 'alphafold.fasta'
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135 self.formatted_line_len = 60
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136
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137 def write(self, fasta: Fasta):
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138 with open(self.outfile, 'w') as fp:
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139 header = fasta.header
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140 seq = self.format_sequence(fasta.aa_seq)
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141 fp.write(header + '\n')
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142 fp.write(seq + '\n')
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143
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144 def format_sequence(self, aa_seq: str):
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145 formatted_seq = ''
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146 for i in range(0, len(aa_seq), self.formatted_line_len):
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147 formatted_seq += aa_seq[i: i + self.formatted_line_len] + '\n'
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148 return formatted_seq
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149
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150
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151 def main():
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152 # load fasta file
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153 args = parse_args()
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154 fas = FastaLoader(args.input_fasta)
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155
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156 # validate
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157 fv = FastaValidator(fas.fastas)
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158 fv.validate()
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159
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160 # write cleaned version
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161 fw = FastaWriter()
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162 fw.write(fas.fastas[0])
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163
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164
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165 def parse_args() -> argparse.Namespace:
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166 parser = argparse.ArgumentParser()
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167 parser.add_argument(
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168 "input_fasta",
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169 help="input fasta file",
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170 type=str
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171 )
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172 return parser.parse_args()
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173
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174
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175
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176 if __name__ == '__main__':
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177 main()