Mercurial > repos > galaxy-australia > alphafold2

annotate validate_fasta.py @ 12:7fbec959cf2b draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 6fdbb269efd97b6f5c6ab40db4ab0b23459f884b
author galaxy-australia
date Fri, 16 Sep 2022 06:14:06 +0000
parents 3bd420ec162d
children d00e15139065
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1 """Validate input FASTA sequence."""
0
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3 import re
6
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4 import sys
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5 import argparse
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6 from typing import List
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8 MULTIMER_MAX_SEQUENCE_COUNT = 10
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9
0
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11 class Fasta:
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12 def __init__(self, header_str: str, seq_str: str):
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13 self.header = header_str
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14 self.aa_seq = seq_str
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17 class FastaLoader:
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18 def __init__(self, fasta_path: str):
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19 """Initialize from FASTA file."""
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20 self.fastas = []
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21 self.load(fasta_path)
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23 def load(self, fasta_path: str):
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24 """Load bare or FASTA formatted sequence."""
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25 with open(fasta_path, 'r') as f:
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26 self.content = f.read()
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27
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28 if "__cn__" in self.content:
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29 # Pasted content with escaped characters
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30 self.newline = '__cn__'
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31 self.read_caret = '__gt__'
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32 else:
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33 # Uploaded file with normal content
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34 self.newline = '\n'
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35 self.read_caret = '>'
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36
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37 self.lines = self.content.split(self.newline)
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38
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39 if not self.lines[0].startswith(self.read_caret):
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40 # Fasta is headless, load as single sequence
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41 self.update_fastas(
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42 '', ''.join(self.lines)
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43 )
1
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44
0
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45 else:
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46 header = None
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47 sequence = None
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48 for line in self.lines:
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49 if line.startswith(self.read_caret):
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50 if header:
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51 self.update_fastas(header, sequence)
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52 header = '>' + self.strip_header(line)
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53 sequence = ''
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54 else:
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55 sequence += line.strip('\n ')
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56 self.update_fastas(header, sequence)
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57
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58 def strip_header(self, line):
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59 """Strip characters escaped with underscores from pasted text."""
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60 return re.sub(r'\_\_.{2}\_\_', '', line).strip('>')
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61
0
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62 def update_fastas(self, header: str, sequence: str):
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63 # if we have a sequence
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64 if sequence:
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65 # create generic header if not exists
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66 if not header:
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67 fasta_count = len(self.fastas)
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68 header = f'>sequence_{fasta_count}'
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69
1
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70 # Create new Fasta
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71 self.fastas.append(Fasta(header, sequence))
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72
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74 class FastaValidator:
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75 def __init__(
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76 self,
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77 min_length=None,
9
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78 max_length=None,
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79 multiple=False):
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80 self.multiple = multiple
6
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81 self.min_length = min_length
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82 self.max_length = max_length
0
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83 self.iupac_characters = {
1
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84 'A', 'B', 'C', 'D', 'E', 'F', 'G',
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85 'H', 'I', 'K', 'L', 'M', 'N', 'P',
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86 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
0
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87 'Y', 'Z', '-'
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88 }
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89
9
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90 def validate(self, fasta_list: List[Fasta]):
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diff changeset
91 """Perform FASTA validation."""
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92 self.fasta_list = fasta_list
0
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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 return self.fasta_list
0
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100
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101 def validate_num_seqs(self) -> None:
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102 """Assert that only one sequence has been provided."""
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galaxy-australia
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103 fasta_count = len(self.fasta_list)
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diff changeset
104
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diff changeset
105 if self.multiple:
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106 if fasta_count < 2:
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diff changeset
107 raise ValueError(
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
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108 'Error encountered validating FASTA:\n'
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galaxy-australia
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109 'Multimer mode requires multiple input sequence.'
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galaxy-australia
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110 f' Only {fasta_count} sequences were detected in'
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
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diff changeset
111 ' the provided file.')
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112 self.fasta_list = self.fasta_list
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113
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114 elif fasta_count > MULTIMER_MAX_SEQUENCE_COUNT:
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galaxy-australia
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115 sys.stderr.write(
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116 f'WARNING: detected {fasta_count} sequences but the'
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galaxy-australia
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117 f' maximum allowed is {MULTIMER_MAX_SEQUENCE_COUNT}'
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galaxy-australia
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118 ' sequences. The last'
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galaxy-australia
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119 f' {fasta_count - MULTIMER_MAX_SEQUENCE_COUNT} sequence(s)'
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
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120 ' have been discarded.\n')
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galaxy-australia
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121 self.fasta_list = self.fasta_list[:MULTIMER_MAX_SEQUENCE_COUNT]
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
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122 else:
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galaxy-australia
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123 if fasta_count > 1:
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galaxy-australia
parents: 8
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124 sys.stderr.write(
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
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125 'WARNING: More than 1 sequence detected.'
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galaxy-australia
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126 ' Using first FASTA sequence as input.\n')
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galaxy-australia
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127 self.fasta_list = self.fasta_list[:1]
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128
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129 elif len(self.fasta_list) == 0:
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130 raise ValueError(
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
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131 'Error encountered validating FASTA:\n'
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132 ' no FASTA sequences detected in input file.')
0
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133
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134 def validate_length(self):
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135 """Confirm whether sequence length is valid."""
0
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136 fasta = self.fasta_list[0]
6
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137 if self.min_length:
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galaxy-australia
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138 if len(fasta.aa_seq) < self.min_length:
7
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139 raise ValueError(
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galaxy-australia
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140 'Error encountered validating FASTA:\n Sequence too short'
6
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141 f' ({len(fasta.aa_seq)}AA).'
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142 f' Minimum length is {self.min_length}AA.')
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143 if self.max_length:
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144 if len(fasta.aa_seq) > self.max_length:
7
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145 raise ValueError(
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galaxy-australia
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diff changeset
146 'Error encountered validating FASTA:\n'
6
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galaxy-australia
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147 f' Sequence too long ({len(fasta.aa_seq)}AA).'
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galaxy-australia
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148 f' Maximum length is {self.max_length}AA.')
1
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galaxy-australia
parents: 0
diff changeset
149
0
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150 def validate_alphabet(self):
7
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151 """Confirm whether the sequence conforms to IUPAC codes.
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diff changeset
152
6
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153 If not, report the offending character and its position.
1
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galaxy-australia
parents: 0
diff changeset
154 """
0
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galaxy-australia
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155 fasta = self.fasta_list[0]
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galaxy-australia
parents:
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156 for i, char in enumerate(fasta.aa_seq.upper()):
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galaxy-australia
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157 if char not in self.iupac_characters:
7
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galaxy-australia
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diff changeset
158 raise ValueError(
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galaxy-australia
parents: 6
diff changeset
159 'Error encountered validating FASTA:\n Invalid amino acid'
6
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galaxy-australia
parents: 1
diff changeset
160 f' found at pos {i}: "{char}"')
0
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galaxy-australia
parents:
diff changeset
161
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galaxy-australia
parents:
diff changeset
162 def validate_x(self):
6
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galaxy-australia
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163 """Check for X bases."""
0
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galaxy-australia
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164 fasta = self.fasta_list[0]
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galaxy-australia
parents:
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165 for i, char in enumerate(fasta.aa_seq.upper()):
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galaxy-australia
parents:
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166 if char == 'X':
7
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galaxy-australia
parents: 6
diff changeset
167 raise ValueError(
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galaxy-australia
parents: 6
diff changeset
168 'Error encountered validating FASTA:\n Unsupported AA code'
6
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galaxy-australia
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169 f' "X" found at pos {i}')
0
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galaxy-australia
parents:
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170
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galaxy-australia
parents:
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171
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galaxy-australia
parents:
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172 class FastaWriter:
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galaxy-australia
parents:
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173 def __init__(self) -> None:
6
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galaxy-australia
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174 self.line_wrap = 60
0
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galaxy-australia
parents:
diff changeset
175
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galaxy-australia
parents:
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176 def write(self, fasta: Fasta):
6
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177 header = fasta.header
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galaxy-australia
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178 seq = self.format_sequence(fasta.aa_seq)
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galaxy-australia
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diff changeset
179 sys.stdout.write(header + '\n')
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galaxy-australia
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diff changeset
180 sys.stdout.write(seq)
0
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181
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182 def format_sequence(self, aa_seq: str):
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183 formatted_seq = ''
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184 for i in range(0, len(aa_seq), self.line_wrap):
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185 formatted_seq += aa_seq[i: i + self.line_wrap] + '\n'
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186 return formatted_seq.upper()
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187
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188
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189 def main():
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190 # load fasta file
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191 try:
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192 args = parse_args()
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193 fas = FastaLoader(args.input)
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194
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195 # validate
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196 fv = FastaValidator(
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197 min_length=args.min_length,
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198 max_length=args.max_length,
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199 multiple=args.multimer,
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200 )
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201 clean_fastas = fv.validate(fas.fastas)
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202
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203 # write clean data
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204 fw = FastaWriter()
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205 for fas in clean_fastas:
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206 fw.write(fas)
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207
7
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208 except ValueError as exc:
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209 sys.stderr.write(f"{exc}\n\n")
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210 raise exc
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211
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212 except Exception as exc:
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213 sys.stderr.write(
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214 "Input error: FASTA input is invalid. Please check your input.\n\n"
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215 )
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216 raise exc
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217
1
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218
0
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219 def parse_args() -> argparse.Namespace:
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220 parser = argparse.ArgumentParser()
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221 parser.add_argument(
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222 "input",
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223 help="input fasta file",
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224 type=str
1
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225 )
6
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226 parser.add_argument(
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227 "--min_length",
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228 dest='min_length',
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229 help="Minimum length of input protein sequence (AA)",
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230 default=None,
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231 type=int,
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232 )
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233 parser.add_argument(
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234 "--max_length",
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235 dest='max_length',
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236 help="Maximum length of input protein sequence (AA)",
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237 default=None,
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238 type=int,
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239 )
9
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240 parser.add_argument(
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241 "--multimer",
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242 action='store_true',
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243 help="Require multiple input sequences",
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244 )
0
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245 return parser.parse_args()
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246
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247
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248 if __name__ == '__main__':
1
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249 main()