Mercurial > repos > galaxy-australia > alphafold2

annotate validate_fasta.py @ 7:eb085b3dbaf8 draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
author galaxy-australia
date Tue, 19 Apr 2022 00:39:29 +0000
parents 04e95886cf24
children ca90d17ff51b
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1 """Validate input FASTA sequence."""
0
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2
1
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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, TextIO
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7
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8
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9 class Fasta:
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10 def __init__(self, header_str: str, seq_str: str):
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11 self.header = header_str
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12 self.aa_seq = seq_str
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7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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15 class FastaLoader:
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16 def __init__(self, fasta_path: str):
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17 """Initialize from FASTA file."""
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18 self.fastas = []
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19 self.load(fasta_path)
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21 def load(self, fasta_path: str):
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22 """Load bare or FASTA formatted sequence."""
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23 with open(fasta_path, 'r') as f:
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24 self.content = f.read()
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26 if "__cn__" in self.content:
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27 # Pasted content with escaped characters
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28 self.newline = '__cn__'
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29 self.read_caret = '__gt__'
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30 else:
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31 # Uploaded file with normal content
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32 self.newline = '\n'
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33 self.read_caret = '>'
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34
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35 self.lines = self.content.split(self.newline)
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36
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37 if not self.lines[0].startswith(self.read_caret):
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38 # Fasta is headless, load as single sequence
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39 self.update_fastas(
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40 '', ''.join(self.lines)
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41 )
1
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42
0
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43 else:
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44 header = None
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45 sequence = None
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46 for line in self.lines:
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47 if line.startswith(self.read_caret):
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48 if header:
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49 self.update_fastas(header, sequence)
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50 header = '>' + self.strip_header(line)
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51 sequence = ''
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52 else:
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53 sequence += line.strip('\n ')
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54 self.update_fastas(header, sequence)
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55
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56 def strip_header(self, line):
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57 """Strip characters escaped with underscores from pasted text."""
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58 return re.sub(r'\_\_.{2}\_\_', '', line).strip('>')
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59
0
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60 def update_fastas(self, header: str, sequence: str):
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61 # if we have a sequence
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62 if sequence:
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63 # create generic header if not exists
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64 if not header:
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65 fasta_count = len(self.fastas)
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66 header = f'>sequence_{fasta_count}'
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67
1
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68 # Create new Fasta
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69 self.fastas.append(Fasta(header, sequence))
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70
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71
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72 class FastaValidator:
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73 def __init__(
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74 self,
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75 fasta_list: List[Fasta],
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76 min_length=None,
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77 max_length=None):
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78 self.min_length = min_length
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79 self.max_length = max_length
0
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80 self.fasta_list = fasta_list
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81 self.iupac_characters = {
1
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82 'A', 'B', 'C', 'D', 'E', 'F', 'G',
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83 'H', 'I', 'K', 'L', 'M', 'N', 'P',
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84 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
0
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85 'Y', 'Z', '-'
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86 }
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87
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88 def validate(self):
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diff changeset
89 """Perform FASTA validation."""
0
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galaxy-australia
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90 self.validate_num_seqs()
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galaxy-australia
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91 self.validate_length()
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92 self.validate_alphabet()
6
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93
1
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galaxy-australia
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94 # not checking for 'X' nucleotides at the moment.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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95 # alphafold can throw an error if it doesn't like it.
6
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96 # self.validate_x()
0
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97
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98 def validate_num_seqs(self) -> None:
6
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galaxy-australia
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99 """Assert that only one sequence has been provided."""
0
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100 if len(self.fasta_list) > 1:
7
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101 raise ValueError(
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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102 'Error encountered validating FASTA:\n'
6
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galaxy-australia
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103 f' More than 1 sequence detected ({len(self.fasta_list)}).'
7
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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104 ' Please use single FASTA sequence as input.')
0
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galaxy-australia
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105 elif len(self.fasta_list) == 0:
7
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galaxy-australia
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106 raise ValueError(
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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diff changeset
107 'Error encountered validating FASTA:\n'
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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108 ' input file has no FASTA sequences')
0
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109
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110 def validate_length(self):
6
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111 """Confirm whether sequence length is valid."""
0
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112 fasta = self.fasta_list[0]
6
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113 if self.min_length:
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114 if len(fasta.aa_seq) < self.min_length:
7
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115 raise ValueError(
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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116 'Error encountered validating FASTA:\n Sequence too short'
6
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galaxy-australia
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117 f' ({len(fasta.aa_seq)}AA).'
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galaxy-australia
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118 f' Minimum length is {self.min_length}AA.')
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119 if self.max_length:
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galaxy-australia
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120 if len(fasta.aa_seq) > self.max_length:
7
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galaxy-australia
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121 raise ValueError(
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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diff changeset
122 'Error encountered validating FASTA:\n'
6
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galaxy-australia
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123 f' Sequence too long ({len(fasta.aa_seq)}AA).'
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galaxy-australia
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124 f' Maximum length is {self.max_length}AA.')
1
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galaxy-australia
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125
0
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126 def validate_alphabet(self):
7
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127 """Confirm whether the sequence conforms to IUPAC codes.
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128
6
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129 If not, report the offending character and its position.
1
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galaxy-australia
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130 """
0
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131 fasta = self.fasta_list[0]
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132 for i, char in enumerate(fasta.aa_seq.upper()):
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galaxy-australia
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133 if char not in self.iupac_characters:
7
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galaxy-australia
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diff changeset
134 raise ValueError(
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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diff changeset
135 'Error encountered validating FASTA:\n Invalid amino acid'
6
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galaxy-australia
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136 f' found at pos {i}: "{char}"')
0
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137
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galaxy-australia
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138 def validate_x(self):
6
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139 """Check for X bases."""
0
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galaxy-australia
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140 fasta = self.fasta_list[0]
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galaxy-australia
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141 for i, char in enumerate(fasta.aa_seq.upper()):
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142 if char == 'X':
7
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143 raise ValueError(
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
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144 'Error encountered validating FASTA:\n Unsupported AA code'
6
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galaxy-australia
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145 f' "X" found at pos {i}')
0
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146
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147
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148 class FastaWriter:
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149 def __init__(self) -> None:
6
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150 self.line_wrap = 60
0
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151
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152 def write(self, fasta: Fasta):
6
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153 header = fasta.header
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galaxy-australia
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154 seq = self.format_sequence(fasta.aa_seq)
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galaxy-australia
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diff changeset
155 sys.stdout.write(header + '\n')
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galaxy-australia
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diff changeset
156 sys.stdout.write(seq)
0
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157
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galaxy-australia
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158 def format_sequence(self, aa_seq: str):
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159 formatted_seq = ''
6
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160 for i in range(0, len(aa_seq), self.line_wrap):
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galaxy-australia
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161 formatted_seq += aa_seq[i: i + self.line_wrap] + '\n'
0
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162 return formatted_seq
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163
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galaxy-australia
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164
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165 def main():
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166 # load fasta file
7
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diff changeset
167 try:
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diff changeset
168 args = parse_args()
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169 fas = FastaLoader(args.input)
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170
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diff changeset
171 # validate
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172 fv = FastaValidator(
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173 fas.fastas,
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diff changeset
174 min_length=args.min_length,
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175 max_length=args.max_length,
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diff changeset
176 )
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diff changeset
177 fv.validate()
0
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178
7
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179 # write cleaned version
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180 fw = FastaWriter()
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181 fw.write(fas.fastas[0])
0
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182
7
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183 except ValueError as exc:
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184 sys.stderr.write(f"{exc}\n\n")
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185 raise exc
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186
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187 except Exception as exc:
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188 sys.stderr.write(
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189 "Input error: FASTA input is invalid. Please check your input.\n\n"
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190 )
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191 raise exc
0
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192
1
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193
0
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194 def parse_args() -> argparse.Namespace:
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195 parser = argparse.ArgumentParser()
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196 parser.add_argument(
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197 "input",
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198 help="input fasta file",
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199 type=str
1
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200 )
6
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201 parser.add_argument(
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202 "--min_length",
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203 dest='min_length',
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204 help="Minimum length of input protein sequence (AA)",
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205 default=None,
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206 type=int,
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207 )
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208 parser.add_argument(
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209 "--max_length",
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210 dest='max_length',
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211 help="Maximum length of input protein sequence (AA)",
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212 default=None,
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213 type=int,
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214 )
0
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215 return parser.parse_args()
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216
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217
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218 if __name__ == '__main__':
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219 main()