Coverage for src/python/ensembl/io/genomio/genome_metadata/prepare.py: 87%

1# See the NOTICE file distributed with this work for additional information 

2# regarding copyright ownership. 

3# 

4# Licensed under the Apache License, Version 2.0 (the "License"); 

5# you may not use this file except in compliance with the License. 

6# You may obtain a copy of the License at 

7# 

8# http://www.apache.org/licenses/LICENSE-2.0 

9# 

10# Unless required by applicable law or agreed to in writing, software 

11# distributed under the License is distributed on an "AS IS" BASIS, 

12# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 

13# See the License for the specific language governing permissions and 

14# limitations under the License. 

15"""Expand the genome metadata file adding information about the provider, taxonomy, and assembly and 

16gene build versions. 

17""" 

18 

19__all__ = [ 

20 "add_provider", 

21 "add_assembly_version", 

22 "add_genebuild_metadata", 

23 "add_species_metadata", 

24 "prepare_genome_metadata", 

25 "PROVIDER_DATA", 

26 "MissingNodeError", 

27 "MetadataError", 

28] 

29 

30import datetime 

31from os import PathLike 

32from typing import Dict 

33 

34import ensembl.io.genomio 

35from ensembl.io.genomio.utils import get_json, print_json 

36from ensembl.utils.argparse import ArgumentParser 

37from ensembl.utils.logging import init_logging_with_args 

38 

39 

40PROVIDER_DATA = { 

41 "GenBank": { 

42 "assembly": { 

43 "provider_name": "GenBank", 

44 "provider_url": "https://www.ncbi.nlm.nih.gov/datasets/genome", 

45 }, 

46 "annotation": { 

47 "provider_name": "GenBank", 

48 "provider_url": "https://www.ncbi.nlm.nih.gov/datasets/genome", 

49 }, 

50 }, 

51 "RefSeq": { 

52 "assembly": { 

53 "provider_name": "RefSeq", 

54 "provider_url": "https://www.ncbi.nlm.nih.gov/datasets/genome", 

55 }, 

56 "annotation": { 

57 "provider_name": "RefSeq", 

58 "provider_url": "https://www.ncbi.nlm.nih.gov/datasets/genome", 

59 }, 

60 }, 

61} 

62 

63 

64class MissingNodeError(Exception): 

65 """When a taxon XML node cannot be found.""" 

66 

67 

68class MetadataError(Exception): 

69 """When a metadata value is not expected.""" 

70 

71 

72def add_provider(genome_metadata: Dict, ncbi_data: Dict) -> None: 

73 """Updates the genome metadata adding provider information for assembly and gene models. 

74 

75 Assembly provider metadata will only be added if it is missing, i.e. neither `"provider_name"` or 

76 `"provider_url"` are present. The gene model metadata will only be added if `gff3_file` is provided. 

77 

78 Args: 

79 genome_data: Genome information of assembly, accession and annotation. 

80 ncbi_data: Report data from NCBI datasets. 

81 

82 Raises: 

83 MetadataError: If accession's format in genome metadata does not match with a known provider. 

84 """ 

85 # Get accession provider 

86 accession = genome_metadata["assembly"]["accession"] 

87 if accession.startswith("GCF"): 

88 provider = PROVIDER_DATA["RefSeq"] 

89 elif accession.startswith("GCA"): 

90 provider = PROVIDER_DATA["GenBank"] 

91 else: 

92 raise MetadataError(f"Accession does not look like an INSDC or RefSeq accession: {accession}") 

93 

94 # Add assembly provider (if missing) 

95 assembly = genome_metadata["assembly"] 

96 if ("provider_name" not in assembly) and ("provider_url" not in assembly): 

97 assembly["provider_name"] = provider["assembly"]["provider_name"] 

98 assembly["provider_url"] = f'{provider["assembly"]["provider_url"]}/{accession}' 

99 

100 # Add annotation provider if there are gene models 

101 if "annotation_info" in ncbi_data: 

102 annotation = genome_metadata.setdefault("annotation", {}) 

103 if ("provider_name" not in annotation) and ("provider_url" not in annotation): 

104 annotation["provider_name"] = provider["annotation"]["provider_name"] 

105 annotation["provider_url"] = f'{provider["annotation"]["provider_url"]}/{accession}' 

106 

107 

108def add_assembly_version(genome_data: Dict) -> None: 

109 """Adds version number to the genome's assembly information if one is not present already. 

110 

111 Args: 

112 genome_data: Genome information of assembly, accession and annotation. 

113 """ 

114 assembly = genome_data["assembly"] 

115 if "version" not in assembly: 

116 accession = assembly["accession"] 

117 version = accession.partition(".")[2] 

118 if version: 

119 assembly["version"] = int(version) 

120 

121 

122def add_genebuild_metadata(genome_data: Dict) -> None: 

123 """Adds genebuild metadata to genome information if not present already. 

124 

125 The default convention is to use the current date as `"version"` and `"start_date"`. 

126 

127 Args: 

128 genome_data: Genome information of assembly, accession and annotation. 

129 """ 

130 genebuild = genome_data.setdefault("genebuild", {}) 

131 current_date = datetime.date.today().isoformat() 

132 if "version" not in genebuild: 

133 genebuild["version"] = current_date 

134 if "start_date" not in genebuild: 

135 genebuild["start_date"] = current_date 

136 

137 

138def add_species_metadata(genome_metadata: Dict, ncbi_data: Dict) -> None: 

139 """Adds taxonomy ID, scientific name and strain (if present) from the NCBI dataset report. 

140 

141 Args: 

142 genome_metadata: Genome information of assembly, accession and annotation. 

143 ncbi_data: Report data from NCBI datasets. 

144 

145 """ 

146 species = genome_metadata.setdefault("species", {}) 

147 try: 

148 organism = ncbi_data["organism"] 

149 except KeyError: 

150 return 

151 

152 if "tax_id" in organism: 152 ↛ 154line 152 didn't jump to line 154 because the condition on line 152 was always true

153 species.setdefault("taxonomy_id", organism["tax_id"]) 

154 if "organism_name" in organism: 

155 species.setdefault("scientific_name", organism["organism_name"]) 

156 

157 try: 

158 species.setdefault("strain", organism["infraspecific_names"]["strain"]) 

159 except KeyError: 

160 pass 

161 

162 

163def prepare_genome_metadata( 

164 input_file: PathLike, 

165 output_file: PathLike, 

166 ncbi_meta: PathLike, 

167) -> None: 

168 """Updates the genome metadata JSON file with additional information. 

169 

170 In particular, more information is added about the provider, the assembly and its gene build version, 

171 and the taxonomy. 

172 

173 Args: 

174 input_file: Path to JSON file with genome metadata. 

175 output_file: Output directory where to generate the final `genome.json` file. 

176 ncbi_meta: JSON file from NCBI datasets. 

177 

178 """ 

179 genome_data = get_json(input_file) 

180 ncbi_data = {} 

181 if ncbi_meta: 181 ↛ 185line 181 didn't jump to line 185 because the condition on line 181 was always true

182 ncbi_data = get_json(ncbi_meta)["reports"][0] 

183 

184 # Amend any missing metadata 

185 add_provider(genome_data, ncbi_data) 

186 add_assembly_version(genome_data) 

187 add_genebuild_metadata(genome_data) 

188 add_species_metadata(genome_data, ncbi_data) 

189 # Dump updated genome metadata 

190 print_json(output_file, genome_data) 

191 

192 

193def main() -> None: 

194 """Module's entry-point.""" 

195 parser = ArgumentParser(description=__doc__) 

196 parser.add_argument_src_path("--input_file", required=True, help="Genome metadata JSON file") 

197 parser.add_argument_dst_path( 

198 "--output_file", required=True, help="Output path for the new genome metadata file" 

199 ) 

200 parser.add_argument_src_path( 

201 "--ncbi_meta", required=True, help="JSON file from NCBI datasets for this genome." 

202 ) 

203 parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__) 

204 parser.add_log_arguments() 

205 args = parser.parse_args() 

206 init_logging_with_args(args) 

207 

208 prepare_genome_metadata( 

209 input_file=args.input_file, output_file=args.output_file, ncbi_meta=args.ncbi_meta 

210 )