manifest_stats
ensembl.io.genomio.manifest.manifest_stats
¶
Representation of the statistics of the set of files listed in the manifest file provided.
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 |
|
accession = accession
instance-attribute
¶
check_ncbi = False
instance-attribute
¶
datasets_bin = datasets_bin
instance-attribute
¶
errors = []
instance-attribute
¶
errors_file = Path(manifest_dir) / 'stats_diff.log'
instance-attribute
¶
manifest = f'{manifest_dir}/manifest.json'
instance-attribute
¶
manifest_parent = manifest_dir
instance-attribute
¶
biotypes_stats(biotypes)
¶
Prepare biotype stats in order of their name.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
biotypes
|
Dict[str, BiotypeCounter]
|
Biotypes counters. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
A list with the computed statistics in a printable format. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 |
|
check_ncbi_stats(biotypes)
¶
Use the dataset tool from NCBI to get stats and compare with what we have
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 |
|
compare_ncbi_counts(biotypes, ncbi)
¶
Compare specific gene stats from NCBI
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 |
|
coord_systems_stats(coord_systems)
¶
For each coord_system compute various stats
- number of sequences
- sequence length sum, minimum, maximum, mean
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coord_systems
|
Dict[str, List[int]]
|
Coordinate system dictionary of lengths. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
A list with the computed statistics in a printable format. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 |
|
count_biotypes(gff3_path)
¶
Count the biotypes in a GFF3 file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gff3_path
|
Path
|
Path to the GFF3 file. |
required |
Returns:
Type | Description |
---|---|
Dict[str, BiotypeCounter]
|
Dictionary of biotype counters. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 |
|
get_gff3_stats(gff3_path)
¶
Extract the gene models from the GFF3 file and compute stats.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gff3_path
|
Path
|
the GFF3 file. |
required |
Returns:
Name | Type | Description |
---|---|---|
List |
List[str]
|
Stats from the gene model. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 |
|
get_manifest()
¶
Get the files metadata from the manifest json file.
Returns:
Name | Type | Description |
---|---|---|
Dict |
Dict
|
A representation of the manifest json data. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 |
|
get_seq_region_stats(seq_region_path)
¶
Compute stats from the seq_region json file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
seq_region_path
|
Path
|
the seq_region json file. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
List[str]: Stats from the seq_regions. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 |
|
increment_biotype(biotypes, feature_id, feature_biotype)
staticmethod
¶
Add the feature to their respective biotype counter.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
biotypes
|
Dict[str, BiotypeCounter]
|
All current biotypes, with their counter. |
required |
feature_id
|
str
|
Feature id to be counted. |
required |
feature_biotype
|
str
|
The biotype of the feature. |
required |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
397 398 399 400 401 402 403 404 405 406 407 408 |
|
run(stats_path)
¶
Compute stats in the files and output a stats.txt file in the same folder.
Raises:
Type | Description |
---|---|
StatsError
|
Could not compute some stats. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 |
|
seq_region_special_stats(circular=0, locations=None, codon_tables=None)
¶
Prepare stats in case there are circular regions, specific locations and codon_tables. stats.append(f"{count: 9f} {name}")
Parameters:
Name | Type | Description | Default |
---|---|---|---|
circular
|
int
|
Number of circular regions. Defaults to 0. |
0
|
locations
|
Optional[List[str]]
|
The regions and their location. Defaults to None. |
None
|
codon_tables
|
Optional[List[str]]
|
The regions and their codon_table. Defaults to None. |
None
|
Returns:
Type | Description |
---|---|
List[str]
|
A list with the computed statistics in a printable format. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 |
|