check_integrity
ensembl.io.genomio.manifest.check_integrity
¶
Compare the genomic data in a DNA FASTA file, seq_region JSON, gene models GFF3 and peptide FASTA to ensure their contents are in sync.
IntegrityTool
¶
Check the integrity of sequence and annotation files in the genome
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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errors = []
instance-attribute
¶
ignore_final_stops = False
instance-attribute
¶
manifest = ManifestStats(manifest_file)
instance-attribute
¶
no_fail = no_fail
instance-attribute
¶
add_errors(errors)
¶
Store the given errors (list or single string) in the list of all errors.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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check_ids(list1, list2, name)
¶
Compare the ids in list1 and list2.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
list1
|
dict[str, Any]
|
Sequence IDs retrieved from |
required |
list2
|
dict[str, Any]
|
Sequence IDs retrieved from the GFF3 file. |
required |
name
|
str
|
Source name. |
required |
Return
List of message errors of sequence IDs found only in one of the lists provided.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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check_integrity()
¶
Load files listed in the manifest.json and check the integrity. Check if the files are correct by verifying the MD5 hash. Check if translation, functional annotation and sequence region ids and lengths are consistent with the information in gff. Compare sequence length from fasta_dna file to seq_region.json metadata.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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check_lengths(list1, list2, name, *, allowed_len_diff=None, special_diff=False)
¶
Check the difference in ids and length between list1 and list2. There are a few special cases here where we allow a certain asymmetry by changing the values of the arguments.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
list1
|
dict[str, int]
|
dict containing length and id of the sequence from fasta files. |
required |
list2
|
dict[str, int]
|
dict containing length and id in the retrieved from the gff. |
required |
name
|
str
|
string |
required |
None to to not accept differences in length between list1 and list2.
The value can be changed based on how much difference in sequence length we are wanting to accept.
set as False when no special length difference is expected between the lists.
This can be changed if we want to report common sequences with 1 BP difference.
Returns:
Type | Description |
---|---|
list[str]
|
Error if there is a difference in length or ids between the lists. |
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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check_seq_region_lengths(seqrs, feats, name, circular=None)
¶
Check the integrity of seq_region.json file by comparing the length of the sequence to fasta files and the gff.
Seq_region file is in json format containing the metadata of the sequence.
It contains sequence id, length, location and the synonyms for the sequence name
from different sources.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
seqs
|
Sequence name and length retrieved from seq_region.json file. |
required | |
feats
|
dict[str, Any] | None
|
Sequence name and length retrieved from the fasta and gff file. |
required |
name
|
str
|
Name of the check to show in the logs. |
required |
circular
|
dict[str, Any] | None
|
Whether any sequence is circular. |
None
|
Returns:
Type | Description |
---|---|
None
|
Error if there are common sequences with difference in ids |
None
|
and if the sequences are not consistent in the files. |
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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set_ignore_final_stops(ignore_final_stops)
¶
Set ignore_final_stops (when calculating peptide length) for this tool and the manifest.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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main()
¶
Main entrypoint.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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