extend
ensembl.io.genomio.genome_metadata.extend
¶
Update a genome metadata file to include additional sequence regions (e.g. MT chromosome).
amend_genome_metadata(genome_infile, genome_outfile, report_file=None, genbank_file=None)
¶
Parameters:
Name | Type | Description | Default |
---|---|---|---|
genome_infile
|
PathLike
|
Genome metadata following the |
required |
genome_outfile
|
PathLike
|
Amended genome metadata file. |
required |
report_file
|
Optional[PathLike]
|
INSDC/RefSeq sequences report file. |
None
|
genbank_file
|
Optional[PathLike]
|
INSDC/RefSeq GBFF file. |
None
|
Source code in src/python/ensembl/io/genomio/genome_metadata/extend.py
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|
get_additions(report_path, gbff_path)
¶
Returns all seq_regions
that are mentioned in the report but that are not in the data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
report_path
|
PathLike
|
Path to the report file. |
required |
gbff_path
|
Optional[PathLike]
|
Path to the GBFF file. |
required |
Source code in src/python/ensembl/io/genomio/genome_metadata/extend.py
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|
get_gbff_regions(gbff_path)
¶
Returns the seq_region
data from a GBFF file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gbff_path
|
Optional[PathLike]
|
GBFF file path to use. |
required |
Source code in src/python/ensembl/io/genomio/genome_metadata/extend.py
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|
get_report_regions_names(report_path)
¶
Returns a list of GenBank-RefSeq seq_region
names from the assembly report file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
report_path
|
PathLike
|
Path to the assembly report file from INSDC/RefSeq. |
required |
Source code in src/python/ensembl/io/genomio/genome_metadata/extend.py
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|
main()
¶
Module's entry-point.
Source code in src/python/ensembl/io/genomio/genome_metadata/extend.py
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