assembly
ensembl.io.genomio.assembly
¶
Assembly preparation module.
FTPConnectionError
¶
Bases: Exception
Error while initialising an FTP connection.
Source code in src/python/ensembl/io/genomio/assembly/download.py
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FileDownloadError
¶
Bases: Exception
When a file download fails or there is a problem with that file.
Source code in src/python/ensembl/io/genomio/assembly/download.py
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UnsupportedFormatError
¶
Bases: Exception
When a string does not have the expected format.
Source code in src/python/ensembl/io/genomio/assembly/download.py
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download_files(ftp_connection, accession, dl_dir, max_redo)
¶
Given an INSDC accession, download all available files from the ftp to the download dir
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ftp_connection
|
FTP
|
An open FTP connection object |
required |
accession
|
str
|
Genome assembly accession. |
required |
dl_dir
|
Path
|
Path to downloaded FTP files. |
required |
max_redo
|
int
|
Maximum FTP connection retry attempts. |
required |
Source code in src/python/ensembl/io/genomio/assembly/download.py
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|
establish_ftp(ftp_conn, ftp_url, accession)
¶
Return an FTP connection based on the provided accession
and sub_dir
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ftp_conn
|
FTP
|
FTP class object. |
required |
ftp_url
|
str
|
Specific FTP URL in connection request. |
required |
accession
|
str
|
Genome accession required data for download. |
required |
Raises:
Type | Description |
---|---|
UnsupportedFormatError
|
If |
Source code in src/python/ensembl/io/genomio/assembly/download.py
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|
extract_assembly_metadata(assembly_reports)
¶
Parse assembly reports and extract specific key information on status and related fields.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
assembly_reports
|
dict[str, dict]
|
Key value pair of source name <> assembly report. |
required |
Returns:
Type | Description |
---|---|
dict[str, ReportStructure]
|
Parsed assembly report meta (source, meta). |
Source code in src/python/ensembl/io/genomio/assembly/status.py
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|
fetch_accessions_from_core_dbs(src_file, server_url)
¶
Obtain the associated INSDC accession given a set of core database names and a database server URL.
The accession information is obtained from the meta
table's meta key assembly.accession
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
src_file
|
StrPath
|
File path with list of core database names. |
required |
server_url
|
URL
|
Database server URL. |
required |
Returns:
Type | Description |
---|---|
dict[str, str]
|
Dict of core database names (key) and their corresponding INSDC assembly accession (value). |
Source code in src/python/ensembl/io/genomio/assembly/status.py
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fetch_datasets_reports(sif_image, assembly_accessions, download_directory, batch_size)
¶
Obtain assembly reports in JSON format for each assembly accession via datasets
CLI.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
sif_image
|
Client
|
Instance of |
required |
assembly_accessions
|
dict[str, str]
|
Dictionary of accession source <> assembly accessions pairs. |
required |
download_directory
|
StrPath
|
Directory path to store assembly report JSON files. |
required |
batch_size
|
int
|
Number of assembly accessions to batch submit to |
required |
Returns:
Type | Description |
---|---|
dict[str, dict]
|
Dictionary of accession source and its associated assembly report. |
Raises:
Type | Description |
---|---|
ValueError
|
If result returned by |
RuntimeError
|
If there was an error raised by |
Source code in src/python/ensembl/io/genomio/assembly/status.py
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|
generate_report_tsv(parsed_asm_reports, query_type, output_directory=Path(), outfile_name='AssemblyStatusReport')
¶
Generate and write the assembly report to a TSV file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
parsed_asm_reports
|
dict[str, ReportStructure]
|
Parsed assembly report meta. |
required |
query_type
|
str
|
Type of query (either core databases or accessions). |
required |
output_directory
|
StrPath
|
Directory to store report TSV file. |
Path()
|
outfile_name
|
str
|
Name to give to the output TSV file. |
'AssemblyStatusReport'
|
Source code in src/python/ensembl/io/genomio/assembly/status.py
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get_assembly_accessions(src_file)
¶
Returns the list of assembly accessions found in the provided file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
src_file
|
StrPath
|
Path to file with one line per INSDC assembly accession. |
required |
Raises:
Type | Description |
---|---|
UnsupportedFormatError
|
If an accession does not match the INSDC assembly accession format. |
Source code in src/python/ensembl/io/genomio/assembly/status.py
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get_checksums(checksum_path)
¶
Get a dict of checksums from a file, with file names as keys and sums as values
Parameters:
Name | Type | Description | Default |
---|---|---|---|
checksum_path
|
Path
|
Path location to MD5 checksum file. |
required |
Source code in src/python/ensembl/io/genomio/assembly/download.py
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get_files_selection(dl_dir)
¶
Returns a dictionary with the relevant downloaded files classified.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dl_dir
|
Path
|
Local path to downloaded FTP files. |
required |
Returns:
Type | Description |
---|---|
Dict[str, str]
|
Dictionary of file type (e.g. |
Raises:
Type | Description |
---|---|
FileDownloadError
|
If |
Source code in src/python/ensembl/io/genomio/assembly/download.py
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get_root_name(dl_dir)
¶
Returns the root name, i.e. shared files basename prefix, using the assembly report file as base.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dl_dir
|
Path
|
Path location of downloaded FTP files. |
required |
Source code in src/python/ensembl/io/genomio/assembly/download.py
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md5_files(dl_dir, md5_path=None, md5_filename='md5checksums.txt')
¶
Check all files checksums with the sums listed in a checksum file, if available. Return False if there is no checksum file, or a file is missing, or has a wrong checksum.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dl_dir
|
Path
|
Path location to containing downloaded FTP files. |
required |
md5_path
|
Optional[Path]
|
Full path to an MD5 checksum file. |
None
|
md5_filename
|
str
|
Name of a checksum file in the |
'md5checksums.txt'
|
Source code in src/python/ensembl/io/genomio/assembly/download.py
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retrieve_assembly_data(accession, download_dir, max_increment=0, max_redo=3)
¶
Establishes an FTP connection and downloads a predefined subset of assembly data files from either INSDC or RefSeq.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
accession
|
str
|
Genome assembly accession. |
required |
download_dir
|
PathLike
|
Path to where to download FTP files. |
required |
max_increment
|
int
|
If you want to allow assembly versions. |
0
|
max_redo
|
int
|
Maximum FTP connection retry attempts. |
3
|
Raises:
Type | Description |
---|---|
FileDownloadError
|
If no files are downloaded or if any does not match its MD5 checksum. |
Source code in src/python/ensembl/io/genomio/assembly/download.py
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singularity_image_setter(sif_cache_dir, datasets_version)
¶
Parse ENV and User specified variables related to datasets
singularity SIF
container and define version and location of container.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
sif_cache_dir
|
Path | None
|
Path to locate existing, or download new SIF container image. |
required |
datasets_version
|
str | None
|
URL of singularity container (custom |
required |
Returns:
Type | Description |
---|---|
Client
|
|
Source code in src/python/ensembl/io/genomio/assembly/status.py
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