download
ensembl.io.genomio.assembly.download
¶
Download an assembly data files from INSDC or RefSeq.
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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|
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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|
main()
¶
Module's entry-point.
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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