pyega3 3.0.33

EGA python client - pyEGA3
pyEGA3 uses the EGA REST API to download authorized datasets and files

Currently works only with Python3

REQUIREMENTS:
Python "requests" module
http://docs.python-requests.org/en/master/
pip3 install requests

Firewall Ports
This client makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443/) and to the EGA Data API (https://ega.ebi.ac.uk:8051). Both ports 8443 and 8051 must be reachable from the location where this client script is run. Otherwise you will experience timeouts.
(e.g. https://ega.ebi.ac.uk:8443/ega-openid-connect-server/, https://ega.ebi.ac.uk:8051/elixir/central/stats/load should not time out).
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INSTALLATION via Pip:
sudo pip3 install pyega3
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INSTALLATION via Conda(Bioconda channel):
conda config --add channels bioconda
conda config --add channels conda-forge
conda install pyega3
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USAGE:
pyega3 [-h] [-d] -cf CREDENTIALS_FILE [-c CONNECTIONS] {datasets,files,fetch} ...

Download from EMBL EBI's EGA (European Genome-phenome Archive)

positional arguments:
{datasets,files,fetch}
subcommands
datasets List authorized datasets
files List files in a specified dataset
fetch Fetch a dataset or file

optional arguments:
-h, --help show this help message and exit
-d, --debug Extra debugging messages
-cf CREDENTIALS_FILE, --credentials-file CREDENTIALS_FILE
JSON file containing credentials
e.g.{'username':'user1','password':'toor'}
-c CONNECTIONS, --connections CONNECTIONS
Download using specified number of connections

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Credentials file supposed to be in json format e.g:
{
"username": "my.email@domain.edu",
"password": "mypassword",
"client_secret":"AMenuDLjVdVo4BSwi0QD54LL6NeVDEZRzEQUJ7hJOM3g4imDZBHHX0hNfKHPeQIGkskhtCmqAJtt_jm7EKq-rWw"
}

Your username and password are provided to you by EGA.
Specifying password is not mandatory - if password is not provided
the user will be asked to enter it from the console

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Parallelism ( download via multiple connections ) works on the file level,
but still usable while downloading whole dataset.
If -c command line switch is provided all big files (>100Mb) in the
dataset will be downloaded using specified # of connections.

The number of connections breaks down individual file downloads into segments,
which are then downloaded in parallel. So using a very high number actually
introduces overhead that slows down the download of the file.
Files are still downloaded in sequence – so multiple connections doesn't mean
downloading multiple files in parallel, if an entire dataset is being downloaded.

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GENOMIC RANGE REQUESTS ( via Htsget protocol ) :

usage: pyega3 fetch [-h] [--reference-name REFERENCE_NAME]
[--reference-md5 REFERENCE_MD5] [--start START]
[--end END] [--format {BAM,CRAM}] [--saveto [SAVETO]]
identifier

positional arguments:
identifier Id for dataset (e.g. EGAD00000000001) or file (e.g.
EGAF12345678901)

optional arguments:
-h, --help show this help message and exit
--reference-name REFERENCE_NAME, -r REFERENCE_NAME
The reference sequence name, for example 'chr1', '1',
or 'chrX'. If unspecified, all data is returned.
--reference-md5 REFERENCE_MD5, -m REFERENCE_MD5
The MD5 checksum uniquely representing the requested
reference sequence as a lower-case hexadecimal string,
calculated as the MD5 of the upper-case sequence
excluding all whitespace characters.
--start START, -s START
The start position of the range on the reference,
0-based, inclusive. If specified, reference-name or
reference-md5 must also be specified.
--end END, -e END The end position of the range on the reference,
0-based exclusive. If specified, reference-name or
reference-md5 must also be specified.
--format {BAM,CRAM}, -f {BAM,CRAM}
The format of data to request.
--max-retries MAX_RETRIES, -M MAX_RETRIES
The maximum number of times to retry a failed
transfer. Any negative number means infinite number of
retries( default value = 5 ).
--retry-wait RETRY_WAIT, -W RETRY_WAIT
The number of seconds to wait before retrying a failed
transfer( default value = 5 ).
--saveto [SAVETO] Output file(for files)/output dir(for datasets)