Command Line Interface to fetch data from OmicsDI
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OmicsDi fetcher makes use of the OmicsDi API to find the data file links that belong to a data set accession number.
By default it gives these data links back. Using the -d
flag it is possible to download the files itself in the working directory or in a specified output directory using the -o
option. Files are placed in a folder with the accession number as name.
Simply use following command line to install OmicsDi fetcher on linux/macOS:
sudo python3 -m pip install git+git://github.com/bedroesb/omicsdi-cli.git
or this command for Windows (be sure that Python is installed):
pip install git+git://github.com/bedroesb/omicsdi-cli.git
When OmicsDI fetcher is installed correctly it should be available through the command omicsdi_fetcher
. You can easily test which version is installed with omicsdi_fetcher -v
. The tool has one mandatory parameter 'accession number' and several options:
omicsdi_fetcher [OPTIONS] ACC_NUMBER
Option | Type | Description |
---|---|---|
-v, --version | FLAG | Print version number |
-d, --download | FLAG | Use this flag to download the files in the current directory or a specified output directory |
-o, --output | PATH | Output directory when downloading files (default: CWD) |
-h, --help | FLAG | Show this message and exit. |
- A microarray dataset with ftp links:
omicsdi_fetcher E-MTAB-5612
- Downloading the microarray dataset with ftp links:
omicsdi_fetcher E-MTAB-5612 -d
- A BioModels dataset with https links:
omicsdi_fetcher BIOMD0000000048
- Downloading a dataset in a different directory than CWD:
omicsdi_fetcher BIOMD0000000048 -d -o <path to directory>