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

• 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>