When data is uploaded to PipeBio, we parse it and display the results to users. Sequence and related data can then be exported in a wide range of common bioinformatic formats, such as Genbank, Fasta, Fastq and more.
But what if you want the original, un-parsed file out? Many PipeBio customers require an audit trail of the sequences for taking drug candidates to clinical trials.
Exporting the originally uploaded files from PipeBio is easy via the UI. Simply select the file to export, choose File > export from the menu and select “Source files” from the dropdown.
You can also export these source files using the PipeBio REST API. A full working example with daily integration tests is available in the public PipeBio Github repo, here.
Here’s how to download the original files from PipeBio Bioinformatics cloud in 3 steps:
1. Authenticate with PipeBio
2. Request a pre-signed url for the document you want to export
3. Download data from the pre-signed url.
That’s it! Your raw un-parsed files will be downloaded to the directory you have specified by destination_filename above.
To see it running in action check out our test suite, here: https://github.com/pipebio/api-examples/actions
To try PipeBio, visit our website for a free trial.
