1 / 9

Downloading Datasets

Fetching datasets from the Internet. Downloading Datasets. Let's Get Data. http://www.emboss.org. Downloading From The Web. $ man wget. Using wget to download PDB data-files. $ mkdir structures $ cd structures $ wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1m7t.ent.Z

erv
Télécharger la présentation

Downloading Datasets

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Fetching datasets from the Internet Downloading Datasets

  2. Let's Get Data http://www.emboss.org

  3. Downloading From The Web $ man wget

  4. Using wget to download PDB data-files $ mkdir structures $ cd structures $ wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1m7t.ent.Z $ wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1lqt.ent.Z $ gzip -d pdb1m7t.ent.Z pdb1lqt.ent.Z

  5. Mirroring a dataset $ wget --mirror ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb

  6. Only download a dataset when absolutely necessary. Consider the implications of doing so first Maxim 9.1

  7. Smarter mirroring structures/ftp.rcsb.org/pub/pdb/data/structures/all/pdb $ wget --output-file=log --mirror --http-user=anonymous --http-passwd=email@where.ever.net --directory-prefix=structures/mmCIF --no-host-directories --cut-dirs=6 ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb

  8. Downloading a subset of a dataset $ wget ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/all/1ger.cif.Z

  9. Where To From Here

More Related