Downloading%20Datasets

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Downloading Datasets

• Fetching datasets from the Internet

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Let's Get Data
http//www.emboss.org
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Downloading From The Web

• man wget

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Using wget to download PDB data-files
mkdir structures cd structures wget
ftp//ftp.rcsb.org/pub/pdb/data/structures/all/pdb
1m7t.ent.Z wget ftp//ftp.rcsb.org/pub/pdb/dat
a/structures/all/pdb1lqt.ent.Z gzip -d
pdb1m7t.ent.Z pdb1lqt.ent.Z
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Mirroring a dataset

• wget --mirror ftp//ftp.rcsb.org/pub/pdb/data/st
  ructures/all/pdb

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Maxim 9.1

• Only download a dataset when absolutely
  necessary. Consider the implications of doing so
  first

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Smarter mirroring

• structures/ftp.rcsb.org/pub/pdb/data/structures/al
  l/pdb
• wget --output-filelog --mirror
  --http-useranonymous
• --http-passwdemail_at_where.ever.net
• --directory-prefixstructures/mmCIF
• --no-host-directories
• --cut-dirs6 ftp//ftp.rcsb.org/pub/pdb/data/st
  ructures/all/pdb

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Downloading a subset of a dataset

• wget ftp//beta.rcsb.org/pub/pdb/uniformity/data
  /mmCIF/all/1ger.cif.Z

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Where To From Here