A Command Line Tool for downloading protein structures, protein sequences and multiple sequence alignments.

Easy install from github using pip.

$ pip install --upgrade http://github.com/biomadeira/BioDownloader/zipball/master

If you want to mess up with the source code.

$ git clone https://github.com/biomadeira/BioDownloader.git
$ cd BioDownloader
$ sudo python setup.py install

Printing help information...

$ BioDownloader -h
Usage: BioDownloader [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...

  BioDownloader: a Command Line Tool for downloading protein structures,
  protein sequences and multiple sequence alignments.

      $ BioDownloader COMMAND --help for additional help

Options:
  --version      Show the version and exit.
  -h, --help     Show this message and exit.

Commands:
  cath     Multiple sequence alignments (fasta) from...
  pdb      Macromolecular structures from the PDBe.
  pfam     Multiple sequence alignments (fasta) from...
  sifts    SIFTS xml structure-sequence mappings from...
  uniprot  Sequences (fasta) and sequence annotations in...

Printing help information for one of the available commands...

$ BioDownloader uniprot -h
Usage: BioDownloader uniprot [OPTIONS] IDS...

  Sequences (fasta) and sequence annotations in SwissProt (txt) or GFF (gff)
  format from the UniProt.

  Pass one or more accession IDs (e.g. 'P00439' or 'P00439 P12345').

Options:
  --fasta        UniProt sequence in fasta format (expects UniProt ID).
  --gff          UniProt record in gff format (expects UniProt ID).
  --txt          UniProt record in txt format (expects UniProt ID).
  -v, --verbosity LVL  Either CRITICAL, ERROR, WARNING, INFO or DEBUG
  --override     Overrides any existing file, if available.
  --output TEXT  Directory path to which the files will be written.
  -h, --help     Show this message and exit.

Downloading a bunch of structure files...

# Downloads structures in PDB and mmCIF format
$ BioDownloader pdb --pdb --mmcif 2pah 3pah 4pah

Changing where the files will be downloaded to...

# Downloads a UniProt sequence in FASTA and sequence annotations in GFF
$ BioDownloader uniprot --fasta --gff --output /path/to/output/dir/ P00439

See the necessary requirements for this module.

Feel free to fork, clone, share and distribute. If you find any bugs or issues please log them in the issue tracker.

• Fábio Madeira
• Felix Simkovic

GNU General Public License v3 (GPLv3). See license for details.