BioDownloader

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

Setup

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

Quickstart

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

Dependencies

See the necessary requirements for this module.

Contributing and Bug tracking

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

Contributors

• Fábio Madeira
• Felix Simkovic

License

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