A Command Line Tool for downloading protein structures, protein sequences and multiple sequence alignments.
Easy install from github using pip.
$ pip install --upgrade https://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.
GNU General Public License v3 (GPLv3). See license for details.