Skip to content
Snippets Groups Projects
Select Git revision
  • master default protected
1 result
Compare
Name Last commit Last update
__pycache__
examples
examples_multimers
LICENSE
README.md
barrOs.py
barrOs_library.py
README.md

barrOs

Dependencies

barrOs is written in Python 3.7. It requires mostly core Python modules and only three external packages are required:

  • Seaborn
  • Pandas
  • Networkx

It also requires DSSP (https://swift.cmbi.umcn.nl/gv/dssp/) to be installed.

Installation

Installing from Source

Download the zip archive or clone the repository with git:

# To download
git clone https://github.com/JoanaMPereira/barrOs
cd barrOs

# To update
git pull origin master

Allowed inputs

Usage

Usage: python3 barrOs.py -in:<type>:<input_file> -out:<mode>

Parameters:
     -in:<type>  	an input string (or list of strings) with one of the following types: ['pdb_file', 'pdbID', 'hhpred', 'pdbsum_fasta']
                 	for example: -in:pdbID:1LML_A,3XML_A or -in:pdb_file:1LML_A.pdb,3XML_A.pdb
                 	ATENTION: barrOs only works with monomeric proteins, so always provide the target chain
     -mode:      	defines the mode of running, i.e. either we want to deal only with membrane proteins, all, or non-membrane proteins
                 	values accepted: ['membrane', 'non-membrane', 'all']

Examples

barrOs can take different input types (i.e., PDB files, PDB IDs including chain ID, HHpred result files, of fasta files with PDB IDs in the headers), as well as different modes that allow the focus on membrane proteins if necessary:

# For a single pdbID
python3 barrOs.py -in:pdbID:1BXW_A -mode:membrane


# For a list of hhr files
python3 barrOs.py -in:hhpred:examples/hhpred_3686809.hhr,examples/hhpred_3686809_10.hhr,examples/hhpred_3686809_12.hhr,examples/hhpred_3686809_2.hhr,examples/hhpred_3686809_4.hhr,examples/hhpred_3686809_6.hhr,examples/hhpred_3686809_8.hhr,examples/hhpred_3686809_1.hhr,examples/hhpred_3686809_11.hhr,examples/hhpred_3686809_13.hhr,examples/hhpred_3686809_3.hhr,examples/hhpred_3686809_5.hhr,examples/hhpred_3686809_7.hhr,examples/hhpred_3686809_9.hhr -mode:membrane

Acknowledgements

barrOs started in 2018 while Joana Pereira was a postdoc with Andrei Lupas at the Dept. of Protein Evolution of the Max Planck Institute for Developmental Biology. Its further development is now being carried out at Trosten Schwede's group at the Biozentrum of the University of Basel. Special thanks to Jens Bassler and Andrei Lupas for helpful discussions and brainstormings when barrOs was being born, and to Roger Bamert for contributing to the implementation of the shear number calculation into the pipeline.