COPAL -- COmplexome Profile ALignment

Synopsis

COPAL is a tool that aligns complexome profiling samples using a multi-dimensional adaptation of the dynamic time warping algorithm. After alignment it can quantify differences in protein migration patterns between sample groups using the hausdorff effect size.

Installation

COPAL source code can be accessed by cloning this repository. To run the tool with python, run the copal/COPAL_main.py module. To run the tool with the Graphical user interface (GUI) wrapper with python, run the COPAL_gui.py module. To use the packaged tool (with GUI), download the latest release, and run the executable single file (Windows or Mac).

requirements

• python 3 (for python2.7 switch to py2_version branch)
• numpy
• pandas
• xlsxwriter
• xlrd

requirements.txt: can be used to create (conda) virtual environment with all necessary requirements

example command: conda create --name env_name --file requirements.txt

Test Example

test data:

• Gel1_unaligned_samples_500_rows.csv
• Gel2_unaligned_samples_500_rows.csv
• Gel3_unaligned_samples_500_rows.csv

To run COPAL on test data, run example_run.py For documentation on how to run an analysis using the GUI, refer to the user guide

Modules:

COPAL main modules

• COPAL_main -- Contains higher level functions running steps of the analysis specified below. run this module to run COPAL analysis without GUI wrapper
• COPAL_gui -- Contains code that wraps COPAL analysis with a GUI. run this module to run COPAL with GUI wrapper

Progressive alignment modules

• localdist -- Contains functions that calculate local distances between samples. These distances are then used in dynamic time warping
• timewarp -- Contains core dynamic time warping function. This function performs dynamic time warping between two samples or two alignments.
• multipletimewarp -- Contains functions that perform progressive alignment procedure. Pairwise alignments to determine order, and multiple alignment to get final alignment

hausdorff scoring modules

• hausdorff -- Computes the hausdorff distance between two protein migration patterns
• findshift -- Calculates hausdorff distances between sample pairs for all proteins using hausdorff module
• shiftscore -- Calculates hausdorff effect sizes between sample groups

data preparation modules

• dataprep -- Prepares data for complexome alignment, complementing the provided datasets and normalising data
• complement_frames -- Complements uneven datasets, generating rows for missing proteins

output modules

• datatoexcel -- Produces excel output of COPAL results
• txtoutput -- Produces text output with information on COPAL process. writes to file and to stdout

License

COPAL -- COmplexome Profile ALignment Tool
Copyright (C) 2018  Radboud universitair medisch centrum

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.

Contact

Joeri van Strien Msc

email: Joeri.vanStrien@radboudumc.nl

Citing COPAL

Van Strien, J., Guerrero-Castillo, S., Chatzispyrou, I. A., Houtkooper, R. H., Brandt, U., & Huynen, M. A. COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome. Bioinformatics, 2019, 1–9