Combining DSD (Cao et al. 2013, 2014) runtime optimizations from reemagit for a fast, optimized version of DSD / cDSD
git clone git@github.com:samsledje/fastDSD.git
cd fastDSD
pip install .or
pip install fastdsdusage: fastdsd [-h] [--converge] [-n NRW] [-w PPIP] [-r PATHPROB] [-o OUTFILE] [-q] [-f] [-m {1,2,3}] [--outformat {matrix,list,top}] [-k NTOP] [-t THRESHOLD] [-c]
[-a] [-p]
infile
parses PPIs from infile and calculates DSD
positional arguments:
infile read PPIs from tab-delimited edge list (with optional weights)
optional arguments:
-h, --help show this help message and exit
--converge calculate converged DSD
-n NRW, --nRW NRW length of random walks, 5 by default
-w PPIP, --ppip PPIP directory containing PPI pathway files
-r PATHPROB, --pathprob PATHPROB
probability of remaining on a path given that you are already on it
-o OUTFILE, --outfile OUTFILE
output DSD file name, tab delimited tables, stdout by default
-q, --quiet turn off status message
-f, --force calculate DSD for the whole graph despite it is not connected if it is turned on; otherwise, calculate DSD for the largest component
-m {1,2,3}, --outFMT {1,2,3}
the format of output DSD file: type 1 for matrix; type 2 for pairs at each line; type 3 for top K proteins with lowest DSD. Type 1 by default
--outformat {matrix,list,top}
the format of output DSD file: 'matrix' for matrix, type 1; 'list' for pairs at each line, type 2; 'top' for top K proteins with lowest DSD,
type 3. 'matrix' by default
-k NTOP, --nTop NTOP if chosen to output lowest DSD nodes, output at most K nodes with lowest DSD, 10 by default
-t THRESHOLD, --threshold THRESHOLD
threshold for PPIs' confidence score, if applied
-c, --confidence use information about interaction confidence (cDSD)
-a, --augment augment with high-confidence signaling pathway data (caDSD: requires -c)
-p, --properties make use of topological properties of signaling pathways (capDSD: requireds -ca)