This release is a pre-release and may not be stable for production use.
bigmcl
Large scale Markov clustering (MCL) via subgraph extraction
bigmcl will isolate disconnected subgraphs from a large graph file and execute
MCL on the subgraphs. bigmcl enables MCL on large, highly disconnected graphs,
such as those used in orthogroup inference. Not recommended for graphs that are
manageable with typical MCL.
Important to note that the inflation parameter is affected by this approach - I have noted clusters are more granular if anything. In the future, I plan on implementing a systematic approach option for identifying ideal inflations for each subgraph.
Please cite this git repository and MCL when this software contributes to your analysis.
DISCLAIMER
bigmcl is currently in a beta state, and while I appreciate bringing issues to
my attention, I am currently focused on getting things working well for my own
research, so I cannot guarantee timely issue resolution. My hope is bigmcl will
be in a longterm stable state by publication 2022.
INSTALL
pip install bigmcl
Clone mcl from here, compile, and add to your path.
USE
Input and go:
bigmcl -i <GRAPH.imx> -I 1.5
More elaborate options:
usage: bigmcl.py [-h] -i INPUT -I INFLATION [-s] [-r ROW_FILE] [-m] [-o OUTPUT] [-c CORES]
[-v]
Isolates disconnected graphs and runs MCL on the subgraphs. Input data must be numerical.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
MCL graph file in imx format
-I INFLATION, --inflation INFLATION
-s, --symmetric Matrix is symmetric (throughput increase)
-r ROW_FILE, --row_file ROW_FILE
Continue from finished row.txt
-m, --mcl_format Output clusters in MCL format
-o OUTPUT, --output OUTPUT
Alternative output directory
-c CORES, --cores CORES
-v, --verbose
1 maintainer
Metadata
1 maintainer
Release files for bigmcl 0.2b2
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| File | Size | Uploaded | |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bigmcl-0.2b2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 34.9 kB
Release files / bigmcl-0.2b2.tar.gz
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| Size | 13.3 kB |
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