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execute_all.sh
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execute_all.sh
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#!/usr/bin/env bash
# This bash script can be used to run all python files
# sequentially for the mexcowalk algorithm. The required
# python libraries are numpy, scipy and networkx. The
# input files are provided within the data folder. If
# the user wishes to use a different input file, the
# filenames in the utils.py file need to be changes.
cd src
#########################################################
#
# Compute Edge Weights
#
#########################################################
# following arguments can be passed onto this python file
#
# -m str Name of the model | default 'mexcowalk'
# -t float Mutex threshold | default 0.7
# -v Verbose, prints additional data during
# runtime
#
#########################################################
printf "Computing Edge Weights...\n\n"
python compute_edge_weights.py \
-v
#########################################################
#
# Perform Random Walk
#
#########################################################
# following arguments can be passed onto this python file
#
# -m str Name of the model | default 'mexcowalk'
# -s Stores all random walk matrices when
# called
# -v Verbose, prints additional data during
# runtime
#
#########################################################
printf "\nRunning Random Walk...\n\n"
python random_walk.py \
-s \
-v
#########################################################
#
# Find Connected Components and Split
#
#########################################################
# following arguments can be passed onto this python file
#
# -m str Name of the model | default 'mexcowalk'
# -k int Minimum length of a module | default 3
# -ns int Maximum number of genes | default 1000
# -ne int Minimum number of genes | default 100
# -step int Stepsize of decrement from num_start to
# num_end | default 100
# -ts float Starting threshold | default 0.0002 for
# 1000 genes
# -cc Outputs modules before splitting when
# called
# -v Verbose, prints additional data during
# runtime
#
#########################################################
# Change -ts to 0.00008 and ns to 2500 in order to find
# top 2500 genes. -ts to 0.0002 and ns to 1000 for top
# 1000 genes.
#
#########################################################
printf "\nFinding Connected Components...\n\n"
python connected_components_isolarge.py \
-k 3 \
-ns 1000 \
-ne 100 \
-step 100 \
-ts 0.0002 \
-v
printf "\nDONE!!!\n"