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pipeline2.sh
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pipeline2.sh
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#!/bin/bash
set -e
help() {
echo "usage: ./pipeline.sh [-p [ppinfile]] [-r [reffile]] [-o [outputdir]] [-f [filter]] [-h]
Runs P5COMP on the given PPIN file (ppinfile) and evaluates against the given gold standard (reffile).
Final predicted clusters will be written in outputdir.
Important: Protein names (PID) should be in gene name (ordered locus) or KEGG format (ex. YLR075W) to match gold standards.
options:
-p [ppinfile] path to PPIN file (.txt) where each row is (u v w) (required)
-r [reffile] path to gold standard or reference complexes file (.txt) (required)
-o [outputdir] path to output directory (required)
-f [filter] filtering type (perpair or perprotein)
-a [attribs] attributes for evaluation file name of format 'algo-goldstd-ppin', ex: P5COMP-CYC-Collins
-h show this help information"
}
log() {
echo "$@" >> ./debug.txt
}
validate_file() {
if [[ ! -f $1 ]]; then
echo "$1 is not a valid file."
exit 1
fi
}
validate_dir() {
if [[ ! -d $1 ]]; then
echo "$1 is not a valid directory."
exit 1
fi
}
if [ $# -eq 0 ]; then
echo "Error: No options supplied. See help below."
help
exit 1
fi
# Developer parameters
filteredfile="data/Interm/filtered_ppin.txt"
# Parse user-defined parameters
ppinfile=
reffile=
outputdir=
filtering=
attribs=
resfile=
while getopts ":hp:r:o:f:a:R:" opt; do
case ${opt} in
h)
help
exit 0
;;
f)
filtering=$OPTARG
;;
R)
resfile=$OPTARG
;;
a)
attribs=$OPTARG
;;
p)
ppinfile=$OPTARG
;;
r)
reffile=$OPTARG
;;
o)
outputdir=$OPTARG
;;
\?)
echo "Error: Invalid option: -$OPTARG."
exit 1
;;
:)
echo "Error: Option -$OPTARG requires an argument."
exit 1
;;
esac
done
if [[ -z $ppinfile || -z $reffile || -z $outputdir ]]; then
echo "Error: Missing -p, -r, and/or -o arguments. See help (-h)."
exit 1
fi
mkdir -p $outputdir
validate_file $ppinfile && validate_file $reffile && validate_dir $outputdir
echo "RUNNING INDEPENDENT CLUSTERING ALGO: ${attribs}"
echo "Denoising..."
python code/filtering.py $ppinfile $reffile $filteredfile --filtering $filtering
method=${attribs%%-*}
case "$method" in
"PC2P")
echo "IND 1: Running PC2P..."
predictsfile="${outputdir}/PC2P_predicted.txt"
postprocessed="${outputdir}/PC2P_postprocessed.txt"
python code/PC2P/PC2P.py $filteredfile $predictsfile -p mp
python code/PC2P/PC2P_scoring.py $filteredfile $predictsfile $postprocessed
python code/remove_duplicates.py $postprocessed
python code/eval2.py $postprocessed $reffile $resfile auc_pts.csv --attribs $attribs
;;
"CUBCO+")
echo "IND 2: Running CUBCO+..."
predictsfile="${outputdir}/CUBCO+_predicted.txt"
postprocessed="${outputdir}/CUBCO+_postprocessed.txt"
python code/CUBCO+/CUBCO.py $filteredfile $outputdir $predictsfile
python code/CUBCO+/cubco_scoring.py $filteredfile $predictsfile $postprocessed
python code/remove_duplicates.py $postprocessed
python code/eval2.py $postprocessed $reffile $resfile auc_pts.csv --attribs $attribs
;;
"ClusterOne")
echo "IND 3: Running ClusterOne..."
predictsfile="${outputdir}/ClusterOne_predicted.txt"
postprocessed="${outputdir}/ClusterOne_postprocessed.txt"
jarPath="code/ClusterOne/cluster_one-1.0.jar"
java -jar $jarPath $filteredfile > $predictsfile
## Score ClusterOne clusters
python code/ClusterOne/cluster_one_scoring.py $ppinfile $predictsfile $postprocessed
python code/remove_duplicates.py $postprocessed
python code/eval2.py $postprocessed $reffile $resfile auc_pts.csv --attribs $attribs
;;
esac