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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,58 @@ | ||
| import argparse | ||
| import pandas as pd | ||
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| if __name__ == "__main__": | ||
| # parse command-line arguments | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument("--emx", required=True, help="expression matrix file", dest="EMX") | ||
| parser.add_argument("--cmx", required=True, help="correlation matrix file", dest="CMX") | ||
| parser.add_argument("-o", "--output", required=True, help="output net file", dest="OUTPUT") | ||
| parser.add_argument("--mincorr", type=float, default=0, help="minimum absolute correlation threshold", dest="MINCORR") | ||
| parser.add_argument("--maxcorr", type=float, default=1, help="maximum absolute correlation threshold", dest="MAXCORR") | ||
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| args = parser.parse_args() | ||
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| # load data | ||
| emx = pd.read_table(args.EMX) | ||
| cmx = pd.read_table(args.CMX, header=None, names=[ | ||
| "x", | ||
| "y", | ||
| "Cluster", | ||
| "Num_Clusters", | ||
| "Cluster_Samples", | ||
| "Missing_Samples", | ||
| "Cluster_Outliers", | ||
| "Pair_Outliers", | ||
| "Too_Low", | ||
| "sc", | ||
| "Samples" | ||
| ]) | ||
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| # extract correlations within thresholds | ||
| cmx = cmx[(args.MINCORR <= abs(cmx["sc"])) & (abs(cmx["sc"]) <= args.MAXCORR)] | ||
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| # insert additional columns used in netlist format | ||
| cmx.insert(len(cmx.columns), "Source", [emx.index[x] for x in cmx["x"]]) | ||
| cmx.insert(len(cmx.columns), "Target", [emx.index[y] for y in cmx["y"]]) | ||
| cmx.insert(len(cmx.columns), "Interaction", ["co" for idx in cmx.index]) | ||
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| # reorder columns to netlist format | ||
| cmx = cmx[[ | ||
| "Source", | ||
| "Target", | ||
| "sc", | ||
| "Interaction", | ||
| "Cluster", | ||
| "Num_Clusters", | ||
| "Cluster_Samples", | ||
| "Missing_Samples", | ||
| "Cluster_Outliers", | ||
| "Pair_Outliers", | ||
| "Too_Low", | ||
| "Samples" | ||
| ]] | ||
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| # save output data | ||
| cmx.to_csv(args.OUTPUT, sep="\t", index=False) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| #!/bin/bash | ||
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| # parse command-line arguments | ||
| if [[ $# != 1 ]]; then | ||
| echo "usage: $0 <infile>" | ||
| exit -1 | ||
| fi | ||
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| # define analytic flags | ||
| DO_SIMILARITY=1 | ||
| DO_THRESHOLD=1 | ||
| DO_EXTRACT=1 | ||
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| # define input/output files | ||
| DATA="data" | ||
| EMX_FILE="$1" | ||
| CMX_FILE="$DATA/$(basename $EMX_FILE .txt)-cmx-py.txt" | ||
| NET_FILE="$DATA/$(basename $EMX_FILE .txt)-net-py.txt" | ||
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| # similarity | ||
| if [[ $DO_SIMILARITY = 1 ]]; then | ||
| CLUSMETHOD="gmm" | ||
| CORRMETHOD="pearson" | ||
| MINEXPR="-inf" | ||
| MINCLUS=1 | ||
| MAXCLUS=5 | ||
| CRITERION="bic" | ||
| PREOUT="--preout" | ||
| POSTOUT="--postout" | ||
| MINCORR=0 | ||
| MAXCORR=1 | ||
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| python scripts/similarity.py \ | ||
| -i $EMX_FILE \ | ||
| -o $CMX_FILE \ | ||
| --clusmethod $CLUSMETHOD \ | ||
| --corrmethod $CORRMETHOD \ | ||
| --minexpr=$MINEXPR \ | ||
| --minclus $MINCLUS --maxclus $MAXCLUS \ | ||
| --crit $CRITERION \ | ||
| $PREOUT $POSTOUT \ | ||
| --mincorr $MINCORR --maxcorr $MAXCORR | ||
| fi | ||
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| # threshold | ||
| if [[ $DO_THRESHOLD = 1 ]]; then | ||
| NUM_GENES=$(expr $(cat $EMX_FILE | wc -l) - 1) | ||
| METHOD="rmt" | ||
| TSTART=0.99 | ||
| TSTEP=0.001 | ||
| TSTOP=0.50 | ||
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| python scripts/threshold.py \ | ||
| -i $CMX_FILE \ | ||
| --genes $NUM_GENES \ | ||
| --method $METHOD \ | ||
| --tstart $TSTART \ | ||
| --tstep $TSTEP \ | ||
| --tstop $TSTOP | ||
| fi | ||
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| # extract | ||
| if [[ $DO_EXTRACT = 1 ]]; then | ||
| MINCORR=0 | ||
| MAXCORR=1 | ||
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| python scripts/extract.py \ | ||
| --emx $EMX_FILE \ | ||
| --cmx $CMX_FILE \ | ||
| --output $NET_FILE \ | ||
| --mincorr $MINCORR \ | ||
| --maxcorr $MAXCORR | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| #!/bin/bash | ||
|
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| # parse command-line arguments | ||
| if [[ $# != 1 ]]; then | ||
| echo "usage: $0 <infile>" | ||
| exit -1 | ||
| fi | ||
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| GPU=1 | ||
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| # define analytic flags | ||
| DO_IMPORT_EMX=1 | ||
| DO_SIMILARITY=1 | ||
| DO_EXPORT_CMX=1 | ||
| DO_THRESHOLD=1 | ||
| DO_EXTRACT=1 | ||
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| # define input/output files | ||
| INFILE="$1" | ||
| DATA="data" | ||
| EMX_FILE="$DATA/$(basename $INFILE .txt).emx" | ||
| CCM_FILE="$DATA/$(basename $EMX_FILE .emx).ccm" | ||
| CMX_FILE="$DATA/$(basename $EMX_FILE .emx).cmx" | ||
| LOGS="logs" | ||
| RMT_FILE="$LOGS/$(basename $CMX_FILE .cmx).txt" | ||
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| # apply settings | ||
| if [[ $GPU == 1 ]]; then | ||
| kinc settings set opencl 0:0 | ||
| kinc settings set threads 4 | ||
| kinc settings set logging off | ||
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| NP=1 | ||
| else | ||
| kinc settings set opencl none | ||
| kinc settings set logging off | ||
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| NP=$(nproc) | ||
| fi | ||
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| # import emx | ||
| if [[ $DO_IMPORT_EMX = 1 ]]; then | ||
| kinc run import-emx \ | ||
| --input $INFILE \ | ||
| --output $EMX_FILE \ | ||
| --nan NA | ||
| fi | ||
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| # similarity | ||
| if [[ $DO_SIMILARITY = 1 ]]; then | ||
| CLUSMETHOD="gmm" | ||
| CORRMETHOD="pearson" | ||
| MINEXPR="-inf" | ||
| MINCLUS=1 | ||
| MAXCLUS=5 | ||
| CRITERION="BIC" | ||
| PREOUT="--preout" | ||
| POSTOUT="--postout" | ||
| MINCORR=0.5 | ||
| MAXCORR=1 | ||
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| mpirun -np $NP kinc run similarity \ | ||
| --input $EMX_FILE \ | ||
| --ccm $CCM_FILE \ | ||
| --cmx $CMX_FILE \ | ||
| --clusmethod $CLUSMETHOD \ | ||
| --corrmethod $CORRMETHOD \ | ||
| --minexpr $MINEXPR \ | ||
| --minclus $MINCLUS --maxclus $MAXCLUS \ | ||
| --crit $CRITERION \ | ||
| $PREOUT $POSTOUT \ | ||
| --mincorr $MINCORR --maxcorr $MAXCORR | ||
| fi | ||
|
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| # export cmx | ||
| if [[ $DO_EXPORT_CMX = 1 ]]; then | ||
| OUTFILE="$DATA/$(basename $CMX_FILE .cmx)-cmx.txt" | ||
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| kinc run export-cmx \ | ||
| --emx $EMX_FILE \ | ||
| --ccm $CCM_FILE \ | ||
| --cmx $CMX_FILE \ | ||
| --output $OUTFILE | ||
| fi | ||
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| # threshold | ||
| if [[ $DO_THRESHOLD = 1 ]]; then | ||
| mkdir -p $LOGS | ||
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| kinc run rmt \ | ||
| --input $CMX_FILE \ | ||
| --log $RMT_FILE | ||
| fi | ||
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| # extract | ||
| if [[ $DO_EXTRACT = 1 ]]; then | ||
| NET_FILE="$DATA/$(basename $EMX_FILE .emx)-net.txt" | ||
| MINCORR=0 | ||
| MAXCORR=1 | ||
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| kinc run extract \ | ||
| --emx $EMX_FILE \ | ||
| --ccm $CCM_FILE \ | ||
| --cmx $CMX_FILE \ | ||
| --output $NET_FILE \ | ||
| --mincorr $MINCORR \ | ||
| --maxcorr $MAXCORR | ||
| fi |
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